DNA Breaks, Single-Stranded
Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.
A genotoxicological technique for measuring DNA damage in an individual cell using single-cell gel electrophoresis. Cell DNA fragments assume a "comet with tail" formation on electrophoresis and are detected with an image analysis system. Alkaline assay conditions facilitate sensitive detection of single-strand damage.
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Nucleic Acid Denaturation
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
DNA-Directed DNA Polymerase
DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.
A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.
Immunoglobulin Class Switching
Gene rearrangement of the B-lymphocyte which results in a substitution in the type of heavy-chain constant region that is expressed. This allows the effector response to change while the antigen binding specificity (variable region) remains the same. The majority of class switching occurs by a DNA recombination event but it also can take place at the level of RNA processing.
Somatic Hypermutation, Immunoglobulin
DNA Breaks, Double-Stranded
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Impaired translesion synthesis in xeroderma pigmentosum variant extracts. (1/5092)Xeroderma pigmentosum variant (XPV) cells are characterized by a cellular defect in the ability to synthesize intact daughter DNA strands on damaged templates. Molecular mechanisms that facilitate replication fork progression on damaged DNA in normal cells are not well defined. In this study, we used single-stranded plasmid molecules containing a single N-2-acetylaminofluorene (AAF) adduct to analyze translesion synthesis (TLS) catalyzed by extracts of either normal or XPV primary skin fibroblasts. In one of the substrates, the single AAF adduct was located at the 3' end of a run of three guanines that was previously shown to induce deletion of one G by a slippage mechanism. Primer extension reactions performed by normal cellular extracts from four different individuals produced the same distinct pattern of TLS, with over 80% of the products resulting from the elongation of a slipped intermediate and the remaining 20% resulting from a nonslipped intermediate. In contrast, with cellular extracts from five different XPV patients, the TLS reaction was strongly reduced, yielding only low amounts of TLS via the nonslipped intermediate. With our second substrate, in which the AAF adduct was located at the first G in the run, thus preventing slippage from occurring, we confirmed that normal extracts were able to perform TLS 10-fold more efficiently than XPV extracts. These data demonstrate unequivocally that the defect in XPV cells resides in translesion synthesis independently of the slippage process. (+info)
The DNA binding activity of Translin is mediated by a basic region in the ring-shaped structure conserved in evolution. (2/5092)DNA binding proteins, for the most part, function as dimers or tetramers which recognize their target sequences. Here we show that Translin, a novel single-stranded DNA end binding protein, forms a ring-shaped structure conserved throughout evolution and that this structure is responsible for its DNA binding activity. Point mutations at Leu184 and Leu191 in the leucine zipper motif of human Translin resulted in loss of the multimeric structure and abrogation of DNA binding. Point mutations at R86, H88, H90 to T86, N88, N90 in one of the basic regions, however, completely inhibited the DNA binding activity without affecting the multimeric structure. These results support the view that the DNA binding domain of Translin is formed in the ring-shaped structure in combination with its basic region (amino acids 86-97) polypeptides. (+info)
Mutations and allelic deletions of the MEN1 gene are associated with a subset of sporadic endocrine pancreatic and neuroendocrine tumors and not restricted to foregut neoplasms. (3/5092)Endocrine pancreatic tumors (EPT) and neuroendocrine tumors (NET) occur sporadically and rarely in association with multiple endocrine neoplasia type 1 (MEN1). We analyzed the frequency of allelic deletions and mutations of the recently identified MEN1 gene in 53 sporadic tumors including 30 EPT and 23 NET (carcinoids) of different locations and types. Allelic deletion of the MEN1 locus was identified in 18/49 (36.7%) tumors (13/30, 43.3% in EPT and 5/19, 26.3% in NET) and mutations of the MEN1 gene were present in 8/52 (15.3%) tumors (4/30 (13.3%) EPT and 4/22 (18.1%) NET). The somatic mutations were clustered in the 5' region of the coding sequence and most frequently encompassed missense mutations. All tumors with mutations exhibited a loss of the other allele and a wild-type sequence of the MEN1 gene in nontumorous DNA. In one additional patient with a NET of the lung and no clinical signs or history of MEN1, a 5178-9G-->A splice donor site mutation in intron 4 was identified in both the tumor and blood DNA, indicating the presence of a thus far unknown MEN1 syndrome. In most tumor groups the frequency of allelic deletions at 11q13 was 2 to 3 times higher than the frequency of identified MEN1 gene mutations. Some tumor types, including rare forms of EPT and NET of the duodenum and small intestine, exhibited mutations more frequently than other types. Furthermore, somatic mutations were not restricted to foregut tumors but were also detectable in a midgut tumor (15.2% versus 16.6%). Our data indicate that somatic MEN1 gene mutations contribute to a subset of sporadic EPT and NET, including midgut tumors. Because the frequency of mutations varies significantly among the investigated tumor subgroups and allelic deletions are 2 to 3 times more frequently observed, factors other than MEN1 gene inactivation, including other tumor-suppressor genes on 11q13, may also be involved in the tumorigenesis of these neoplasms. (+info)
An allosteric synthetic DNA. (4/5092)Allosteric DNA oligonucleotides are potentially useful diagnostic reagents. Here we develop a model system for the study of allosteric interactions in DNAs. A DNA that binds either Cibacron blue or cholic acid was isolated and partially characterized. Isolation was performed using a multi-stage SELEX. First, short oligos that bind either Cibacron blue or cholic acid were enriched from random oligonucleotide pools. Then, members of the two pools were fused to form longer oligos, which were then selected for theability to bind Cibacron blue columns and elute with cholic acid. One resulting isolate (A22) was studied. Dye- and cholate-binding functions can be separated on sequences from the 5'- and 3'-regions, respectively. Ligand-column affinity assays indicate that each domain binds only its respective ligand. However, the full-length A22 will bind either dye or cholate columns and elute with the other ligand, as if binding by the ligands is mutually exclusive. Furthermore, S1 nuclease protection assays show that Cibacron blue causes a structural change in A22 and that cholic acid inhibits this change. This system will be useful for elucidating mechanisms of allosteric interactions in synthetic DNAs. (+info)
The binding affinity of Ff gene 5 protein depends on the nearest-neighbor composition of the ssDNA substrate. (5/5092)The Ff gene 5 protein (g5p) is considered to be a nonspecific single-stranded DNA binding protein, because it binds cooperatively to and saturates the Ff bacteriophage single-stranded DNA genome and other single-stranded polynucleotides. However, the binding affinity Komega (the intrinsic binding constant times a cooperativity factor) differs by over an order of magnitude for binding to single-stranded polynucleotides such as poly[d(A)] and poly[d(C)]. A polynucleotide that is more stacked, like poly[d(A)], binds more weakly than one that is less stacked, like poly[d(C)]. To test the hypothesis that DNA base stacking, a nearest-neighbor property, is involved in the binding affinity of the Ff g5p for different DNA sequences, Komega values were determined as a function of NaCl concentration for binding to six synthetic sequences 48 nucleotides in length: dA48, dC48, d(AAC)16, d(ACC)16, d(AACC)12, and d(AAACC)9A3. The binding affinities of the protein for these sequences were indeed found to be related to the nearest-neighbor compositions of the sequences, rather than to simple base compositions. That is, the g5p binding site, which is spanned by four nucleotides, discriminates among these sequences on the basis of the relative numbers of nearest neighbors (AA, CC, and AC plus CA) in the sequence. The results support the hypothesis that the extent of base stacking/unstacking of the free, nonbound ssDNA plays an important role in the binding affinity of the Ff gene 5 protein. (+info)
Identification of RNase T as a high-copy suppressor of the UV sensitivity associated with single-strand DNA exonuclease deficiency in Escherichia coli. (6/5092)There are three known single-strand DNA-specific exonucleases in Escherichia coli: RecJ, exonuclease I (ExoI), and exonuclease VII (ExoVII). E. coli that are deficient in all three exonucleases are abnormally sensitive to UV irradiation, most likely because of their inability to repair lesions that block replication. We have performed an iterative screen to uncover genes capable of ameliorating the UV repair defect of xonA (ExoI-) xseA (ExoVII-) recJ triple mutants. In this screen, exonuclease-deficient cells were transformed with a high-copy E. coli genomic library and then irradiated; plasmids harvested from surviving cells were used to seed subsequent rounds of transformation and selection. After several rounds of selection, multiple plasmids containing the rnt gene, which encodes RNase T, were found. An rnt plasmid increased the UV resistance of a xonA xseA recJ mutant and uvrA and uvrC mutants; however, it did not alter the survival of xseA recJ or recA mutants. RNase T also has amino acid sequence similarity to other 3' DNA exonucleases, including ExoI. These results suggest that RNase T may possess a 3' DNase activity capable of substituting for ExoI in the recombinational repair of UV-induced lesions. (+info)
Nuclear foci of mammalian recombination proteins are located at single-stranded DNA regions formed after DNA damage. (7/5092)A sensitive and rapid in situ method was developed to visualize sites of single-stranded (ss) DNA in cultured cells and in experimental test animals. Anti-bromodeoxyuridine antibody recognizes the halogenated base analog incorporated into chromosomal DNA only when substituted DNA is in the single strand form. After treatment of cells with DNA-damaging agents or gamma irradiation, ssDNA molecules form nuclear foci in a dose-dependent manner within 60 min. The mammalian recombination protein Rad51 and the replication protein A then accumulate at sites of ssDNA and form foci, suggesting that these are sites of recombinational DNA repair. (+info)
Structure of DNA-dependent protein kinase: implications for its regulation by DNA. (8/5092)DNA double-strand breaks are created by ionizing radiation or during V(D)J recombination, the process that generates immunological diversity. Breaks are repaired by an end-joining reaction that requires DNA-PKCS, the catalytic subunit of DNA-dependent protein kinase. DNA-PKCS is a 460 kDa serine-threonine kinase that is activated by direct interaction with DNA. Here we report its structure at 22 A resolution, as determined by electron crystallography. The structure contains an open channel, similar to those seen in other double-stranded DNA-binding proteins, and an enclosed cavity with three openings large enough to accommodate single-stranded DNA, with one opening adjacent to the open channel. Based on these structural features, we performed biochemical experiments to examine the interactions of DNA-PKCS with different DNA molecules. Efficient kinase activation required DNA longer than 12 bp, the minimal length of the open channel. Competition experiments demonstrated that DNA-PKCS binds to double- and single-stranded DNA via separate but interacting sites. Addition of unpaired single strands to a double-stranded DNA fragment stimulated kinase activation. These results suggest that activation of the kinase involves interactions with both double- and single-stranded DNA, as suggested by the structure. A model for how the kinase is regulated by DNA is described. (+info)
Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear...
Single-stranded DNA (ssDNA) binding protein (SSB) is an essential protein to protect ssDNA and recruit specific ssDNA-processing proteins. Escherichia coli SSB forms a tetramer at neutral pH, comprising a structurally well-defined ssDNA binding domain (OB-domain) and a disordered C-terminal domain (C-domain) of ∼64 amino acid residues. The C-terminal eight-residue segment of SSB (C-peptide) has been shown to interact with the OB-domain, but crystal structures failed to reveal any electron density of the C-peptide. Here we show that SSB forms a monomer at pH 3.4, which is suitable for studies by high-resolution nuclear magnetic resonance (NMR) spectroscopy. The OB-domain retains its 3D structure in the monomer, and the C-peptide is shown by nuclear Overhauser effects and lanthanide-induced pseudocontact shifts to bind to the OB-domain at a site that harbors ssDNA in the crystal structure of the SSB-ssDNA complex. 15N relaxation data demonstrate high flexibility of the polypeptide segment ...
Isolation and characterization of the gene encoding single-stranded-DNA-binding protein (SSB) from four marine Shewanella...
The ssb gene, coding for single-stranded-DNA-binding protein (SSB), was cloned from four marine Shewanella strains that differed in their temperature and pressure optima and ranges of growth. All four Shewanella ssb genes complemented Escherichia coli ssb point and deletion mutants, with efficiencies that varied with temperature and ssb gene source. The Shewanella SSBs are the largest bacterial SSBs identified to date (24.9-26.3 kDa) and may be divided into conserved amino- and carboxy-terminal regions and a highly variable central region. Greater amino acid sequence homology was observed between the Shewanella SSBs as a group (72-87%) than with other bacterial SSBs (52-69%). Analysis of the amino acid composition of the Shewanella SSBs revealed several features that could correlate with pressure or temperature adaptation. SSBs from the three low-temperature-adapted Shewanella strains were an order of magnitude more hydrophilic than that from the mesophilic strain, and differences in the distribution of
Molecular mechanism of DNA association with single-stranded DNA binding protein | The Aksimentiev Group
Genome replication and maintenance occurs through the collective action of proteins that operate on single-stranded DNA (ssDNA). All cells express single-stranded DNA binding proteins (SSBs), which prevent errors by sequestering ssDNA with high-affinity, keeping it free from transient structures and protecting it from unwanted chemical modification. SSBs must be easily repositioned, or else risk stalling DNA replication and repair processes. How does a protein simulataneously bind DNA tightly yet diffuse rapidly?. Through a set of extensive all-atom molecular dynamics (MD) simulations, we have elucidated the molecular mechanism of SSB association with ssDNA. First, we showed that the same SSB-ssDNA complex can both spontaneously rearrange its structure and maintain its stable conformation depending on whether it is surrounded by physiological solution or a protein-crystal environment. Next, we probed the local interaction between ssDNA and SSB through simulations of mechanical unraveling of the ...
Crystal structure of a distinct viral capsid/ssDNA complex illuminates how viruses assemble into infectious virions
Crystal structure of a distinct viral capsid/ssDNA complex illuminates how viruses assemble into infectious virions Conference Paper ...
EP1501944A4 - Amplification of dna to produce single-stranded product of defined sequence and length - Google Patents
The present disclosure relates to methods for generating single-stranded DNA molecules of defined sequence and length. Specifically, a region of template containing target sequence is amplified by PCR or RCA, exogenous sequence is introduced by primers or probes used in amplification, double-stranded amplification products are converted to single-stranded amplification products, and single-stranded amplification products are trimmed to produce short single-stranded DNA molecules of defined sequence and length.
The 3 Genomic Numbers Discovery: How Our Genome Single-Stranded DNA Sequence Is Self-Designed as a Numerical Whole
This article proves the existence of a hyper-precise global numerical meta-architecture unifying, structuring, binding and controlling the billion triplet codons constituting the sequence of single-stranded DNA of the entire human genome. Beyond the evolution and erratic mutations like transposons within the genome, its as if the memory of a fossil genome with multiple symmetries persists. This recalls the
Research Article: Concentration-Dependent Exchange of Replication Protein A on Single-Stranded DNA Revealed by Single-Molecule...
Date Published: February 3, 2014. Publisher: Public Library of Science. Author(s): Bryan Gibb, Ling F. Ye, Stephanie C. Gergoudis, YoungHo Kwon, Hengyao Niu, Patrick Sung, Eric C. Greene, Maria Spies.. http://doi.org/10.1371/journal.pone.0087922. Abstract. Replication protein A (RPA) is a ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein necessary for all aspects of DNA metabolism involving an ssDNA intermediate, including DNA replication, repair, recombination, DNA damage response and checkpoint activation, and telomere maintenance , , . The role of RPA in most of these reactions is to protect the ssDNA until it can be delivered to downstream enzymes. Therefore a crucial feature of RPA is that it must bind very tightly to ssDNA, but must also be easily displaced from ssDNA to allow other proteins to gain access to the substrate. Here we use total internal reflection fluorescence microscopy and nanofabricated DNA curtains to visualize the behavior of Saccharomyces ...
Alexander Mazin | Profiles
List of Publications, The asterisk (*) marks peer reviewed publications.. 1. *Dianov G, Mazin A, Vavilin V, Zajtsev A and Salganik R (1980) Addressed modification of T7 phage early DNA by its alkylation in the R-loop formed with modified transcript Mol. Biol. 14: 261-264. (Russian).. 2. *Salganik R, Dianov G, Ovchinnikova L, Voronina E, Kokoza E and Mazin A (1980) Gene-directed mutagenesis in bacteriophage T7 provided by polyalkylating RNAs complementary to selected DNA sites. Proc. Natl. Acad. Sci. USA 77: 2796-2800.. 3. *Mazin A, Dianov G and Salganik R (1981) Application of alkylating DNA derivatives for addressed modification of genome. Mol. Biol. 15: 252-256. (Russian).. 4. *Mazin A, Dianov G, Ovchinnikova L and Salganik R (1983) Induction of directed mutation in the tetracycline resistance gene of plasmid pBR322 by complementary single-stranded DNA fragments carrying alkylating groups. Dokl. Acad. Nauk SSSR [Proceedings of the Academy of Science of the USSR] 268: 979-982. (Russian).. 5. ...
High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein
Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA replication, recombination, and repair. SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to bring multiple OB fold domains together in the functional SSB. SSBs from hyperthermophilic crenarchaea, such as Sulfolobus solfataricus, have an unusual structure with a single OB fold coupled to a flexible C-terminal tail. The OB fold resembles those in RPA, whilst the tail is reminiscent of bacterial SSBs and mediates interaction with other proteins. One paradigm in the field is that SSBs bind specifically to ssDNA and much less strongly to RNA, ensuring that their functions are restricted to DNA metabolism. Here, we use a combination of biochemical and biophysical approaches to demonstrate that the binding properties of S. solfataricus SSB are essentially identical for ssDNA and ssRNA. These features may ...
Method of targeting DNA - Patent # 5460941 - PatentGenius
The present invention relates to a method of forming a three-stranded DNA molecule wherein each strand of the three-stranded DNA molecule is hybridized (that is, non-covalently bound) to at least one other strand of the three-stranded DNA molecule. The method comprises:contacting a recombination protein with a double-stranded DNA molecule and with a single-stranded DNA molecule sufficiently complementary to one strand of the double-stranded DNA molecule to hybridize therewith, which contacting is effected under conditions such that the single-stranded DNA molecule hybridizes to the double-stranded molecule so that the three stranded DNA molecule is formed.
Jacobs:Protocol 10 bp DNA Ladder - OpenWetWare
The 10 bp DNA Ladder consists of thirty-three 10-bp repeats plus a fragment at 1668 bp and is suitable for sizing both double-stranded and single-stranded DNA fragments from 10 bp to 200 bp. The 100-bp band is approximately two to three times brighter than other ladder bands to provide internal orientation. In addition, because both DNA strands are of the same nucleotide composition, this product can be denatured to produce a set of single-stranded oligonucleotides increasing in length by 10-nucleotide increments. The double-stranded ladder can be visualized on 4% to 5% agarose gels after ethidium bromide staining. The single-stranded ladder can be visualized on an 8% urea-polyacrylamide gel after electrophoresis. This ladder can be easily radiolabeled using T4 polynucleotide kinase. ...
J-STORE SYSTEM(～Nucleic acid-encapsulating polymer micelle complex and method for producing same KATAOKA KAZUNORI 2920328～)
(CA2920328)This nucleic acid-encapsulating polymer micelle complex is characterized in being formed of: a block copolymer containing an uncharged hydrophilic polymer chain block and a cationic polymer chain block; and two single-stranded DNA molecules comprising mutually complementary base sequences of 1000 or more bases in length, double-stranded DNA of 1000 or more base pairs in length in which at least a part of the double helix structure has dissociated and taken on a single-stranded structure, or one single-stranded DNA molecule of 1000 or more bases in length.
J-STORE(～Nucleic acid-encapsulating polymer micelle complex and method for producing same KATAOKA KAZUNORI 201480043775～)
(CN105451719)This nucleic acid-encapsulating polymer micelle complex is characterized in being formed of: a block copolymer containing an uncharged hydrophilic polymer chain block and a cationic polymer chain block; and two single-stranded DNA molecules comprising mutually complementary base sequences of 1000 or more bases in length, double-stranded DNA of 1000 or more base pairs in length in which at least a part of the double helix structure has dissociated and taken on a single-stranded structure, or one single-stranded DNA molecule of 1000 or more bases in length.
The Escherichia coli single-strand binding protein  (gene ssb), also known as the helix-destabilizing protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterized in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB. Proteins currently known to belong to this subfamily are listed below : ...
RADX interacts with single‐stranded DNA to promote replication fork stability | EMBO Reports
Single‐stranded DNA (ssDNA) regions form as an intermediate in many DNA‐associated transactions. Multiple cellular proteins interact with ssDNA via the oligonucleotide/oligosaccharide‐binding (OB) fold domain. The heterotrimeric, multi‐OB fold domain‐containing Replication Protein A (RPA) complex has an essential genome maintenance role, protecting ssDNA regions from nucleolytic degradation and providing a recruitment platform for proteins involved in responses to replication stress and DNA damage. Here, we identify the uncharacterized protein RADX (CXorf57) as an ssDNA‐binding factor in human cells. RADX binds ssDNA via an N‐terminal OB fold cluster, which mediates its recruitment to sites of replication stress. Deregulation of RADX expression and ssDNA binding leads to enhanced replication fork stalling and degradation, and we provide evidence that a balanced interplay between RADX and RPA ssDNA‐binding activities is critical for avoiding these defects. Our findings establish ...
Purification and Analysis of Single-Stranded Binding Protein Tail Mutants
Single stranded binding protein (SSB) is a prokaryotic DNA protein that binds to single stranded DNA during times when the DNA is rendered from its double stranded form during times of genetic recombination or DNA damage in order to stabilize and protect it from further unnecessary harm. The protein exists as a tetramer with each monomer being made of an N-terminal and Cterminal domain. The C-terminal domain is made of two smaller sub-domains, both of which have yet to resolve properly in a crystal structure, named the intrinsically disordered linker and the acidic tip, with limited understanding on how they function and relate to other proteins and SSB itself. Due to the disordered nature of its C-terminal domain limiting the ability to yield a concise crystal structure, much of the function and nearly all of the structure of the C-terminal domain has yet to be identified. While some function has been determined for these disordered regions, its relationship with other binding partners, DNA, ...
golden ratio and numbers in DNA- CODEX BIOGENESIS: les 13 codes de lADN (13 codes of DNA): October 2013: the first proof that...
This article proves the existence of a hyper-precise global numerical meta-architecture unifying, structuring, binding and controlling the billion triplet codons comprising the sequence of single-stranded DNA of the entire human genome. Beyond the evolution and erratic mutations like transposons within the genome, its as if the memory of a fossil genome with multiple symmetries persists. This recalls the intermingling of information characterizing the fractal universe of chaos theory. The result leads to a balanced and perfect tuning between the masses of the two strands of the huge DNA molecule that constitute our genome. We show here how codon populations forming the single-stranded DNA sequences can constitute a critical approach to the understanding of junk DNA function. Then, we suggest revisiting certain methods published in our 2009 book Codex Biogenesis. In fact, we demonstrate here how the universal genetic code table is a powerful analytical filter to characterize single-stranded ...
ISIS Solving the structure of fundamental bacterial protein
The protein, known as a single-stranded DNA binding protein (SSB),is involved in a variety of essential DNA mechanisms such as replication and repair. Now the structure of this messy protein has been found, it could present a new bullseye for future antibiotics to hit bacteria right at its heart.. In 2014, 700,000 deaths were attributable to antimicrobial resistance, and this number is estimated to rise to 10 million fatalities by 2050 according to a review that the UK government commissioned on antimicrobial resistance in collaboration with the Wellcome Trust.. As we approach an era of antibiotic resistance, the ability to target a key protein behind bacterial growth may offer a solution for delivering new and effective antibiotics.. Single-stranded DNA binding proteins, or SSBs are fundamental proteins in molecular biology. Every time there is a transaction in the genome there is single strand of DNA that needs to be protected by these proteins. Seeing as these proteins are essential to ...
m13 phage manipulation protocols »
Synthesis of Single-stranded DNA Probes of Heterogeneous Length from Bacteriophage M13 Templates Technique yields a heterogeneous population of short radiolabeled molecules 200-300 nucleotides in length. These probes are synthesized, as in Synthesis of Single-stranded DNA Probes of Defined Length from Bacteriophage M13 Templates, by extension of an oligonucleotide primer on a single-stranded DNA template. The radiolabeled products of the reaction are then separated from the template by electrophoresis through a denaturing gel from which they are eluted directly into hybridization buffer. ...
An improved filamentous helper phage for generating single-stranded plasmid DNA. - PubMed - NCBI
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
In ,9209101632.AA03158 at anolis.bnr.usu.edu, thsiao at ANOLIS.BNR.USU.EDU writes: , Dear Netters, , , I am interested in the use of PCR enhancers. I would like to know if any one , has experience with the use of Stratagenes Perfect Match Polymerase Enhancer. , Is this a single-stranded DNA binding protein? What is the difference with , USBs single-stranded DNA binding protein or GP 32? How effective are these , products in getting better PCR yields? Any suggestion and tips will be , appreciated. , , +---------------Ting H. Hsiao ---------------+ , , Dept. of Biology, Utah State University , , , Logan, UT 84322-5303, U.S.A. , , , PHONE: (801) 750-2549; FAX: (801) 750-1575 , , , E-MAIL: thsiao at anolis.bnr.usu.edu , , +--------------------------------------------+ An issue of Biotechniques (I think, not absolutely sure) a couple of years ago revealed that Stratagenes Perfect Match is actually a 5x10E-5 M solution of tetra-methyl-ammonium chloride. ...
Characterization and application to the detection of single-stranded DNA binding protein of fluorescent DNA-templated copper...
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E Bochkareva, V Belegu, S Korolev, A Bochkarev (2001). Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding. EMBO J, 20:612-8 [Medline info for 11157767 ...
ssDNA Antibody | Single-Stranded DNA Antibody | Anti Single Stranded DNA Antibody
ssDNA Antibody is an affinity-purified IgG that recognizes ssDNA. The ssDNA Antibody was raised in rabbit and can be used for IHC detection of apoptotic cells.
The effect of various DNA dyes and enhancers on ssDNA f | Open-i
The effect of various DNA dyes and enhancers on ssDNA fluorescence and dsDNA melting temperature. (A) TNF-1 oligonucleotide (ssDNA, 45.5% GC; 1 μM final concen
Mitokondriaalsed nukleoidid - Vikipeedia
Imetajatest on mitokondriaalsed nukleoidid kõige paremini kirjeldatud inimeses. Samuti on nukleoidid leitud roti, rohepärdiku ja potoroo maksarakkude mitokondritest. Imetajate mtDNA paiknemine diskreetsete üksustena oli esmakordselt näidatud 1991. aastal inimrakkude mtDNA värvimisel DAPI-ga ning see oli hiljem kinnitatud ka immunofluorestsentsi katsetes, kus kasutati anti-DNA antikehi. mtDNA kompleksid valkudega olid imetajates kirjeldatud siis, kui näidati mtDNA seondumist DNA helikaasiga Twinkle inimrakkudes. Seejärel demonstreeriti mitme uuringu käigus ka teiste valkude esinemine mtDNA-ga, peaaegu alati esinesid koos mtDNA-ga mitokondriaalne transkriptsioonifaktor A (TFAM, ingl. mitochondrial transcription factor A), pagaripärmi Apf2p valgu homoloog, ning mitokondriaalne üheahelalise DNA-ga seonduv valk mtSSB (ingl. mitochondrial single strand binding protein), mis on pagaripärmi Rim1p homoloog. TFAM on seejuures valk, mille põhiline funktsioon seisneb mtDNA ...
In higher plants, mitochondrial genomes are large (367 and 570 kb in Arabidopsis thaliana and maize [Zea mays], respectively) (Unseld et al., 1997; Clifton et al., 2004), and their complete genetic repertoire can theoretically assemble in a genome-size circular chromosome. However, electrophoresis and electron microscopy studies showed that plant mitochondrial DNA (mtDNA) is a heterogeneous population of circular, linear, and complex double- and single-stranded molecules (Oldenburg and Bendich, 1996; Backert et al., 1997; Backert and Börner, 2000). These structures exist in dynamic equilibrium and probably result from a rolling-circle mechanism of DNA replication, but also from a recombination-dependent mechanism of DNA replication, similar to the replication of phage T4 (Backert and Börner, 2000). In addition, numerous recombination events between large and small repeats result in a multipartite structure of the plant mtDNA (Adams and Daley, 2004). Because the plant mtDNA is rich in repeated ...
RMI1 | Loqate
Subunit of the RecQ (Sgs1p) - Topo III (Top3p) complex; stimulates superhelical relaxing and ssDNA binding activities of Top3p; involved in response to DNA damage; null mutants display increased rates of recombination and delayed S ...
Library Quantification: Fluorometric Quantitation of Double-Stranded or Single-Stranded DNA Samples Using the Qubit System
Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
RCSB PDB - 1AE3: MUTANT R82C OF GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN) Macromolecule Annotations Page
1AE3: Analyses of the stability and function of three surface mutants (R82C, K69H, and L32R) of the gene V protein from Ff phage by X-ray crystallography.
RCSB PDB - 1GVP: GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN) Macromolecule Annotations Page
1GVP: Analyses of the stability and function of three surface mutants (R82C, K69H, and L32R) of the gene V protein from Ff phage by X-ray crystallography.
Messenger RNA definition, a single-stranded molecule of RNA that is synthesized in the nucleus from a DNA template and then enters the cytoplasm, where its genetic code specifies the amino acid sequence for protein synthesis. See more.
Ssbp3 (house mouse) | Gene Target - PubChem
Gene target information for Ssbp3 - single-stranded DNA binding protein 3 (house mouse). Find diseases associated with this biological target and compounds tested against it in bioassay experiments.
Make a d-strand from ss oligonucleotide ?
WANGNN at UCBEH.SAN.UC.EDU wrote: : Hi Netters: : I am going run the gel retardation to show the band shifting using my protein : and a small fragment DNA. The small fragment is about 20 bases, which is : planned to be synthesized. For sure, the synthesis of a 20-mer of : oligonucleotide is much cheaper than that of two strands to make a ds DNA. : My question is if some methods can be used to synthesis such small ds DNA : fragment (20bp) from the single strand oligonucleotide. : Any suggestion will be appreciated. Dear Hong, All DNA polymerases require a short primer to initiate synthesis. Even RNA polymerases require a promoter site. If you were really clever, you could design a DNA hairpin structure which would fold back on itself to give you a double-stranded region (really just a big stem-loop). You could use the Zucker folding program (available on several computer platforms) to help predict the folding, and you would have to be sure to anneal at low concentration to avoid intermolecular ...
Reverse Transcriptases | NEB
Reverse transcriptases can synthesize a complementary DNA strand initiating from a primer using RNA (cDNA synthesis) or single-stranded DNA as a template.
S1 - oi
S1 nuclease (EC 184.108.40.206, ~300 aa) is a fungal nuclease that degrades single-stranded nucleic acids and is preferentially active against DNA. Used experimentally to analyse the structure of DNA:RNA hybrids (S1 nuclease mapping, Berk-Sharp technique), and to remove single-stranded extensions from DNA to produce blunt ends (see restriction endonucleases). ...
IDT Oligo Analyzer | ProgrammableWeb
Integrated DNA Technologies (IDT) is a company that manufactures and sells oligonucleotides (short, single-stranded DNA or RNA molecules). On their website, they provide the Oligo Analyzer service, which can be used to examine an oligonucleotide (oligo) in a variety of ways. This service is primarily available through a web interface, but the Analyze, Hetero-Dimer, and Self-Dimer functions are also available as SOAP functions. The Analyze service returns physical properties of a given oligo sequence. The Hetero-Dimer examines possible duplexes when one oligo is combined with another. The Self-Dimer reports possible duplexes and their stabilities when an oligo hybridizes with itself ...
Difference between revisions of CH391L/S13/BioBricksAndRegistry - OpenWetWare
For example, to join together two BioBricks, you would first cut both plasmids with restriction enzymes, turning one into an insert by getting rid of the rest of the plasmid, and turning the other into a vector by opening a space in the plasmid in front of the BioBrick. Because As always pair with Ts and Gs always pair with Cs, the overhanging edges of single-stranded DNA that your restriction enzymes left behind will match up to make double stranded DNA. You then mix together the insert and vector with a special enzyme called a ligase that can join together two broken pieces of DNA. The result is a composite plasmid that contains two BioBricks, now side by side . It is important to note that this new larger composite part has the same restriction sites as the smaller parts it was originally made from. This is what is meant by preserving key structural elements that allow one component of any size to be easily connected to any other component. Also note that the scar ...
The first model describes the dynamic behavior of the virus production in terms of the law of mass action (Sidorenko & Reichl 2004). Therefore the temporal changes in concentrations of titrated plasmids, synthesized proteins, replicated single-stranded DNA and formed virus capsids and finally concentration of viral particles are simulated using MathWorks® MATLAB R2010b ...
Manual Screening Of Aggregates
Screening is an important part of processing and is used to separate material according to its size. Material is typically fed to a single-, double- or triple-deck screen to make the required sizes. Screens can be considered the cashbox of the operation, because while crushers make the gradation, screens make the specification. Material must go through or over a specified size to Get price ...
ChefsChoice Trizor XV EdgeSelect Sharpener Gray 15 - Best Buy
CHEFSCHOICE Trizor XV EdgeSelect Sharpener: 3-stage process; combines the power of the triple-bevel Trizor edge with 15-degree, EdgeSelect technology; converts 20-degree edges, as well as double- and single-bevel edges, into Trizor edges
Disassembly of Escherichia coli RecA E38K/DeltaC17 nucleoprotein filaments is required to complete DNA strand exchange. -...
Disassembly of RecA protein subunits from a RecA filament has long been known to occur during DNA strand exchange, although its importance to this process has been controversial. An Escherichia coli RecA E38K/DeltaC17 double mutant protein displays a unique and pH-dependent mutational separation of DNA pairing and extended DNA strand exchange. Single strand DNA-dependent ATP hydrolysis is catalyzed by this mutant protein nearly normally from pH 6 to 8.5. It will also form filaments on DNA and promote DNA pairing. However, below pH 7.3, ATP hydrolysis is completely uncoupled from extended DNA strand exchange. The products of extended DNA strand exchange do not form. At the lower pH values, disassembly of RecA E38K/DeltaC17 filaments is strongly suppressed, even when homologous DNAs are paired and available for extended DNA strand exchange. Disassembly of RecA E38K/DeltaC17 filaments improves at pH 8.5, whereas complete DNA strand exchange is also restored. Under these sets of conditions, a tight ...
A novel pairing process promoted by Escherichia coli RecA protein: inverse DNA and RNA strand exchange. - Semantic Scholar
Traditionally, recombination reactions promoted by RecA-like proteins initiate by forming a nucleoprotein filament on a single-stranded DNA (ssDNA), which then pairs with homologous double-stranded DNA (dsDNA). In this paper, we describe a novel pairing process that occurs in an unconventional manner: RecA protein polymerizes along dsDNA to form an active nucleoprotein filament that can pair and exchange strands with homologous ssDNA. Our results demonstrate that this inverse reaction is a unique, highly efficient DNA strand exchange reaction that is not due to redistribution of RecA protein from dsDNA to the homologous ssDNA partner. Finally, we demonstrate that the RecA protein-dsDNA filament can also pair and promote strand exchange with ssRNA. This inverse RNA strand exchange reaction is likely responsible for R-loop formation that is required for recombination-dependent DNA replication.
Host genes involved in the replication of single-stranded DNA phage ϕK | SpringerLink
Using various replication mutants of E. coli, the host genes that participate in the replication of some K12-specific single-stranded DNA phages have been
Molecular determinants responsible for recognition of the single-stranded DNA regulatory sequence, χ, by RecBCD enzyme<...
TY - JOUR. T1 - Molecular determinants responsible for recognition of the single-stranded DNA regulatory sequence, χ, by RecBCD enzyme. AU - Handa, Naofumi. AU - Yang, Liang. AU - Dillingham, Mark S.. AU - Kobayashi, Ichizo. AU - Wigley, Dale B.. AU - Kowalczykowski, Stephen C.. PY - 2012/6/5. Y1 - 2012/6/5. N2 - The RecBCD enzyme is important for both restriction of foreign DNA and recombinational DNA repair. Switching enzyme function from the destructive antiviral state to the productive recombinational state is regulated by the recombination hotspot, χ (5′-GCTGGTGG-3′). Recognition of χ is unique in that it is recognized as a specific sequence within single-stranded DNA (ssDNA) during DNA translocation and unwinding by RecBCD. The molecular determinants of χ recognition and the subsequent alteration in function are unknown. Consequently, we mutated residues within the RecC subunit that comprise a channel where ssDNA is thought to be scanned for a χ sequence. These mutants were ...
Mammalian single-stranded DNA binding protein UP I is derived from the hnRNP core protein A1. - Fingerprint - University...
Fingerprint Dive into the research topics of Mammalian single-stranded DNA binding protein UP I is derived from the hnRNP core protein A1.. Together they form a unique fingerprint. ...
The meiosis-specific recombinase hDmc1 forms ring structures and interacts with hRad51. - Lancaster EPrints
Eukaryotic cells encode two homologs of Escherichia coli RecA protein, Rad51 and Dmc1, which are required for meiotic recombination. Rad51, like E.coli RecA, forms helical nucleoprotein filaments that promote joint molecule and heteroduplex DNA formation. Electron microscopy reveals that the human meiosis-specific recombinase Dmc1 forms ring structures that bind single-stranded (ss) and double-stranded (ds) DNA. The protein binds preferentially to ssDNA tails and gaps in duplex DNA. hDmc1-ssDNA complexes exhibit an irregular, often compacted structure, and promote strand-transfer reactions with homologous duplex DNA. hDmc1 binds duplex DNA with reduced affinity to form nucleoprotein complexes. In contrast to helical RecA/Rad51 filaments, however, Dmc1 filaments are composed of a linear array of stacked protein rings. Consistent with the requirement for two recombinases in meiotic recombination, hDmc1 interacts directly with hRad51.. ...
JCI - Dominant mutations in mtDNA maintenance gene SSBP1 cause optic atrophy and foveopathy
Mutations in genes encoding components of the mitochondrial DNA (mtDNA) replication machinery cause mtDNA depletion syndromes (MDSs), which associate ocular features with severe neurological syndromes. Here, we identified heterozygous missense mutations in single-strand binding protein 1 (SSBP1) in 5 unrelated families, leading to the R38Q and R107Q amino acid changes in the mitochondrial single-stranded DNA-binding protein, a crucial protein involved in mtDNA replication. All affected individuals presented optic atrophy, associated with foveopathy in half of the cases. To uncover the structural features underlying SSBP1 mutations, we determined a revised SSBP1 crystal structure. Structural analysis suggested that both mutations affect dimer interactions and presumably distort the DNA-binding region. Using patient fibroblasts, we validated that the R38Q variant destabilizes SSBP1 dimer/tetramer formation, affects mtDNA replication, and induces mtDNA depletion. Our study showing that mutations in ...
U.S. Patent: 5532001 - Stimulation of tanning by DNA fragments or single-stranded DNA - July 2, 1996
In one method, DNA fragments, of approximately 2-200 bases in length, or deoxynucleotides (single bases), are administered topically to the epidermis, either in a liposome preparation or in another appropriate vehicle, such as propylene glycol, in a quantity sufficient to enhance melanin production. As used herein, DNA fragments refers to single-stranded DNA fragments, double-stranded DNA fragments, a mixture of both single-and double-stranded DNA fragments, or deoxynucleotides. Deoxynucleotides refers to either a single type of deoxynucleotide or a mixture of different deoxynucleotides. The DNA fragments or deoxynucleotides can come from any appropriate source. For example, salmon sperm DNA can be dissolved in water, and then the mixture can be autoclaved to fragment the DNA. The fragments can additionally be UV-irradiated. The liposome preparation can be comprised of any liposomes which penetrate the stratum corneum and fuse with the cell membrane, resulting in delivery of the contents of ...
The structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus - University of St...
Canonical single-stranded DNA-binding proteins (SSBs) from the oligosaccharide/oligonucleotide-binding (OB) domain family are present in all known organisms and are critical for DNA replication, recombination and repair. The SSB from the hyperthermophilic crenarchaeote Sulfolobus solfataricus (SsoSSB) has a simple domain organization consisting of a single DNA-binding OB fold coupled to a flexible C-terminal tail, in contrast with other SSBs in this family that incorporate up to four OB domains. Despite the large differences in the domain organization within the SSB family, the structure of the OB domain is remarkably similar all cellular life forms. However, there are significant differences in the molecular mechanism of ssDNA binding. We have determined the structure of the SsoSSB OB domain bound to ssDNA by NMR spectroscopy. We reveal that ssDNA recognition is modulated by base-stacking of three key aromatic residues, in contrast with the OB domains of human RPA and the recently discovered ...
Simultaneous targeted exchange of two nucleotides by single-stranded oligonucleotides clusters within a region of about...
Transfection of cells with gene-specific, single-stranded oligonucleotides can induce the targeted exchange of one or two nucleotides in the targeted gene. To characterize the features of the DNA-repair mechanisms involved, we examined the maximal distance for the simultaneous exchange of two nucleotides by a single-stranded oligonucleotide. The chosen experimental system was the correction of a hprt- point mutation in a hamster cell line, the generation of an additional nucleotide exchange at a variable distance from the first exchange position and the investigation of the rate of simultaneous nucleotide exchanges. The smaller the distance between the two exchange positions, the higher was the probability of a simultaneous exchange. The detected simultaneous nucleotide exchanges were found to cluster in a region of about fourteen nucleotides upstream and downstream from the first exchange position. We suggest that the mechanism involved in the repair of the targeted DNA strand utilizes only a short
Enzymatic production of single-stranded DNA as a target for fluorescence in situ hybridization<...
TY - JOUR. T1 - Enzymatic production of single-stranded DNA as a target for fluorescence in situ hybridization. AU - van Dekken, H.. AU - Pinkel, D.. AU - Mullikin, J.. AU - Gray, J. W.. PY - 1988/9/1. Y1 - 1988/9/1. N2 - This study demonstrates that Exonuclease III (Exo III) can be used to produce sufficient single-stranded (ss)DNA in chromosomes and cells to allow in situ hybridization. In this study, all of the probes were modified with biotin and the probe binding was visualized with fluorescein-labeled avidin. Exo III digestion starting at naturally occurring breaks in methanol-acetic acid preparations produced enough ssDNA for strong hybridization when human genomic DNA was used to probe human chromosomes. Pretreatment with the endonucleases EcoRI, Hind III and BamHI was used to produce more sites for initiation of Exo III digestion when using a chromosome-specific repetitive probe specific to a small chromosomal subregion near the telomere of human chromosome 1(1p36). The fluorescence ...
IMPC Paper Archives - IMPC | International Mouse Phenotyping Consortium
The CRISPR/Cas9 system used in conjunction with single stranded DNA donors is revolutionising our ability to generate targeted mutations directly in the embryo. Whilst short synthetic DNA molecules facilitate this, the use of longer single-stranded DNA donors is a more recent addition to the genome editing toolbox. The two new articles summarised here compare long and short single-stranded donors in a high-throughput setting, both look at conditional knock-out mutants while also presenting advances for the generations of point mutations.. In the first study, led by researchers in Lydia Tebouls group at the MRC Harwell institute, long single-stranded molecules are utilised to facilitate the generation of conditional alleles. They also apply the system to the introduction of point mutations remote from the recognition site of active Cas9/sgRNA complexes, which up to now has not been possible. This last technique is particularly valuable for human genomic sequencing since it enhances our ability ...
Nucleic acid hybridization - Wikipedia
In molecular biology, hybridization (or hybridisation) is a phenomenon in which single-stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) molecules anneal to complementary DNA or RNA. Though a double-stranded DNA sequence is generally stable under physiological conditions, changing these conditions in the laboratory (generally by raising the surrounding temperature) will cause the molecules to separate into single strands. These strands are complementary to each other but may also be complementary to other sequences present in their surroundings. Lowering the surrounding temperature allows the single-stranded molecules to anneal or hybridize to each other. DNA replication and transcription of DNA into RNA both rely upon nucleotide hybridization, as do molecular biology techniques including Southern blots and Northern blots, the polymerase chain reaction (PCR), and most approaches to DNA sequencing. Hybridization is a basic property of nucleotide sequences and is taken advantage of ...
Frontiers | A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection...
The initiation of an immune response is dependent on the activation and maturation of dendritic cells after sensing pathogen associated molecular patterns by pattern recognition receptors. However, the response needs to be balanced as excessive pro-inflammatory cytokine production in response to viral or stress-induced pattern recognition receptor signaling has been associated with severe influenza A virus (IAV) infection. Here, we use an inhibitor of Toll-like receptor (TLR)3, a single-stranded oligonucleotide (ssON) with the capacity to inhibit certain endocytic routes, or a TLR3 agonist (synthetic double-stranded RNA PolyI:C), to evaluate modulation of innate responses during H1N1 IAV infection. Since IAV utilizes cellular endocytic machinery for viral entry, we also assessed ssONs capacity to affect IAV infection. We first show that IAV infected human monocyte-derived dendritic cells (MoDC) were unable to up-regulate the co-stimulatory molecules CD80 and CD86 required for T cell activation.
Biology | Free Full-Text | A Comparison of Two Single-Stranded DNA Binding Models by Mutational Analysis of APOBEC3G
APOBEC3G is the best known of several DNA cytosine deaminases that function to inhibit the replication of parasitic genetic elements including the lentivirus HIV. Several high-resolution structures of the APOBEC3G catalytic domain have been generated, but none reveal how this enzyme binds to substrate single-stranded DNA. Here, we constructed a panel of APOBEC3G amino acid substitution mutants and performed a series of biochemical, genetic, and structural assays to distinguish between
recA - Protein RecA - Mycobacterium avium (strain 104) - recA gene & protein
Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage.
recA - Protein RecA - uncultured bacterium - recA gene & protein
Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage.
Programming nanoparticle valence bonds with single-stranded DNA encoders | Nature Materials
Nature has evolved strategies to encode information within a single biopolymer to program biomolecular interactions with characteristic stoichiometry, orthogonality and reconfigurability. Nevertheless, synthetic approaches for programming molecular reactions or assembly generally rely on the use of multiple polymer chains (for example, patchy particles). Here we demonstrate a method for patterning colloidal gold nanoparticles with valence bond analogues using single-stranded DNA encoders containing polyadenine (polyA). By programming the order, length and sequence of each encoder with alternating polyA/non-polyA domains, we synthesize programmable atom-like nanoparticles (PANs) with n-valence that can be used to assemble a spectrum of low-coordination colloidal molecules with different composition, size, chirality and linearity. Moreover, by exploiting the reconfigurability of PANs, we demonstrate dynamic colloidal bond-breaking and bond-formation reactions, structural rearrangement and even the
Detection of cell cycle stages in situ in growing cell populations - Oxford Neuroscience
Microscopic in situ detection of the cell cycle stages is based on immunocytochemical techniques and allows one to determine the stage of the cell cycle of individual cells. Based on pKi-67 immunostaining, one can distinguish between proliferating and quiescent cells and identify cells in early G1. Denaturation is a critical step of detection because it can negatively affect preservation of cell morphology. In particular, incubation of cells in 2N HCl for 30-60 min strongly impairs cell and nuclear morphology and, therefore, should be avoided in assays where the conservation of cell morphology is important. Epitops of Ki-67 protein is stable and the protein can be detected after 0.1N HCl and denaturation steps with heat denaturation or DNase. Therefore, pKi-67 immunostaining can be performed either simultaneously or after detection of incorporated halogenated thymidine analogs. The antibody to BrdU supplied with the kit contains nucleases generating single-stranded DNA fragments in the nucleus. © 2006
Omics analysis nurtures the creation of functional plants
Omics is a science that comprehensively embraces the four disciplines of genomics, transcriptomics, proteomics and metabolomics (Fig. 2), and has developed rapidly in the past decade triggered by improvements in genome decoding techniques and processing speed. These improvements have led to some remarkable milestones in genomic research, including sequencing of the complete genomes of the flowering plant Arabidopsis thaliana, rice and soy-bean.. Similarly, the DNA microarray technique used in transcriptome analysis, the analysis of RNA transcribed from DNA, has also improved dramatically over the past decade. In this technique, hundreds of thousands of single-stranded DNA fragments are fixed in holes or spots on a glass substrate, and fluorescently labeled RNA are dropped onto the substrate surface. RNA complementary to a DNA fragment will become bound to the DNA, which causes the combined compound to emit fluorescent light. From the fluorescence intensity of each spot, researchers can ...
All authors have read and approved the manuscript Backgro | FLT-3 inhibitors
Background Single-stranded DNA-binding (SSB) proteins play an essential role in all in vivo processes involving ssDNA. They interact with ssDNA and RNA, in an independent from sequence manner, preventing single-stranded nucleic acids from hybridization and degradation. by nucleases . SSB proteins play a central role in DNA replication, repair and recombination [2-4]. They have been identified in all classes of organisms, performing similar functions but displaying little sequence similarity and very different ssDNA binding properties. Based on their oligomeric state, SSBs can be classified into four groups: monomeric, homodimeric, heterotrimeric and homotetrameric. A prominent feature of all SSBs is that the DNA-binding domain is made up of a conserved motif, the OB (oligonucleotide binding) ICG-001 chemical structure fold . Most of the bacterial SSBs exist as homotetramers. However, recent discoveries have shown that. SSB proteins from the genera Thermus and Deinococcus possess a ...
For about 10 years until 2000, my labs research activities were focused on the mechanism of recombinational repair of double-strand breaks in DNA. We focused our efforts on two model systems: one involved the repair of restriction enzyme cleavages at specific mammalian chromosomal loci and the second explored the biochemical properties of purified yeast Rad51 protein, an essential catalyst for synapsing the broken ends of DNA with an intact homologue of that sequence. We also explored the roles of Rad52 and PRA (single-strand DNA binding protein) in the repair process.In 2000, I became Emeritus Professor in Biochemistry and stepped down from the Directorship of the Beckman Center. Much of my activities since then have been involved in writing a biography of the genetics pioneer George Beadle, published in 2003, plus articles for other publications elaborating on Beadles legacy for todays science. Over the years I have been and continue to be an activist in public policy issues affecting ...
Most recent papers with the keyword mT | Read by QxMD
Hypertrophic pancreatic islets (PI) of Goto Kakizaki (GK) diabetic rats contain a lower number of β-cells vs. non-diabetic Wistar rat PI. Remaining β-cells contain reduced mitochondrial (mt) DNA per nucleus (copy number), probably due to declining mtDNA replication machinery, decreased mt biogenesis or enhanced mitophagy. We confirmed mtDNA copy number decrease down to ,30% in PI of one-year-old GK rats. Studying relations to mt nucleoids sizes, we employed 3D superresolution fluorescent photoactivable localization microscopy (FPALM) with lentivirally transduced Eos conjugate of mt single-stranded-DNA-binding protein (mtSSB) or transcription factor TFAM; or by 3D immunocytochemistry ...
Immunologic Detection of Single-Stranded DNA in Adeno-Associated Satellite Virions | The Journal of Immunology
Double diffusion experiments with antibodies to single-stranded (s-s) DNA confirmed physicochemical data that adeno-associated satellite virions contain s-s DNA but the DNA extracted from such virions is double-stranded. Positive immunologic reactions of intact virions with sera from man and mouse with autoimmune disease and specifically immunized rabbits are consistent with the hypothetical role if viruses as immunogens or as the antigenic participants of immunecomplex vasculitis.. ...
Meiosis-specific with OB domain-containing protein
Single-stranded DNA-binding protein required for homologous recombination in meiosis I. Required for double strand breaks (DSBs) repair and crossover formation and promotion of faithful and complete synapsis. Not required for the initial loading of recombinases but required to maintain a proper number of RAD51 and DMC1 foci after the zygotene stage. May act by ensuring the stabilization of recombinases, which is required for successful homology search and meiotic recombination. Displays Single-stranded DNA 3-5 exonuclease activity in vitro (By similarity ...
BioScience Dictionary :: D loop
A structure that can sometimes be seen on DNA which forms when a small area of the double-stranded molecule comes apart and becomes two single strands. The result is a structure shaped like the letter D. Single-stranded binding protein s are usually present to hold the strands apart for the purpose of DNA replication ...
Study About DNA: Base pairing
king interactions (hydrogen bonding merely provides specificity of the pairing, not stability). As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA. Long DNA helices with a high GC content have stronger-interacting strands, while short helices with high AT content have weaker-interacting strands. In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in some promoters, tend to have a high AT content, making the strands easier to pull apart. In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called Tm value). When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules have no single common shape, but some ...
E-Z 96® M13 DNA Kit - Omega Bio-tek
Omega Bio-teks E.Z.N.A.® M13 DNA Kits are designed to purify up to 10 µg of single-stranded DNA from up to 3 mL of phage supernatant. Yields of single-stranded DNA obtained using E.Z.N.A.® M13 DNA Kits are around 3-10 µg and reproducible when the isolations are performed from the same culture.. The E.Z.N.A.® M13 DNA Kit isolation procedures first call for the infected bacterial culture to be centrifuged to pellet the bacterial cells. MPG buffer is added to the supernatant to precipitate the phage particles. The samples are loaded on HiBind® M13 DNA Mini Columns or on to E-Z 96® DNA Plates. The specially designed HiBind® matrix will retain intact phage particles. These phage particles are lysed and bound to the HiBind® matrix after the addition of MPX Buffer. Contaminants such as protein are efficiently washed away with SPW Wash Buffer and pure ssDNA is eluted with Elution Buffer.. ...
Caratterizzazione funzionale e ricerca di partners proteici cellulari della subunit accessoria, UL44, della DNA polimerasi del...
How UL44 binds to DNA and the role of DNA binding in processivity function have not been yet elucidated. To begin to understand these mechanism, we characterized the interaction of UL44 with DNA by means of filter-binding assays and electrophoretic mobility shift assays (EMSA). We found that, similar to HSV-1 UL42, UL44 binds directly to DNA with nanomolar affinity in a manner that does not require ATP hydrolysis or accessory proteins. UL44 binds DNA as a dimer in a sequence-non specific manner and displays higher affinity for ds DNA compared to ss DNA. Affinity of UL44 for ds DNA decreases with increasing ionic strength and this effect is mediated by ion release, suggesting that DNA binding entails electrostatic interactions between the negatively charged phosphates on DNA backbone and the positive charge of basic residues on the back face and disordered loops of UL44 ...
DNA-Binding Proteins - DNA Binding Protein Summary Report | CureHunter
DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
RecA Homology Search is Promoted by Mechanical Stress Along the Scanned Duplex DNA
A RecA-single-stranded DNA (RecA-ssDNA) filament searches a genome for sequence homology by rapidly binding and unbinding double-stranded DNA (dsDNA) until homology is found. We demonstrate that pulling on the opposite termini (3′ and 5′) of one of the two DNA strands in a dsDNA molecule stabilizes the normally unstable binding of that dsDNA to non-homologous RecA-ssDNA filaments, whereas pulling on the two 3′, the two 5′, or all four termini does not. We propose that the outgoing strand in the dsDNA is extended by strong DNA-protein contacts, whereas the complementary strand is extended by the tension on the base pairs that connect the complementary strand to the outgoing strand. The stress resulting from different levels of tension on its constitutive strands causes rapid dsDNA unbinding unless sufficient homology is present ...
Genes on the rack Meldung Nanosystems Initiative Munich (NIM)
A feather-light touch The members of the Munich group are acknowledged masters of DNA origami. This methodology exploits the base-pairing properties of DNA for the construction of nanostructures from strands that fold up and pair locally in a manner determined by their nucleotide sequences. In the present case, the DNA sequences are programmed to interact with each other in such a way that the final structure is a molecular clamp that can be programmed to exert a defined force on a test molecule. To this end, a single-stranded DNA that contains a specific sequence capable of recruiting the molecule of interest spans from one arm of the clamp to the other. The applied force can then be tuned by changing the length of the single strand base by base. That is equivalent to stretching a spring ever so-o-o slightly, says Nickels. Indeed, by this means it is possible to apply extremely tiny forces between 1 and 15 pN (1 pN = one billionth of a Newton) - comparable in magnitude to those that act on ...
Rapid Editing and Evolution of Bacterial Genomes Using Libraries of Synthetic DNA - PubMed
Multiplex automated genome engineering (MAGE) is a powerful technology for in vivo genome editing that uses synthetic single-stranded DNA (ssDNA) to introduce targeted modifications directly into the Escherichia coli chromosome. MAGE is a cyclical process that involves transformation of ssDNA (by el …
3. Quality control
PhiX is a nontailed bacteriophage with a single-stranded DNA and a genome with 5386 nucleotides. PhiX is used as a quality and calibration control for sequencing runs. PhiX is often added at a low known concentration, spiked in the same lane along with the sample or used as a separate lane. As the concentration of the genome is known, one can calibrate the instruments. Thus, PhiX genomic sequences need to be removed before processing your data further as this constitutes a deliberate contamination [MUKHERJEE2015]. The steps involve mapping all reads to the known PhiX genome, and removing all of those sequence reads from the data.. However, your sequencing provider might not have used PhiX, thus you need to read the protocol carefully, or just do this step in any case.. ...
1. Viruses and other informational parasites are a fact of life 304. 2. Evolution drives diversity in viral strategies and host interactions 304. 3. Cellular defense often involves recognizing nucleic acid structures that are indicative of unwanted information duplication 305. 3.1 Double-stranded RNA (dsRNA) 305. 3.2 Single-stranded DNA (ssDNA) 305. 3.3 Unspliced mRNAs 306. 3.4 Polycistronic mRNAs 306. 3.5 Multi-copy DNAs 306. 3.6 Other structures 306. 4. dsRNA as a case study: building a multilevel response to foreign structure 306. 5. Getting there is half the fun: disseminated immunity in RNAi 308. 6. Viruses strike back … so why do we still get sick? 308. Cells face a constant struggle against unwanted instructions that arrive in the form of viruses and transposons. At the core of this battle are two issues: how can cellular machinery recognize certain informational molecules as unwanted and how can the cell use this recognition to effectively silence malicious genetic activity. While ...
luciferase | AlleleBlog
RNases are an often feared in molecular biology labs because of their high stability and ominous presence in virtually all living systems. Consequently, people who work with RNA are trained to exercise extreme caution to avoid RNA degradation: change gloves often because human hands ooze RNases; use only sterilized labware as microbes may be sources of RNases; for surfaces that cant be autoclaved, use sprays like RNase Zap (SDS- or guanidine-containing solutions). Such cautionary steps are especially necessary when dealing with low abundance RNA samples.. RNAs can be produced by in vitro transcription (IVT), a simple reaction requiring only a DNA template (double-stranded or even single-stranded DNA as long as the promoter region is double-stranded), RNA polymerase (from T7, SP6, or T3 phage), NTPs, and a reaction buffer that provides appropriate salt and pH. Standard NTPs may be replaced with modified ones to either increase stability or to reduce immune-response when transfected into ...
ODN 2088 Control (ODN 2087) - TLR7/8/9 Antagonists - TLR Ligands - Stimulation reagents - MACS Cell Culture and Stimulation -...
TLR7/8/9 antagonists consist of short single-stranded oligodeoxynucleotides. They can inhibit CpG ODN-mediated activation of TLR9 and/or activation of TLR7/8. ODN 2088 Control (ODN 2087) is a TLR7/8 antagonist, but also acts as a TLR9 antagonist control. The sequence does not form G-Tetrads. - USA
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OBFC1, 0.25 mg. CST complex subunit STN1, also known as OBFC1, is a component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation.
ATCC ® 77138™
ATCC ® 77138™ Designation: pRS303 TypeStrain=False Application: YI-type (integrating) shuttle vector shuttle vector vector containing primer sites useful for sequencing vector permitting RNA synthesis in vitro vector permitting production of single-stranded DNA vector permitting visual detection of recombinants
Kavli B et. al. (2002) hUNG2 is the major repair enzyme for removal of uracil from U:A matches, U:G mismatches, and U in single-stranded DNA, with hSMUG1 as a broad specificity backup.. [^] ...
Difference between revisions of Jens Smiatek - ICPWiki
Unfolding pathways and the free energy landscape of a single-stranded DNA i-motif, From Computational Biophysics to Systems Biology (CBSB11), IAS Series 8, 201 (2012 ...
Synthesis of Single-Stranded RNA Probes by In Vitro Transcription
Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
Entecavir (ETV) | Drug Guide - MedSchool
Prevents viral reverse transcription of single-stranded RNA into double-stranded DNA, by inhibiting HIV reverse transcriptase ...
RNase A, without DNase and protease, is an endoribonuclease that specifically degrades the C and U residues of single-stranded RNA. It can cleave the phosphodiester bond between th
DNA Probes: Labelling, Types And Uses
DNA probes are the known short, single-stranded, labelled DNA sequences used to detect the presence or absence of nucleic acid in a sample.
... is single-stranded, and topologically a circle. That is, the DNA single strand extends from one end of the phage particle to ... Wen JD, Gray DM (March 2004). "Ff gene 5 single-stranded DNA-binding protein assembles on nucleotides constrained by a DNA ... Gray CW (July 1989). "Three-dimensional structure of complexes of single-stranded DNA-binding proteins with DNA. IKe and fd ... The single-stranded Ff phage DNA runs down the central core of the phage, and is protected by a cylindrical protein coat built ...
Reineck P, Wienken CJ, Braun D (January 2010). "Thermophoresis of single stranded DNA". Electrophoresis. 31 (2): 279-286. doi: ... A short introduction to thermophoresis, including helpful animated graphics, is at aerosols.wustl.edu Thermophoresis of DNA in ... Thamdrup LH, Larsen NB, Kristensen A (February 2010). "Light-Induced Local Heating for Thermophoretic Manipulation of DNA in ... Furthermore, thermophoresis has been demonstrated as a versatile technique for manipulating single biological macromolecules, ...
Single stranded closed circular DNA. Many begomoviruses have a bipartite genome: this means that the genome is segmented into ... Briddon RW, Stanley J (January 2006). "Subviral agents associated with plant single-stranded DNA viruses". Virology. 344 (1): ... Briddon RW, Patil BL, Bagewadi B, Nawaz-ul-Rehman MS, Fauquet CM (2010). "Distinct evolutionary histories of the DNA-A and DNA- ... of virion strand DNA replication. Component exchange (pseudorecombination) occurs in this genus. The usual mechanism of ...
Class II: Single-stranded DNA. These viruses only replicate in the nucleus. A double-stranded intermediate is formed during the ... Class VI: Single-stranded positive-sense RNA with DNA intermediate. These viruses use reverse transcriptase to convert the ... Class VII: Double-stranded DNA with RNA intermediate. The genome of these viruses are gapped, double-stranded, and subsequently ... replication process that serves as a template for the synthesis of virus's single-stranded DNA. Class III: Double-stranded RNA ...
Reineck P, Wienken CJ, Braun D (2010). "Thermophoresis of single stranded DNA". Electrophoresis. 31 (2): 279-86. doi:10.1002/ ... DNA, RNA, peptides, small molecules, fragments and ions for interactions with high molecular weight complexes, large molecule ... "Thermophoretic melting curves quantify the conformation and stability of RNA and DNA". Nucleic Acids Res. 39 (8): e52. doi: ...
... double-stranded DNA viruses; (II) single-stranded DNA viruses; (III) double-stranded RNA viruses; (IV) positive-sense single- ... negative-sense single-stranded RNA viruses; (VI) positive-sense single-stranded RNA viruses that replicate through a DNA ... double-stranded DNA viruses that replicate through a single-stranded RNA intermediate. The greatest share of bat-associated ... A single bat can host several different kinds of viruses without becoming ill. Bats have also been shown to be more susceptible ...
Partly double-stranded DNA viruses: Hepadnaviridae. These viruses are enveloped. One family of single-stranded DNA viruses ... Both of these taxa are non-enveloped single-stranded DNA viruses. Human-infecting virus families offer rules that may assist ... Double-stranded DNA families: three are non-enveloped (Adenoviridae, Papillomaviridae and Polyomaviridae) and two are enveloped ... Positive single-stranded RNA families: three non-enveloped (Astroviridae, Caliciviridae and Picornaviridae) and four enveloped ...
The Single-Stranded DNA Phages. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. OCLC 4491528, ISBN 0-87969-122-0 ... Comprehensive Virology: Reproduction of Bacterial DNA Viruses. Plenum Press, New York. OCLC 2331482, ISBN 0-306-35147-1, Google ...
Some cleave only double-stranded DNA; others are specific for single-stranded molecules; and still others are active toward ... The resulting DNA-protein extract is highly viscous and difficult to purify, in which case DNase is added. The DNA is ... is an enzyme that catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone, thus degrading DNA. ... DNA absorbs UV light with a wavelength of maximal absorbance near 260 nm. This absorption is due to the pi electrons in the ...
Note that conceptually, DNA single stranded origami is more related to RNA origami than DNA origami. Though RNA nanotechnology ... "Single-stranded DNA and RNA origami". Science. 358 (6369): eaao2648. doi:10.1126/science.aao2648. ISSN 0036-8075. PMC 6384012. ... More recently, RNA origami was extended to the design of long single stranded RNA sequences able to fold into large pre-defined ... TectoRNAs are typically originating from single stranded RNA molecules and once folded, they act like LEGO bricks to build up ...
... double-stranded DNA (persistence length 40-50 nm) and RNA (persistence length 64 nm) single-stranded DNA (persistence length 4 ... Chen, Huimin; Meisburger, Steve P. (2011). "Ionic strength-dependent persistence lengths of single-stranded RNA and DNA". PNAS ... Bernard, Tinland (1997). "Persistence Length of Single-Stranded DNA". Macromolecules. doi:10.1021/ma970381+. ... "Single-Molecule Measurements of the Persistence Length of Double-Stranded RNA". Biophysical Journal. 88: 2737-2744. Bibcode: ...
They have linear, single-stranded DNA (ssDNA) genomes that typically contain two genes encoding for a replication initiator ... Parvoviruses have linear, single-stranded DNA (ssDNA) genomes that are about 4-6 kilobases (kb) in length. The parvovirus ... "Recombination in eukaryotic single stranded DNA viruses". J Gen Virol. 3 (9): 1699-1738. doi:10.3390/v3091699. PMC 3187698. ... Genomic DNA strands in mature virions may be positive-sense or negative-sense. This varies from species to species as some have ...
... double-stranded RNA virus. The genome is segmented. Circoviruses are small single-stranded DNA viruses. There are to genera: ... Parvoviruses are linear, non-segmented single-stranded DNA viruses, with an average genome size of 5000 nucleotides. They are ... Pestiviruses have a single stranded, positive-sense RNA genomes. They cause Classical swine fever (CSF) and Bovine viral ... African swine fever virus (ASFV) is a large double-stranded DNA virus which replicates in the cytoplasm of infected cells and ...
Reverse transcription first generates a DNA template from the mRNA; this single-stranded template is called cDNA. The cDNA ... upstream on the DNA (towards the 5' region of the sense strand). Other important cis-regulatory modules are localized in DNA ... The production of a RNA copy from a DNA strand is called transcription, and is performed by RNA polymerases, which add one ... In prokaryotes, transcription is carried out by a single type of RNA polymerase, which needs to bind a DNA sequence called a ...
PAGEV RNA motif
Single-stranded DNA can occur during plasmid replication. Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins ... its potential relationship to plasmid replication leaves open the possibility that it functions as a single-stranded DNA. In ... terms of secondary structure, RNA and DNA are difficult to distinguish when only sequence information is available. ...
... es have a circular, single-stranded DNA genome. The genome is negative-sense. Postweaning multisystemic wasting ... DNA loads in serum of healthy and postweaning multisystemic wasting syndrome (PMWS) affected pigs" (PDF). Vet. Microbiol. 152 ( ...
"AID mediates hypermutation by deaminating single stranded DNA". The Journal of Experimental Medicine. 197 (10): 1291-1296. doi: ... Papavasiliou, F. Nina; Schatz, David G. (November 2000). "Cell-cycle-regulated DNA double-strand breaks in somatic ... in DNA, which is recognized as DNA damage and repaired in such a way that introduces thymidine (T), effectively mutating Cs to ... She is best known for her work in the fields of DNA and RNA editing. Papavasiliou received her Bachelors of Science from ...
Reduced representation bisulfite sequencing
Bisulfite sequencing only converts single-stranded DNA (ssDNA). Complete bisulfite conversion requires thorough denaturation ... End repair and A-tailing: Due to the nature of how MspI cleaves double stranded DNA, this reaction results in strands with ... Using MspI to digest genomic DNA results in fragments that always start with a C (if the cytosine is methylated) or a T (if a ... End repair is necessary to fill in the 3' terminal of the ends of the strands. The next step is adding an extra adenosine to ...
The encoded protein may bind single-stranded DNA. Model organisms have been used in the study of RTF1 function. A conditional ... De Jong, R. N.; Truffault, V.; Diercks, T.; Ab, E.; Daniels, M. A.; Kaptein, R.; Folkers, G. E. (2008). "Structure and DNA ... DNA Research. 3 (5): 321-329, 341-329. doi:10.1093/dnares/3.5.321. PMID 9039502. v t e. ...
Reduced dimensions form
... and Single-Stranded DNA Polymers". Physical Review Letters. American Physical Society (APS). 92 (4): 048303. doi:10.1103/ ... Tang, Jau; Marcus, R. A. (2005-11-22). "Single particle versus ensemble average: From power-law intermittency of a single ... "Counting statistics of single molecule reaction events and reaction dynamics of a single molecule". Chemical Physics Letters. ... Colquhoun, D.; Hawkes, A. G. (1982-12-24). "On the Stochastic Properties of Bursts of Single Ion Channel Openings and of ...
... single stranded DNA binding protein 3". Wu L (January 2006). "Structure and functional characterization of single-strand ... Single-stranded DNA-binding protein 3 is a protein that in humans is encoded by the SSBP3 gene. GRCh38: Ensembl release 89: ... Raval-Fernandes S, Kickhoefer VA, Rome LH (September 1999). "Cloning of a cDNA encoding a sequence-specific single-stranded-DNA ... evolutionarily conserved gene family with putative sequence-specific single-stranded DNA-binding activity". Genomics. 80 (1): ...
... is a family of single-stranded DNA viruses. The genomes of this family are small (2.3-2.8 kilobases in length). ... The genomes are circular single-stranded DNA and encode rolling-circle replication initiation proteins (Rep) and unique capsid ... These viruses have single stranded genomes of 2.3-2.8 kilobases in length. The genome encodes six proteins including a Rep ( ...
Single-stranded DNA-binding protein 2 is a protein that in humans is encoded by the SSBP2 gene. GRCh38: Ensembl release 89: ... "Entrez Gene: SSBP2 single-stranded DNA binding protein 2". Hu RM, Han ZG, Song HD, et al. (2000). "Gene expression profiling in ... 2007). "Adenoviral E1B55K oncoprotein sequesters candidate leukemia suppressor sequence-specific single-stranded DNA-binding ... evolutionarily conserved gene family with putative sequence-specific single-stranded DNA-binding activity". Genomics. 80 (1): ...
... is a family of single stranded DNA viruses. The genomes of this family are small (2.2-2.4 kilobases in length). ... Krupovic M, Ghabrial SA, Jiang D, Varsani A (2016). "Genomoviridae: a new family of widespread single-stranded DNA viruses". ... The genomes are circular single-stranded DNA and encode rolling-circle replication initiation proteins (Rep) and unique capsid ... "Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae ...
The specific systems studied by him include RecA, RuvA, uracil DNA glycosylase, single stranded DNA binding protein, ribosome ... "Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its ... "Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: ... "Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: Structure of a complex of the ...
Single-stranded DNA-binding protein, mitochondrial is a protein that in humans is encoded by the SSBP1 gene. SSBP 1 is a ... "Entrez Gene: SSBP1 single-stranded DNA binding protein 1". Tiranti V, Rocchi M, DiDonato S, Zeviani M (April 1993). "Cloning of ... Diez-Tascón C, Dodds KG, Crawford AM (December 2002). "Linkage mapping of the ovine single-stranded DNA-binding protein 1 ( ... Yang C, Curth U, Urbanke C, Kang C (February 1997). "Crystal structure of human mitochondrial single-stranded DNA binding ...
This is done to make DNA fragments in blunt ends. HaeIII is not effective for single stranded DNA cleavage. HaeIII has a ... Blakesley RW, Dodgson JB, Nes IF, Wells RD (October 1977). "Duplex regions in "single-stranded" phiX174 DNA are cleaved by a ... HaeIII cuts both strands of DNA in the same location, yielding restriction fragments with blunt ends. Heat denaturation occurs ... The enzyme's recognition site-the place where it cuts DNA molecules-is the GGCC nucleotide sequence which means it cleaves DNA ...
... s bind to either RNA or single stranded DNA. The nucleic acid is bound in an extended conformation across one side of ... The type I KH domains have a three stranded beta-sheet where all three strands are anti-parallel. In the type II domain two of ... "Nucleic acid base-to-protein aromatic side chain stacking interactions which are prevalent in other types of single stranded ... While type I domains are usually found in multiple copies within proteins, the type II are typically found in a single copy per ...
Unlike the diagram, the probe binds to single stranded DNA.) TaqMan probes can be conjugated to a minor groove binder (MGB) ... As the Taq polymerase extends the primer and synthesizes the nascent strand (again, on a single-strand template, but in the ... TaqMan probes are designed such that they anneal within a DNA region amplified by a specific set of primers. ( ... Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures". Nucleic Acids Res. 28 (2): 655-661 ...
DNA polymerase turns single-stranded DNA into double-stranded DNA. Helicases separate double strands of nucleic acids prior to ... cyclically driving it from B-DNA to A-DNA and back again. A-DNA is 23% shorter than B-DNA, and the DNA shrink/expand cycle is ... transitions between A-DNA and B-DNA provide the driving force for genome packaging in double-stranded DNA bacteriophages". ... Viral DNA packaging motors inject viral genomic DNA into capsids as part of their replication cycle, packing it very tightly. ...
1 DNA-Viren *1.1 Doppelsträngige DNA-Viren (dsDNA: double stranded DNA). *1.2 Einzelsträngige DNA-Viren (ssDNA: single stranded ... Einzelsträngige DNA-Viren (ssDNA: single stranded DNA)[Bearbeiten , Quelltext bearbeiten]. Viren mit Einzelstrang-DNA-Genom ... Viren mit DNA-Genom bilden keine taxonomische Einheit. Doppelsträngige DNA-Viren (dsDNA: double stranded DNA)[Bearbeiten , ... Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA ...
... viruses contain single-stranded, non-infectious RNA genomes. Ebolavirus genomes contain seven genes including 3'-UTR- ... December 1999). "Identification of Ebola virus sequences present as RNA or DNA in organs of terrestrial small mammals of the ... Replication of the viral genome results in full-length, positive-strand antigenomes that are, in turn, transcribed into genome ... partially uncoats the nucleocapsid and transcribes the genes into positive-strand mRNAs, which are then translated into ...
DNA becomes susceptible to deamination events when it is single stranded. When replication forks form, the strand not being ... Segments with labels on the inside reside on the B strand of DNA, segments with labels on the outside are on the A strand. ... DNA replicationEdit. Leading model of cpDNA replicationEdit. Chloroplast DNA replication via multiple D loop mechanisms. ... As in prokaryotes, genes in chloroplast DNA are organized into operons. Introns are common in chloroplast DNA molecules, ...
Category:DNA - Simple English Wikipedia, the free encyclopedia
Single nucleotide polymorphism. T. *Tandem repeat. *Transcription factor. Τ. *Template:Single strand DNA discovery ... Pages in category "DNA". The following 33 pages are in this category, out of 33 total. ... Retrieved from "https://simple.wikipedia.org/w/index.php?title=Category:DNA&oldid=4367965" ...
In Inuit creation myths, when 'Big Raven', a deity in human form, found a stranded whale, he was told by the Great Spirit where ... A single specimen can reportedly fetch up to US$100,000 (UK£64,160) on the market. The beluga's popularity is due to its unique ... "More DNA support for a Cetacea/Hippopotamidae clade: the blood-clotting protein gene gamma-fibrinogen" (PDF). Molecular ... Another, unsuccessful, attempt was made by the U.S.  One stranded humpback whale calf was kept in captivity for ...
Fluorescence in situ hybridization
In biology, a probe is a single strand of DNA or RNA that is complementary to a nucleotide sequence of interest. ... Single-molecule RNA FISH. Single-molecule RNA FISH, also known as Stellaris® RNA FISH, is a method of detecting and ... Probe size is important because longer probes hybridize less specifically than shorter probes, so that short strands of DNA or ... Repetitive DNA sequences must be blocked by adding short fragments of DNA to the sample. The probe is then applied to the ...
RNA polymerase - Simple English Wikipedia, the free encyclopedia
With the help of some other molecules, it makes messenger RNA from a strand of a DNA. This is its main function, but it does ... Eukaryotic mitochondria contain an unrelated RNAP (member of the "single-subunit RNAP" protein family). ... It is building a messenger RNA molecule from a DNA helix. Part of the enzyme was made transparent so the RNA and DNA can be ... Herr A.J. et al (2005). "RNA polymerase IV directs silencing of endogenous DNA". Science 308 (5718): 118-20. doi:10.1126/ ...
single-stranded DNA binding. • double-stranded DNA binding. • single-stranded DNA-dependent ATPase activity. ... strand at the DSB to generate a 3' single-strand DNA overhang strand. ... strand displacement. • DNA synthesis involved in DNA repair. • interstrand cross-link repair. • response to glucoside. • DNA ... an ATP dependent DNA strand exchange takes place in which a template strand invades base-paired strands of homologous DNA ...
Their genome single-stranded (+) sense RNA is that functions as mRNA after entry into the cell and all viral mRNA synthesized ... and a poliovirus clone was the first infectious DNA clone made of an RNA virus in animals. Along with rhinovirus, poliovirus ... Step 2: The 3C dimer opens the RNA stem by forming a more stable interaction with single strands forming the stem. Step 3: ... Its genome is linear, single stranded positive sense RNA with a viral genome-linked protein (VPg) covalently linked at the 5' ...
Two groups of single-stranded DNA viruses that infect archaea have been recently isolated. One group is exemplified by the ... "Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome". Proceedings of the National ... Archaea can be infected by double-stranded DNA viruses that are unrelated to any other form of virus and have a variety of ... For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, revolutionized molecular ...
Death of Caylee Anthony
Jacqueline Fell, Adam Longo, Kelli Cook 20: Casey Anthony's defense begins case, challenges DNA evidence[dead link], Central ... Four hundred pieces of evidence were presented. A strand of hair was recovered from the trunk of Casey's car which was ... Mason's response was viewed as especially critical of Nancy Grace, whose news program is cited as having "almost single- ... Her attorney had argued that her false statements constituted a single offense; however, the appeals court noted she gave false ...
Compacting DNA strands. Histones act as spools around which DNA winds. This enables the compaction necessary to fit the ... The single-letter amino acid abbreviation (e.g., K for Lysine) and the amino acid position in the protein ... DNA damage. Marking sites of DNA damage is an important function for histone modifications. It also protects DNA from ... Bekker-Jensen S, Mailand N (Dec 2010). "Assembly and function of DNA double-strand break repair foci in mammalian cells". DNA ...
Nuclear magnetic resonance spectroscopy of nucleic acids
Dynamic properties such as duplex-single strand equilibria and binding rates of other molecules to duplexes can also be ... To overcome sever line-broadening in native DNA, sheer-degraded natural DNA was prepared and studied to learn about the ... "Use of two-dimensional NMR in the study of a double-stranded DNA". J. Am. Chem. Soc. 104 (20): 5540-5541. doi:10.1021/ ... For duplex DNA nonexchangeable protons the H6/H8 protons on the base correlate to their counterparts on neighboring bases and ...
If replacement clutch is laid, usually a single egg is laid which may weigh as little as 112 g (4.0 oz). Average ... An ancient DNA study published in 2015 characterized the rapidly evolving mitochondrial control region of one of these ... In this late summer stage, they may learn quickly to feed on stranded fish or to capture ducks flightless in eclipse. Juvenile ... Single or repeated krlee or similar component of calls used in other circumstances, but this can be very variable. Alarm calls ...
RNA polymerase - Simple English Wikipedia, the free encyclopedia
With the help of some other molecules, it makes messenger RNA from a strand of a DNA. This is its main function, but it does ... Eukaryotic mitochondria contain an unrelated RNAP (member of the "single-subunit RNAP" protein family). ... It is building a messenger RNA molecule from a DNA helix. Part of the enzyme was made transparent so the RNA and DNA can be ... X-ray crystallography of DNA and RNA polymerases show that, other than having a Mg2+ ion at the catalytic site, they are ...
فهرست یهودیان برنده جایزه نوبل - ویکیپدیا، دانشنامهٔ آزاد
"for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA" ... "for their discoveries relating to the highly differentiated functions of single آسهs" ... "for his discovery of آرانای سرکوبگر - gene silencing by double-stranded RNA" ...
This information allows one to be able to single out tea cakes produced using a better batch of máochá. ... and shaped into strands through several steps to lightly bruise the tea and then left to dry in the sun. Unlike green tea ... "Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history ... A small ball-shaped or rolled tea, convenient for a single serving. Generally balls contain between 5 and 10 grams of ...
배아줄기세포 - 위키백과, 우리 모두의 백과사전
... predominantly use homologous recombination to repair double-strand DNA breaks". 》Stem Cells and Development》 19 (11): 1699-1711 ... "MULTIPOTENTIALITY OF SINGLE EMBRYONAL CARCINOMA CELLS". 》Cancer Research》 24: 1544-1551. ISSN 0008-5472. PMID 14234000 ... DNA 손상 복구[편집]. 분화된 체세포와 배아줄기세포는 DNA 손상을 처리하기 위해 다른 전략을 사용한다. 예를 들어, 체세포의 한 유형인 인간 포피 섬유 아세포는 모든 세포주기 단계에서 이중 가닥 파손을 복구하기 위한 ... 결과적으로, DNA 손상을 정확하게 복구하기 위해서는 배아줄기세포에서 강력한 메커니즘이 필요하고, 복구가 실패하면 DNA가 손상된 그 세포를 제거하는 것이 필요하다. 따라서, 마우스 배아줄기세포는 주로 이중 가닥 파손을 고치기 ...
Such viruses are either single stranded RNA (e.g. HIV) or double stranded DNA (e.g. Hepatitis B virus) viruses. ... reverse transcriptase creates a complementary strand of DNA from the retrovirus RNA and the RNA is degraded; this strand of DNA ... The 3' end includes 3 regions, which are PPT (polypurine tract), U3, and R. The PPT is a primer for plus-strand DNA synthesis ... The virions also contain two identical single-stranded RNA molecules 7-10 kilobases in length. Although virions of different ...
... separating it into single DNA strands for later hybridization to the probe (see below), and destroys any residual RNA that may ... A probe that hybridizes only to a single DNA segment that has not been cut by the restriction enzyme will produce a single band ... The membrane is then exposed to a hybridization probe-a single DNA fragment with a specific sequence whose presence in the ... A Southern blot is a method used in molecular biology for detection of a specific DNA sequence in DNA samples. Southern ...
In wild-type S. cerevisiae, DNA damage rates increased 3-fold with age, but more than 5-fold in mutants deleted for either the ... It was the first SOD whose atomic-detail crystal structure was solved, in 1975. It is an 8-stranded "Greek key" beta-barrel ... Second, Mn SODs consist of a homodimer and homotetramer species each containing a single Mn(III) atom per subunit. They are ... Superoxide is known to denature enzymes, oxidize lipids, and fragment DNA. SODs catalyze the production of O2 and H2O2 from ...
ವಂಶವಾಹಿ - ವಿಕಿಪೀಡಿಯ
Belyi, V. A.; Levine, A. J.; Skalka, A. M. (22 September 2010). "Sequences from Ancestral Single-Stranded DNA Viruses in ... DNA study forces rethink of what it means to be a gene". Science 316 (5831): 1556-1557. doi:10.1126/science.316.5831.1556. PMID ... Stanley N. Cohen; Annie C. Y. Chang (1 May 1973). "Recircularization and Autonomous Replication of a Sheared R-Factor DNA ... Koonin, Eugene V.; Dolja, Valerian V.; Morris, T. Jack (January 1993). "Evolution and Taxonomy of Positive-Strand RNA Viruses: ...
... inducing double-strand DNA breaks which, when repaired, could result in a cell homozygous for one of the two alleles. After ... In the more common mosaics, different genotypes arise from a single fertilized egg cell, due to mitotic errors at first or ... "Every Cell in Your Body Has the Same DNA. Except It Doesn't". The New York Times. 21 May 2018. Archived from the original on 23 ... the defect in RecQ an helicase facilitates the defective unwinding of DNA during replication and is thus associated with the ...
The overall structure of RNA and DNA are immensely similar-one strand of DNA and one of RNA can bind to form a double helical ... Eigen et al. and Woese proposed that the genomes of early protocells were composed of single-stranded RNA, and that ... Influenza virus, whose genome consists of 8 physically separated single-stranded RNA segments, is an example of this type ... Main articles: RNA and DNA. The major difference between RNA and DNA is the presence of a hydroxyl group at the 2'-position of ...
Innate immune system
... that attack and destroy specific regions of the viral DNA of invading bacteriophages. Methylation of the host's own DNA marks ... single-cell organisms. Most leukocytes are able to move freely and interact with and capture cellular debris, foreign particles ... Toll-like receptors are located in the endosomal membrane and recognize double-stranded RNA (dsRNA), MDA5 and RIG-I receptors ...
LIG3, a enciclopedia libre
... polymerase 1 in DNA single-strand break repair". Mol. Cell. Biol. 23 (16): 5919-27. PMC 166336. PMID 12897160. doi:10.1128/MCB. ... "Defective DNA single-strand break repair in spinocerebellar ataxia with axonal neuropathy-1". Nature 434 (7029): 108-13. PMID ... "The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway". Annu. Rev. Biochem. 79: 181-211 ... "DNA ligase III is recruited to DNA strand breaks by a zinc finger motif homologous to that of poly(ADP-ribose) polymerase. ...
Tumor necrosis factor alpha
Single nucelotide polymorphism (rs1800629). Empty section References. *^ a b c ENSG00000230108, ENSG00000223952, ... transcription regulatory region DNA binding. • protein binding. • protease binding. • tumor necrosis factor receptor binding. • ... are composed of two antiparallel β-pleated sheets with antiparallel β-strands, forming a 'jelly roll' β-structure, typical for ... positive regulation of transcription, DNA-templated. • positive regulation of transcription from RNA polymerase II promoter. • ...
Гольберг, Дмитрий Викторович - Википедия
Field emission properties of macroscopic single-walled carbon nanotube strands» Appl. Phys. Lett. 86 (2005) 223114-1 DOI: ... C. Zhi, Y. Bando, W. Wang, C. Tang, H. Kuwahara and D. Golberg : «DNA-Mediated Assembly of Boron Nitride Nanotubes» Chem. Asian ... W. L. Wang, X. D. Bai, K. H. Liu, Z. Xu, D. Golberg, Y. Bando and E. G. Wang : «Direct Synthesis of B−C−N Single-Walled ... J. Hu, Z. Chen, H. Chen, H. Chen, Y. Song, Y. Sun, R. Zou, J. Ni, B. Dierre, T. Sekiguchi, D. Golberg and Y. Bando : «Single- ...
Cells have mechanisms for repairing single-strand DNA damage and double-stranded DNA damage. However, double-stranded DNA ... Single-strand DNA damage is then passed on through cell division; damage to the cancer cells' DNA accumulates, causing them to ... Radiation therapy works by damaging the DNA of cancerous cells. This DNA damage is caused by one of two types of energy, photon ... Charged particles such as protons and boron, carbon, and neon ions can cause direct damage to cancer cell DNA through high-LET ...
Replication follows the DNA strand displacement, via replicative transposition model. DNA-templated transcription is the method ... It has three long, kinked terminal fibers around 120 nm in length, and a single straight central fiber attached to a conical ... and degrades the cell wall using viral exolysin enough to eject the viral DNA into the host cytoplasm via long flexible tail ...
Multicopy single-stranded DNA - Wikipedia
Multicopy single-stranded DNA (msDNA) is a type of extrachromosomal satellite DNA that consists of a single-stranded DNA ... further extension of the DNA strand presents a problem: as DNA synthesis progresses, the bulky RNA strand extending from the 3 ... Hsu MY, Inouye M, Inouye S (December 1990). "Retron for the 67-base multicopy single-stranded DNA from Escherichia coli: a ... Yee T, Furuichi T, Inouye S, Inouye M (August 1984). "Multicopy single-stranded DNA isolated from a gram-negative bacterium, ...
Single-strand DNA-binding protein - Wikipedia
... that binds to single-stranded regions of deoxyribonucleic acid (DNA). Single-stranded DNA is produced during all aspects of DNA ... Binding of single-stranded DNA to the tetramer can occur in different "modes", with SSB occupying different numbers of DNA ... It has a structure of three beta-strands to a single six-stranded beta-sheet to form a protein dimer. DNA-binding protein ... "Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined ...
Single-stranded DNA Viruses
... Version 22 December 2005 (temporary). http://tolweb.org/Single-stranded_DNA_Viruses/21829/2005.12. ... Single-stranded DNA Viruses Click on an image to view larger version & data in a new window ... This electron micrograph depicts a number of parvovirus H-1 virions of the Parvoviridae family of DNA viruses. ... Single-stranded DNA Viruses Page Content. *Title Illustrations. *About This Page. articles & notes. *Single-stranded DNA ...
Single Stranded DNA Sequencing
... William R. Morgan wmorgan at ACS.WOOSTER.EDU Mon Sep 13 22:10:17 EST 1993 *Previous message: ... Picard cooperj at nhlbi.nih.gov (John Cooper) asks: ,Does any one know if single stranded sequencing is really superior to ds , ... Although CsCl-prepped DNA is obviously the best, for preparing multiple templates, we DNA prepared with the normal alkaline- ... sequencing? I think that you get the best consistency with single-strand templates. DS templates exhibit more variability. Its ...
Programming nanoparticle valence bonds with single-stranded DNA encoders | Nature Materials
Single-stranded DNA encoders containing polyadenine domains endow colloidal gold nanoparticles with programmable bond valence, ... Here we demonstrate a method for patterning colloidal gold nanoparticles with valence bond analogues using single-stranded DNA ... Nature has evolved strategies to encode information within a single biopolymer to program biomolecular interactions with ... Yao, G., Li, J., Li, Q. et al. Programming nanoparticle valence bonds with single-stranded DNA encoders. Nat. Mater. 19, 781- ...
Single vs. Double Stranded DNA
Double Stranded DNA. Anton Scott Goustin asg at cmb.biosci.wayne.edu Sun Nov 12 16:11:16 EST 1995 *Previous message: Single vs ... or renature as intramolecular ds DNA. This is a problem. *Previous message: Single vs. Double Stranded DNA ... I am looking for a way to distinguish double stranded PCR products from ,,single stranded primers and the unincorporated dNTPs ... Pieces of DS DNA ,1 kb may require heating up to 95oC to denature them. Warning: if the DNA contains any palindromes (invert ...
Single-Stranded DNA Binding Protein
DNA Binding Protein binds with high affinity to single-stranded DNA but does not bind well to double-stranded DNA. ... E. coli Single-Stranded DNA Binding Protein (SSB) consists of four identical 18.9kDa subunits that cooperatively bind to single ... stranded DNA with high affinity. This protein is involved in DNA replication and in recombination in vivo. ... Studying DNA replication and recombination. *DNA sequencing using the primer walking strategy with contiguous oligonucleotides ...
M13mp18 Single-stranded DNA | NEB
The single-stranded DNA is then extracted with phenol. ... M13mp18 is a M13 lac phage vector which contains single HindIII ... SacI and EcoRI sites within the gene encoding β-Galactosidase.This DNA preparation is useful as a standard and has been tested ... as a template in the dideoxy-nucleotide termination method of sequencing DNA. M13mp18 phage is propagated in E. coli ER2738. ... The single-stranded viral DNA is isolated from M13mp18. ... Substrates M13mp18 Single-stranded DNA M13mp18 Single-stranded ...
Anti-Single Stranded DNA Antibody
... , Anti-ssDNA Antibody, Single Stranded DNA antibody, Anti-ssDNA, Anti-Single Stranded DNA ... ss-DNA-Single-stranded DNA ab, antibodies dna single strand, antibody dna single strand, single stranded anti dna antibody, ... deoxyribonucleic acid single strand Antibody, DNA single strand Ab, Single stranded anti DNA antibody, Single-stranded DNA ... Anti-Single Stranded DNA Antibody. Aka: Anti-Single Stranded DNA Antibody, Anti-ssDNA Antibody, Single Stranded DNA antibody, ...
Ionic strength-dependent persistence lengths of single-stranded RNA and DNA | PNAS
Ionic strength-dependent persistence lengths of single-stranded RNA and DNA. Huimin Chen, Steve P. Meisburger, Suzette A. Pabit ... Ionic strength-dependent persistence lengths of single-stranded RNA and DNA. Huimin Chen, Steve P. Meisburger, Suzette A. Pabit ... Ionic strength-dependent persistence lengths of single-stranded RNA and DNA Message Subject (Your Name) has sent you a message ... 2004) Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. Biophys J 86:2530-2537. ...
Association of single-stranded transferred DNA from Agrobacterium tumefaciens with tobacco cells. | PNAS
After vir gene induction, both single-stranded (T-strands) and double-stranded forms of processed T-DNA accumulate in the ... PCR analysis of T-DNA associated with protoplasts indicates that single-stranded, but not double-stranded, T-DNA can be ... Association of single-stranded transferred DNA from Agrobacterium tumefaciens with tobacco cells.. V M Yusibov, T R Steck, V ... Association of single-stranded transferred DNA from Agrobacterium tumefaciens with tobacco cells. ...
An improved filamentous helper phage for generating single-stranded plasmid DNA. - PubMed - NCBI
An improved filamentous helper phage for generating single-stranded plasmid DNA.. Russel M, Kidd S, Kelley MR. ... However, technical difficulties have been a problem, primarily low yields of packaged single stranded (ss) plasmid DNA from the ... plasmid ss DNA is packaged and exported preferentially over phage ss DNA, and the absolute yield of plasmid ss DNA is usually ... and ambiguities in sequencing reactions attributed to the contamination by helper phage ss DNA. We report here the construction ...
RCSB PDB - Gene View - SSBP1 - single stranded DNA binding protein 1
Max Planck Team Reports Single-Stranded NGS Protocol for Ancient DNA | GenomeWeb
... a next-generation sequencing protocol that prepares libraries from single-stranded DNA as opposed to double-stranded DNA, a ... method that is particularly amenable to sequencing ancient DNA. ... from single-stranded DNA as opposed to double-stranded DNA, a ... Max Planck Team Reports Single-Stranded NGS Protocol for Ancient DNA. Apr 09, 2013 ... Home » Max Planck Team Reports Single-Stranded NGS Protocol for Ancient DNA ...
Researchers Characterize Behavior of Single-Stranded DNA Translocating Through a Nanopore | Genomeweb
... that single-stranded DNA produces larger spikes and has a longer translocation time through a nanopore than double-stranded DNA ... Single-stranded DNA behaves completely differently than double-stranded DNA as it translocates through a nanopore, researchers ... Next, the group tested single-stranded viral DNA. They translocated the DNA through a 7-nanometer pore and observed peaks that ... and produced a lower current spike than the single-stranded end. As the length of the single-stranded tail increased, the ...
Control of cross-over by single-strand DNA resection. - PubMed - NCBI
Control of cross-over by single-strand DNA resection.. Prado F1, Aguilera A. ... Extensive DNA resection could be an effective mechanism to prevent reciprocal exchanges between dispersed DNA sequences, and ... Control of DNA cross-overs is necessary for meiotic recombination and genome integrity. The frequency of cross-overs is ... Extensive DNA resection might favor gene conversion without cross-over by channeling recombination events through synthesis- ...
Is the M13mp18 Single-Stranded DNA (N4040S) circular or linear? | NEB
The M13mp18 Single-Stranded DNA is a circular molecule, purified from the M13mp18 phage. The vast majority of the molecules are ... FAQ: Is the M13mp18 Single-Stranded DNA (N4040S) circular or linear?. The M13mp18 Single-Stranded DNA is a circular molecule, ... Home FAQs Is the M13mp18 Single-Stranded DNA (N4040S) circular or linear? ... The presence of linear DNA is inherent to the purification process. Links to this resource. Related Products:. M13mp18 Single- ...
In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element Specific for Bromacil
... and functional aspects of DNA and RNA research. ... In Vitro Selection of a Single-Stranded DNA Molecular ... R. M. Williams, C. L. Crihfield, S. Gattu, L. A. Holland, and L. J. Sooter, "In vitro selection of a single-stranded DNA ... Towards this end, we have utilized a stringent in vitro selection method to identify single-stranded DNA molecular recognition ... This is best achieved through the selection of a stable single-stranded DNA (ssDNA) molecular recognition element (MRE). ...
RCSB PDB - 1AE3: MUTANT R82C OF GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN)
Synthetic long single-stranded and circular DNA
Improvements in DNA and RNA oligonucleotide synthesis methods enabled the production of long single-stranded DNA (ssDNA) and ... as well as circular DNA allow the study of these molecules in vitro and in vivo. ... circular DNA, such as catenanes, chain-like molecules. ... Synthetic long single-stranded and circular DNA. Synthetic long ... Extrachromosomal circular DNA in eukaryotes.. Falanga V, Medsger TA Jr, Reichlin M. Antinuclear and anti-single-stranded DNA ...
AICDA - Single-stranded DNA cytosine deaminase - Bos taurus (Bovine) - AICDA gene & protein
May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation. ... region DNA. Required for several crucial steps of B-cell terminal differentiation necessary for efficient antibody responses. ... Single-stranded DNA-specific cytidine deaminase. Involved in somatic hypermutation (SHM), gene conversion, and class-switch ... Single-stranded DNA cytosine deaminaseAdd BLAST. 199. Amino acid modifications. Feature key. Position(s). DescriptionActions. ...
SSBP2 - Single-stranded DNA-binding protein 2 - Homo sapiens (Human) - SSBP2 gene & protein
... single-stranded DNA binding, transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA ... binding, positive regulation of transcription by RNA polymerase II, regulation of transcription, DNA-templated ... RNA polymerase II proximal promoter sequence-specific DNA binding, ... Cluster: Single-stranded DNA-binding protein 4. 355. P81877-3. Q9BWW4. Q9D032. K7C1B4. H9Z778. K9IJI4. A0A2K5UU13. A0A2J8V926. ...
Cigarette smoke induces DNA single-strand breaks in human cells
... Nature. 1985 Apr 4-10;314(6010):462-4. doi: 10.1038/314462a0. ... However, there has been no previous direct demonstration that cigarette smoke can cause single-strand breaks (SSB) in DNA. Here ... we report that cigarette smoke induces considerable numbers of DNA SSB in cultured human cells, and that such strand breaks may ...
The HRDC domain of E. coli RecQ helicase controls single-stranded DNA translocation and double-stranded DNA unwinding rates...
... translocation along single-stranded (ss)DNA and/or unwinding of double-stranded (ds)DNA. Here, we determined how these ... Our data show that the HRDC domain suppresses the rate of DNA-activated ATPase activity in parallel with those of ssDNA ... These activities, driven by two tandem RecA-like core domains, are thought to be controlled by accessory DNA-binding elements ... DNA-restructuring activities of RecQ-family helicases play key roles in genome maintenance. ...
Addgene: AID mediates hypermutation by deaminating single stranded DNA.
TERRA and hnRNPA1 orchestrate an RPA-to-POT1 switch on telomeric single-stranded DNA
These two processes use two single-stranded DNA (ssDNA)-binding proteins, replication protein A (RPA) and protection of ... Maintenance of telomeres requires both DNA replication and telomere capping by shelterin. ... TERRA and hnRNPA1 orchestrate an RPA-to-POT1 switch on telomeric single-stranded DNA Nature. 2011 Mar 24;471(7339):532-6. doi: ... These two processes use two single-stranded DNA (ssDNA)-binding proteins, replication protein A (RPA) and protection of ...
Polyclonal Antibody Immunofluorescence Immunocytochemistry Single-Stranded Dna Binding from Cell Signaling Technology
RPA is a single stranded DNA binding protein, whose DNA binding activity is believed to reside entirely in the 70 kDa subunit. ... Polyclonal Antibody Immunohistochemistry Paraffin Single-Stranded Dna Binding * Polyclonal Antibody Western Blotting Single- ... Polyclonal Antibody Immunofluorescence Immunocytochemistry Single-Stranded Dna Binding. Polyclonal Antibody - hnRNP A1 (K350) ... Monoclonal Antibody Immunofluorescence Immunocytochemistry Single-Stranded Dna Binding * Polyclonal Antibody Flow Cytometry ...
Single Strand Annealing Induced by DNA Double Strand Break
Deletions of rad50 or xrs2 slow down the formation of single stranded DNA and reduce the amount of product formed. ... to be a DNA binding protein that can anneal ssDNA in vitro and in its absence Rad51 fails to bind to the single-stranded DNA ... Single strand annealing (SSA) is a process that is initiated when a double strand break is made between two repeated sequences ... Purified Rad59 possesses DNA binding properties and strand annealing activity.. RPA. Another DNA binding factor, the RPA ...
DNA, Single-Stranded | Antimicrobial Agents and Chemotherapy
Ssbp3 (single stranded DNA binding protein 3) - Rat Genome Database
SSBP3 (single stranded DNA binding protein 3). NCBI. Ortholog. Mus musculus (house mouse):. Ssbp3 (single-stranded DNA binding ... Ssbp3 (single stranded DNA binding protein 3). Transitive Ortholog Pipeline. Transitive Ortholog Pipeline. ... Ssbp3 (single stranded DNA binding protein 3). Transitive Ortholog Pipeline. Transitive Ortholog Pipeline. ... SSBP3 (single stranded DNA binding protein 3). Transitive Ortholog Pipeline. Transitive Ortholog Pipeline. ...
SsDNAProteinsRecombinationNucleic acidsSequenceVitroDeoxyribonucleic acidGeneGenomicPhageMoleculeSequencesViralM13mp18 Single-Stranded DNAGenomeGenesSynthesisDsDNAPlasmidSkipColiMoleculesFragmentsSSBsIntermediatesRolesNucleotideMitochondrialVirusesDeaminationEnzymesMechanismsAffinityCircularBindingNucleotidesATPaseAntibodiesCytidine deaminaseCytosine deaminasesPathwaysCleavageRole in DNA replicationMolecularTelomeresAntibodyDuplexOccurAPOBEC3GEnzymeDouble-Strand BreaksPolymerase deltaLigaseAccumulationInteractions
- This difficulty motivates our present efforts to measure and directly compare the flexibilities of single-stranded nucleic acids (ssRNA and ssDNA). (pnas.org)
- They translocated the DNA through a 7-nanometer pore and observed peaks that were around 10-fold larger than expected based on the volume of DNA, again due to the fact that the ssDNA hybridizes with itself. (genomeweb.com)
- Stuart Lindsay, director of the center for single molecule biophysics at Arizona State University, said he was surprised that the ssDNA was able to unwind at a neutral pH. (genomeweb.com)
- Synthetic long single-stranded DNA (ssDNA) as well as circular DNA allow functional studies in vitro and in vivo. (biosyn.com)
- Improvements in DNA and RNA oligonucleotide synthesis methods enabled the production of long single-stranded DNA (ssDNA) and circular DNA, such as catenanes, chain-like molecules. (biosyn.com)
- Long synthetic ssDNA may also be of use for the study of DNA repair mechanisms. (biosyn.com)
- Single-stranded DNA (ssDNA) occurs naturally as a transient intermediate during genome maintenance processes. (biosyn.com)
- Single-stranded DNA is known to occur in high incidence and concentrations in the sera of lupus patients (called systemic lupus erythematosus or SLE) at levels as high as 250 μg/ml. ssDNA is known as an immunogen for anti-ssDNA antibodies present in lupus patients. (biosyn.com)
- Trex1 binds to ssDNA in mammalian cells, where it removes mismatched 3'-terminal deoxyribonucleotides at DNA strand breaks. (biosyn.com)
- Compared to double-stranded DNA (dsDNA), the structure of ssDNA is very flexible and usually does not form well-defined secondary structures. (biosyn.com)
- Single molecules of ssDNA can be studied using biophysical methods such as single-molecule fluorescence resonance transfer (smFRET), molecular force spectroscopy, or optical tweezers. (biosyn.com)
- Our data show that the HRDC domain suppresses the rate of DNA-activated ATPase activity in parallel with those of ssDNA translocation and dsDNA unwinding, regardless of the ssDNA binding capability of this domain. (nature.com)
- These two processes use two single-stranded DNA (ssDNA)-binding proteins, replication protein A (RPA) and protection of telomeres 1 (POT1). (nih.gov)
- Together, our data suggest that hnRNPA1, TERRA and POT1 act in concert to displace RPA from telomeric ssDNA after DNA replication, and promote telomere capping to preserve genomic integrity. (nih.gov)
- Rad52 was shown to be a DNA binding protein that can anneal ssDNA in vitro and in its absence Rad51 fails to bind to the single-stranded DNA tails. (brandeis.edu)
- Recent research in CRISPR/Cas9 technology has shown that the use of long single-stranded DNA (ssDNA) donor templates greatly enhances the efficiency of homology directed repair (HDR) enabling researchers to optimize the process of efficiently generating transgenic animal models and cell lines. (genewiz.com)
- Advanced capabilities - Standard ssDNA synthesis service ranging from 150 nt to 8000 nt in length, with difficult stretches, like highly repetitive, AT- or GC-rich DNA. (genewiz.com)
- Includes your ssDNA fragment of interest and the complementary strand, delivered dry in separate tubes. (idtdna.com)
- Megamer ssDNA Fragments are single-stranded genomic blocks for applications such as homology-directed repair of CRISPR-mediated genome editing , in vitro transcription, and more. (idtdna.com)
- Integrated DNA Technologies screens every Megamer ssDNA Fragment for potentially dangerous pathogen sequences, and to verify that IDT's customers are legitimate scientists engaged in beneficial research. (idtdna.com)
- One characteristic of cells undergoing apoptosis is the production of single-stranded DNA (ssDNA). (clontech.com)
- Circular replication initiation protein (Rep)-encoding single-stranded DNA (ssDNA) (CRESS-DNA) genomes are found in diverse group II virus families, which all possess a conserved Rep-encoding gene and a nonenveloped icosahedral capsid, except geminiviruses, which have twinned particles ( 1 ). (cdc.gov)
- Genomic features of gemycircularviruses HV-GcV1 and HV-GcV2 and of a novel circular single-stranded DNA (ssDNA) virus, HV-CV1, including hairpin structure and predicted open reading frames. (cdc.gov)
- Do you have information about the cleanup of single-stranded DNA (ssDNA) with QIAquick columns? (qiagen.com)
- We find that binding of ETAA1 to RPA associated with single-stranded DNA (ssDNA) greatly stimulates its ability to activate ATR-ATRIP. (caltech.edu)
- The Long ssDNA kits use an efficient and simple in vitro protocol for the production of long ssDNA strands. (clontech.com)
- The method involves generating a double-stranded donor template using PCR where only one of the strands is phosphorylated at its 5' end, then selectively digesting the phosphorylated strand using the enzymes supplied in the kit (Strandase A and B). We recommend creating ssDNA for both the sense and antisense strands and using each in separate knockin experiments. (clontech.com)
- We recommend creating ssDNA for both the sense and antisense strand and using each in separate knockin experiments. (clontech.com)
- Sense and antisense ssDNA donor templates were produced for each of the following experiments using the workflow described above, since it is impossible to predict if the sense or the antisense DNA would be more efficient for knockin. (clontech.com)
- Escherichia coli single-stranded (ss)DNA binding (SSB) protein mediates genome maintenance processes by regulating access to ssDNA. (elifesciences.org)
- This homotetrameric protein wraps ssDNA in multiple distinct binding modes that may be used selectively in different DNA processes, and whose detailed wrapping topologies remain speculative. (elifesciences.org)
- Here, we used single-molecule force and fluorescence spectroscopy to investigate E. coli SSB binding to ssDNA. (elifesciences.org)
- Stretching a single ssDNA-SSB complex reveals discrete states that correlate with known binding modes, the likely ssDNA conformations and diffusion dynamics in each, and the kinetic pathways by which the protein wraps ssDNA and is dissociated. (elifesciences.org)
- Previously we demonstrated that Gbp1p binds single-stranded DNA (ssDNA) containing the Chlamydomonas telomeric sequence but not the RNA containing the cognate sequence. (asm.org)
- The G-strand binding protein of Chlamydomonas reinhardtii (Gbp1p) was identified and cloned on the basis of its ability to specifically associate with ssDNA containing the G-strand telomere repeat sequence ( 37 , 38 ), and thus we have classified Gbp1p as a putative telomere-binding protein. (asm.org)
- Nome, Claudia 2018-06-06 00:00:00 A single-stranded DNA (ssDNA) virus was detected in Yerba mate samples showing chlorotic linear patterns, chlorotic rings and vein yellowing. (deepdyve.com)
- In the target cells that these virions infect, encapsidated A3G can deaminate cytosines to uracils in (−)DNA reverse transcribed from the RNA genome, after the reverse transcriptase associated RNaseH activity enables ssDNA regions on the (−)DNA to be accessed by the enzyme  ,  . (prolekare.cz)
- The DNA stimulated ATPase activity of Dda helicase has been used to probe translocation on single-strand DNA (ssDNA). (elsevier.com)
- The direction of translocation on ssDNA is consistent with the direction in which Dda unwinds duplex DNA and is not dependent on duplex structure. (elsevier.com)
- Purine-rich element binding proteins A (Purα) and B (Purβ) are sequence-specific, single-stranded DNA (ssDNA)/RNA-binding proteins that act as transcriptional repressors of ACTA2 expression. (uvm.edu)
- Quantitative DNA-binding assays revealed that Purβ interacts with the purine-rich strand of the ACTA2 MCAT motif via a cooperative, multisite binding mechanism to form a high-affinity 2:1 Purβ-ssDNA complex. (uvm.edu)
- Limited proteolysis of recombinant mouse Purβ in the presence and absence of the purine-rich strand of the ACTA2 MCAT element led to the identification of a core ssDNA-binding region that retains the ability to dimerize in solution. (uvm.edu)
- We have identified an independent Cdc13p domain which retains full ssDNA binding activity and are currently using both biochemical and structural methods to study the determinants of interaction between the isolated domain and single-stranded telomeric DNA. (jbsdonline.com)
- Single-stranded DNA-binding proteins (SSBs) play vital roles in all aspects of DNA metabolism in all three domains of life and are characterized by the presence of one or more OB fold ssDNA-binding domains. (st-andrews.ac.uk)
- Cas3 possesses a single‐stranded DNA (ssDNA)‐stimulated ATPase activity, which is coupled to unwinding of DNA/DNA and RNA/DNA duplexes. (embopress.org)
- As well as stabilizing this single-stranded DNA, SSB proteins bind to and modulate the function of numerous proteins involved in all of these processes. (wikipedia.org)
- The disordered C-terminus of DdrB may mediate interactions with other proteins important for DNA damage recovery. (rcsb.org)
- In addition to the checkpoint partners, RPA interacts with a wide variety of protein partners, including proteins required for normal replication such as RCF, PCNA and Pol α, and also proteins involved in SV40 replication, such as DNA polymerase I and SV40 large T antigen (10,12). (cellsignal.com)
- Background and purpose: Single-stranded DNA-binding proteins participate in all stages of DNA metabolism that involve single-stranded DNA, from replication, recombination, repair of DNA damage, to natural competence in species such as Bacillus subtilis. (srce.hr)
- B. subtilis single-stranded DNA-binding proteins have previously been found to be phosphorylated on tyrosine and arginine residues. (srce.hr)
- The single-stranded-nucleic acid binding (SSB) protein superfamily includes proteins encoded by different organisms from Bacteria and their phages to Eukaryotes. (sigmaaldrich.com)
- However, as other proteins involved in DNA replication, bacterial SSB proteins are clearly different from those found in Archaea and Eukaryotes. (sigmaaldrich.com)
- Cellular proteins specifically bind to single-stranded DNA to prevent their premature recombination. (nanotech-now.com)
- Yen Nee Tan at the A*STAR Institute of Materials Research and Engineering and co-workers1 have now developed a convenient method to characterize the interactions between single-stranded DNA and their binding proteins. (nanotech-now.com)
- For protection, the single-stranded DNA can wrap around single-stranded DNA binding (SSB) proteins, which also control how other maintenance proteins interact with the DNA. (elifesciences.org)
- SSB proteins from the bacteria species Escherichia coli wrap single-stranded DNA into a variety of topologies known as binding modes. (elifesciences.org)
- The unraveling and sliding mechanisms are likely to be used by other proteins to gain access to DNA coated with SSBs. (elifesciences.org)
- Chung, In 2004-10-06 00:00:00 In this work, we have identified and characterized proteins in rice nuclear extracts that specifically bind the single-stranded G-rich telomere sequence. (deepdyve.com)
- These proteins are called rice G-rich telomere binding protein (RGBP) and none of them show binding affinity to double-stranded telomere repeats or single-stranded C-rich sequence. (deepdyve.com)
- Taken together, these studies suggest that RGBPs are new types of telomere-binding proteins that bind in vitro to single-stranded G-rich telomere DNA in the angiosperms. (deepdyve.com)
- Telomeric ss-G-strand binding proteins have been isolated and cloned from Oxytricha nova ( 42 ), Euplotes crassus ( 41 ), Tetrahymena thermophila ( 46 ), and Xenopus laevis ( 8 ). (asm.org)
- The Oxytricha and Euplotes ss-G-strand binding proteins remain bound to telomeric DNA in the presence of extremely high salt concentrations (up to 2 M NaCl) ( 41 , 43 ). (asm.org)
- Two yeast proteins, Est1p ( 48 ) and Cdc13p ( 16 , 35 ), specifically associate with the yeast ss G strand in vitro, and mutations in these proteins affect telomere function in vivo. (asm.org)
- The DNA is maintained by several nuclear-encoded proteins. (spandidos-publications.com)
- Human single-stranded DNA binding proteins: guardians of genome stability. (semanticscholar.org)
- Both Pur proteins interact with the purine-rich strand of a cryptic muscle-CAT (MCAT) enhancer motif in 5'-flanking region of the ACTA2 promoter. (uvm.edu)
- In addition to this, PNKP also helps in other DNA repair pathways through interactions with other DNA repair proteins such as XRCC1 and XRCC4. (wikibooks.org)
- Researchers have also identified that mutations that have lead to changes in PNKP, similar to mutations in other genes that encode other strand break repair proteins, have been connected to a severe autosomal recessive neurological disorder. (wikibooks.org)
- Each of these repeats appears to exhibit the typical RNA recognition motif found in several proteins interacting with RNA or single strand DNA. (pasteur.fr)
- Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination, and repair. (wikipedia.org)
- SSB protein domains in bacteria are important in its function of maintaining DNA metabolism, more specifically DNA replication, repair, and recombination. (wikipedia.org)
- Control of DNA cross-overs is necessary for meiotic recombination and genome integrity. (nih.gov)
- Extensive DNA resection might favor gene conversion without cross-over by channeling recombination events through synthesis-dependent strand-annealing. (nih.gov)
- Genome maintenance is vital during DNA replication, repair, and recombination. (biosyn.com)
- Involved in somatic hypermutation (SHM), gene conversion, and class-switch recombination (CSR) in B-lymphocytes by deaminating C to U during transcription of Ig-variable (V) and Ig-switch (S) region DNA. (uniprot.org)
- The complex is required for almost all aspects of cellular DNA metabolism such as DNA replication (1-3), recombination, cell cycle and DNA damage checkpoints, and all major types of DNA repair including nucleotide excision, base excision, mismatch and double-strand break repairs (4-7). (cellsignal.com)
- Nonhomologous end joining (NHEJ) and homologous recombination (HR) are two pathways for DNA double strand break (DSB) repair. (dissertations.se)
- The yeast K. lactis efficiently integrates DNA by illegitimate recombination (IR). (dissertations.se)
- Homologous recombination between single-stranded DNA and chromosomal genes in Saccharomyces cerevisiae. (asm.org)
- No conversion of single-stranded transforming DNA into duplex forms could be detected during the transformation process, and we conclude that single-stranded DNA may participate directly in recombination with chromosomal sequences. (asm.org)
- Cotransformation with competing heterologous single-stranded DNA specifically inhibited transformation by single-stranded DNA, suggesting that one of the components in the transformation-recombination process has a preferential affinity for single-stranded DNA. (asm.org)
- Lohman and Ferrari, 1994 ) to single stranded (ss)DNA intermediates formed during DNA replication, recombination, and repair, protecting them from both nucleolytic and chemical damage. (elifesciences.org)
- clb2 Δ cells are not sensitive to HU, but the strong synergistic effect of clb2 Δ with most genes tested indicates, unexpectedly, that CLB2 has an important role in DNA replication, in the stability and restart of stalled forks, and in pathways dependent on and independent of homologous recombination. (g3journal.org)
- This unusual distortion of the DNA double helix by RAP1 may contribute to the RAP1-dependent enhancement of recombination rates and promote non-duplex strand interactions at telomeres. (epfl.ch)
- DNA polymerase stalling, sister chromatid recombination and the BRCA genes. (ebscohost.com)
- The T4 bacteriophage Dda helicase is believed to be involved in early events in T4 DNA replication and has been shown to stimulate genetic recombination processes in vitro. (elsevier.com)
- A central function of RecA protein during homologous recombination is to promote sequence recognition and strand exchange between a stretched and unwound single-stranded DNA, to which it is complexed, and a duplex DNA. (jbsdonline.com)
- Previous measurements of flexible single-stranded nucleic acids using fluorescence correlation spectroscopy (FCS) ( 17 ), single molecule Förster resonance energy transfer (smFRET) ( 18 , 19 ), and force spectroscopy ( 20 - 23 ) have not provided a consensus picture of backbone conformations. (pnas.org)
- What are the building blocks for nucleic acids DNA and RNA? (jiskha.com)
- D. Hillemann, A. Pühler, and W. Wohlleben, "Gene disruption and gene replacement in Streptomyces via single stranded DNA transformation of integration vectors", Nucleic Acids Research , vol. 19, 1991, pp. 727-731. (uni-bielefeld.de)
- While RAD52 is clearly required for SSA using ura3 and leu2 substrates it has been reported that RAD52 is not required for SSA events located within the ribosomal DNA array (100 repeats of a 9 kb sequence) and is partially required for SSA within a CUP1 array of repeats. (brandeis.edu)
- Megamer Single-Stranded DNA Fragments are sequence-verified, single-stranded DNA strands of length 201-2000 bases. (idtdna.com)
- Both strands will be delivered for each sequence entry. (idtdna.com)
- In October 2010, the United States government issued final Screening Framework Guidance for Providers of Synthetic Double-Stranded DNA, describing how commercial providers of synthetic genes should perform gene sequence and customer screening. (idtdna.com)
- DNA-EDTA 1 has the sequence 5'-T-A-A-C-G-C-A-G-T*-C-A-G-G-C-A-C-C-G-T-3', which is complementary to a 19-nucleotide sequence in the plasmid pBR322. (caltech.edu)
- In the presence of Fe(II), O2, and dithiothreitol, DNA-EDTA 1 affords specific cleavage (25 degrees C, pH 7.4, 60 min) at its complementary sequence in a heat-denatured 167-base-pair restriction fragment. (caltech.edu)
- These DNA-EDTA-Fe(II) probes should be useful for the sequence-specific cleavage of single-stranded DNA (and most likely RNA) under mild conditions. (caltech.edu)
- Tan and co-workers showed that there was a minimum length of DNA sequence under which the binding protein-DNA adhesion mechanism could operate. (nanotech-now.com)
- They found that the binding protein had a preference for binding to specific chemical units (bases) which make up DNA, and were able to spot DNA sequence variations, called single nucleotide polymorphisms (SNPs), even at the extreme ends of the molecule which are difficult to identify. (nanotech-now.com)
- However, there are many instances when DNA must be separated into its individual strands-for example, when the DNA sequence needs to be copied. (elifesciences.org)
- This double-stranded repeat sequence is bound in vivo by factors such as Rap1p in Saccharomyces cerevisiae ( 29 ) and TRF1 and TRF2 in humans ( 4 , 47 , 53 ), which are important for the regulation of telomere repeat length, the formation of telomeric chromatin, and the integrity of individual chromosome ends. (asm.org)
- hnRNPs A1, A2/B1, D, and E bind ss-G-strand overhang DNA in vitro, although they associate more tightly with RNA of the cognate sequence ( 20 , 31 ). (asm.org)
- how does a change in the sequence of nucleotides in a strand of DNA might cause a protein to malfunction. (jiskha.com)
- Coincident with the RAP1-dependent untwisting, we observe stimulation of the association of a single-stranded yeast telomeric sequence with its homologous double-stranded sequence in a supercoiled plasmid. (epfl.ch)
- Preliminary calculations suggest that sequence homology recognition within the triplex of association is partial and that it is completed during strand exchange and product formation. (jbsdonline.com)
- Telomeric DNA is composed of a non-coding, repetitive sequence, which ends in a single-stranded TG-rich overhang. (jbsdonline.com)
- Cdc13p binds the single-stranded S. cerevisiae telomeric overhangs with high affinity (Kd=0.3 nM) and sequence specificity. (jbsdonline.com)
- The DNA-binding activity of Cj0011c was demonstrated with a variety of DNAs prepared from C. jejuni or Escherichia coli , suggesting that the DNA binding of Cj0011c is not sequence dependent. (iastate.edu)
- For example, the (SSB)65 binding mode, in which approximately 65 nucleotides of DNA wrap around the SSB tetramer and contact all four of its subunits, is favoured at high salt concentrations in vitro. (wikipedia.org)
- Towards this end, we have utilized a stringent in vitro selection method to identify single-stranded DNA molecular recognition elements (MRE) specific for bromacil. (hindawi.com)
- The detected phosphorylation site was assessed for its influence on DNA-binding in vitro, using electrophoretic mobility shift assays. (srce.hr)
- The in vitro assays demonstrated that SsbA is preferentially phosphorylated by the B. subtilis Hanks-type kinase YabT, and phosphorylation of threonine 38 leads to enhanced cooperative binding to DNA. (srce.hr)
- Wickner, S., Hurwitz, J.: Association of ϕX174 DNA-dependent ATPase activity wth an Escherichia coli protein, replication factor Y, required for in vitro synthesis of ϕX174 DNA. (springer.com)
- In vitro, purified Cdc13p binds to single-strand yeast telomeric DNA. (sciencemag.org)
- Replacement of Streptomyces hygroscopicus genomic segments with in vitro altered DNA sequences. (uni-bielefeld.de)
- Single-strand DNA-binding protein (SSB) is a protein found in Escherichia coli (E. coli) bacteria, that binds to single-stranded regions of deoxyribonucleic acid (DNA). (wikipedia.org)
- Purpose: To analyze the short term effects of radiofrequency radiation (RFR) exposure on genomic deoxyribonucleic acid (DNA) of human hair root cells. (buergerwelle.de)
- DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are polymers of nucleotides linked in a chain through phosphodiester bonds. (jiskha.com)
- After a DNA fragment coding for the production of msDNA in E. coli was discovered, it was conjectured that bacteriophages might have been responsible for the introduction of the RT gene into E. coli. (wikipedia.org)
- M13mp18 is a M13 lac phage vector which contains single HindIII, SphI, SbfI, PstI, SalI (AccI/ HincII), XbaI, BamHI, SmaI (XmaI), KpnI (Acc65I), SacI and EcoRI sites within the gene encoding β-Galactosidase.This DNA preparation is useful as a standard and has been tested as a template in the dideoxy-nucleotide termination method of sequencing DNA. (neb.com)
- After vir gene induction, both single-stranded (T-strands) and double-stranded forms of processed T-DNA accumulate in the bacteria. (pnas.org)
- May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation. (uniprot.org)
- Double-stranded DNA has historically been the template of choice for gene insertions, but recent research has shown the superiority of ssODNs as a donor template for HDR. (genewiz.com)
- This genome displayed a typical GcV architecture, with a 2,264-nt circular DNA molecule carrying a capsid gene on 1 strand and 2 genes on the opposite strand, which coded for Rep1 (involved in replication initiation) and Rep2 (involved in replication termination), respectively. (cdc.gov)
- HV-GcV2 (2,262 nt) shares the same stem-loop motif and genomic structure with HV-GcV1, with the exception of the rep gene, which is coded by a single open reading frame. (cdc.gov)
- The Agrobacterium tumefaciens virE2 gene product is a single-stranded-DNA-binding protein that associates with T-DNA. (asm.org)
- In the work described in this report, we used electrophoretic mobility shift assays to show that the purified virE2 gene product binds to single-stranded DNA. (asm.org)
- dnaG gene product, a rifampicin-resistant RNA polymerase, initiates the conversion of a single-stranded coli phage DNA to its duplex replicative form. (springer.com)
- Transformation with single-stranded DNA gave rise to both gene conversion and reciprocal exchange events. (asm.org)
- Disclosed are compositions, methods, and kits for modifying DNA within cells as well as compositions and methods for modifying gene expression in a cell. (patents.com)
- We characterized and purified a protein from rat liver which specifically binds to a DNA motif present in a liver-specific enhancer of the rat tyrosine aminotransferase (TAT) gene, when offered as singlestranded DNA. (uni-muenchen.de)
- Vaccinia virus protein VP8 is a 25 kDa product of the L4R gene and is an abundant virion protein that binds single-stranded (ss) and double-stranded (ds) DNA. (le.ac.uk)
- All together the data support a model in which the way these enzymes scan DNA can predict the magnitude of mutagenesis induced and the target motif can predict ability to cause gene inactivation. (prolekare.cz)
- The protein binds also to a similar polypyrimidine tract present in one of the two strands of a DNA regulatory element of the rat tyrosine aminotransferase gene enhancer. (pasteur.fr)
- Streptomyces viridochromogenes was transformed by single stranded DNA integration vectors in order to replace the pat by the tsr gene and generate mutants unable to synthesize phosphinothricin - tripeptide (PTT). (uni-bielefeld.de)
- Genomic library preparation from highly degraded DNA is more efficient when library molecules are prepared separately from the complementary strands of DNA fragments. (springer.com)
- We plan to further develop this assay into a hassle-free genotyping assay to detect SNPs in real biological samples containing long genomic DNA," says Tan. (nanotech-now.com)
- As such, Strand-seq can be used to assess genomic instability at single cell level, resulting in a much higher sensitivity than previously possible. (futurelearn.com)
- Strand-seq is a very powerful tool for not just detecting DNA strand inheritance patterns, but also for assessing genomic instability at the single cell level. (futurelearn.com)
- An improved filamentous helper phage for generating single-stranded plasmid DNA. (nih.gov)
- However, technical difficulties have been a problem, primarily low yields of packaged single stranded (ss) plasmid DNA from the rapid, small scale procedures usually employed, and ambiguities in sequencing reactions attributed to the contamination by helper phage ss DNA. (nih.gov)
- Using this phage, R408, plasmid ss DNA is packaged and exported preferentially over phage ss DNA, and the absolute yield of plasmid ss DNA is usually increased. (nih.gov)
- The M13mp18 Single-Stranded DNA is a circular molecule, purified from the M13mp18 phage. (neb.com)
- Taketo, A.: Inducibility of lambda phage development in Escherichia coli mutants thermosensitive for DNA replication. (springer.com)
- 32 P-labeled single-stranded DNA phage φX174 was photodynamically inactivated by irradiation in air with visible light in the presence of the acridine dye, proflavine sulfate. (asm.org)
- Multicopy single-stranded DNA (msDNA) is a type of extrachromosomal satellite DNA that consists of a single-stranded DNA molecule covalently linked via a 2'-5'phosphodiester bond to an internal guanosine of an RNA molecule. (wikipedia.org)
- As the hybrid molecule passed through the nanopore, the researchers observed different levels of current spikes, which corresponded to the double-stranded and single-stranded portions of the molecule. (genomeweb.com)
- Multicopy single-stranded DNA (msDNA), a branched DNA-RNA molecule, has been shown in Escherichia coli B and clinical strain Cl-1 to be synthesized by reverse transcriptase. (asm.org)
- By using a technique that uses a laser to exert forces on an individual DNA molecule, Suksombat et al. (elifesciences.org)
- Single-molecule DREEM imaging reveals DNA wrapping around human mitochondrial single-stranded DNA binding protein. (semanticscholar.org)
- Multiple rL4R molecules bound to a single 45mer oligonucleotide, and using oligonucleotides of different lengths it was calculated that one rL4R molecule bound every 17 nt. (le.ac.uk)
- Extensive DNA resection could be an effective mechanism to prevent reciprocal exchanges between dispersed DNA sequences, and thus contribute to the genome stability. (nih.gov)
- Single strand annealing (SSA) is a process that is initiated when a double strand break is made between two repeated sequences oriented in the same direction. (brandeis.edu)
- Single stranded regions are created adjacent to the break that extend to the repeated sequences such that the complementary strands can anneal to each other. (brandeis.edu)
- Cleavage at T-DNA border sequences by the VirD endonuclease generates linear, single-stranded T-DNA molecules. (asm.org)
- The complex III, in addition to binding to telomeric sequences, has a binding affinity to rice nuclear RNA, whereas two other complexes have a binding affinity to only single-stranded G-rich telomere DNA. (deepdyve.com)
- In most organisms, telomeric DNA is composed of simple short repeat sequences which show a strand bias such that there is a G-biased strand (G strand) and a complementary C-biased strand (C strand) ( 25 ). (asm.org)
M13mp18 Single-Stranded DNA1
- Is the M13mp18 Single-Stranded DNA (N4040S) circular or linear? (neb.com)
- Plays a role in DNA repair and genome reconstitution in a RecA-independent process. (rcsb.org)
- DNA-restructuring activities of RecQ-family helicases play key roles in genome maintenance. (nature.com)
- Agrobacterium tumefaciens transfers T-DNA into the plant genome by a process mediated by Ti plasmid-encoded vir genes. (asm.org)
- Each DNA fragment is then amplified, sequenced, and aligned to the correct location in the genome. (futurelearn.com)
- These are the result of a DNA double strand break, and the number of SCEs is an indicator for genome instability. (futurelearn.com)
- Strand-seq can also be used to detect chromosome copy number variations across the genome. (futurelearn.com)
- T-DNA processing and transfer require the induction of vir (virulence) genes by phenolic compounds secreted by wounded plant cells. (pnas.org)
- 2009) The Mycoplasma pneumoniae MPN490 and Mycoplasma genitalium MG339 Genes Encode RecA Homologs That Promote Homologous DNA Strand Exchange. (epibio.com)
- Using various replication mutants of E. coli , the host genes that participate in the replication of some K12-specific single-stranded DNA phages have been determined. (springer.com)
- Mitochondrial (mt) nucleoids as functional units are composed of circular DNA coding 13 genes involved in the electron transport chain. (spandidos-publications.com)
- Streptomyces cloning: useful recombinant DNA systems and a summation of cloned genes. (uni-bielefeld.de)
- The priming of msDNA synthesis offers a fascinating challenge to our understanding of DNA synthesis. (wikipedia.org)
- The synthesis of DNA catenanes, chain-like DNA molecules, allows the study of the secondary structure of these molecules. (biosyn.com)
- The synthesis of a DNA hybridization probe 19 nucleotides in length, equipped with the metal chelator EDTA at C-5 of thymidine in position 10 (indicated by T*) is described. (caltech.edu)
- Bowes, J.M.: Replication of bacteriophage St-1 in Escherichia coli strains temperature sensitive in DNA synthesis. (springer.com)
- Taketo, A.: Replication of ϕA and ϕX174 in Escherichia coli mutants thermosensitive in DNA synthesis. (springer.com)
- However, there are various instances where single-stranded DNA is exposed, such as during replication or transcription, in the synthesis of chromosome ends, and following DNA damage. (semanticscholar.org)
- Synthesis, characterization, DNA-binding studies and acetylcholinesterase inhibition activity of new 3-formyl chromone derivatives. (semanticscholar.org)
- The uracils in the (−)DNA are used as a template by reverse transcriptase during (+)DNA synthesis and result in guanine to adenine mutations. (prolekare.cz)
- Our fragments are derived from clonally purified double-stranded DNA (dsDNA), producing the highest quality results possible. (genewiz.com)
- On binding to a double-stranded DNA (dsDNA), the ratio of the two emission bands of the 3HC conjugates changes up to 16-fold, so that emission of the ESIPT product increases dramatically. (semanticscholar.org)
- These results indicate that DNA ligase 1 functions in both DNA replication and in repair of both ss and dsDNA strand breaks in higher plants. (biomedcentral.com)
- During the inception of crown gall tumorigenesis, the transferred DNA (T-DNA) is processed from the Ti (tumor inducing) plasmid of Agrobacterium tumefaciens and is transferred to plant cells. (pnas.org)
- The effects of the single-strand origins (SSOs) of the broad-host-range streptococcal plasmid pMV158 on (i) the conversion of its single-stranded (ss) DNA replication intermediates to double-stranded (ds) plasmid DNA and (ii) its maintenance were analyzed. (rti.org)
- 1995). In the presence of both SSOs, no ss plasmid DNA was observed in L. lactis. (rti.org)
- Effective cross sections for production of single-strand breaks in plasmid DNA by 0.1 to 4.7 eV electrons. (sigmaaldrich.com)
- We determined effective cross sections for production of single-strand breaks (SSBs) in plasmid DNA [pGEM 3Zf(-)] by electrons of 10 eV and energies between 0.1 and 4.7 eV. (sigmaaldrich.com)
- After purification and lyophilization on a chemically clean tantalum foil, dry plasmid DNA samples were transferred into a high-vacuum chamber and bombarded by a monoenergetic electron beam. (sigmaaldrich.com)
- For the isolation of single stranded plasmid DNA, various E. coli and E. coli- Streptomyces shuttle plasmids were equipped with the f1 replication origin. (uni-bielefeld.de)
- The transformation of some representative Streptomyces species with plasmid vectors occurred irrespective of whether single or double stranded DNA was used. (uni-bielefeld.de)
- 0:01 Skip to 0 minutes and 1 second Strand-seq is a method for single-cell DNA template strand sequencing. (futurelearn.com)
- 0:45 Skip to 0 minutes and 45 seconds However, if cells are pulsed with a dose of the thymidine analogue BrdU for exactly one cell division, the BrdU becomes incorporated into the newly-formed DNA strands, making it possible to distinguish the sister chromatids. (futurelearn.com)
- 1:17 Skip to 1 minute and 17 seconds In order to detect inheritance of template DNA strand at the single cell level, single cells are sorted by means of flow cytometry. (futurelearn.com)
- 1:27 Skip to 1 minute and 27 seconds The DNA is extracted from each cell and then fragmented. (futurelearn.com)
- 2:20 Skip to 2 minutes and 20 seconds Using Strand-seq, we can now determine which template strands were inherited for each chromosome. (futurelearn.com)
- Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. (asm.org)
- In most studies of single molecules, DNA or protein molecules are immobilized to a surface and are often mobilized with fluorophores or tethers to allow observations. (biosyn.com)
- Double-stranded DNA must disentangle itself into single strands during replication or repair to allow functional molecules to bind and perform their various operations. (nanotech-now.com)
- The protein molecules alone are smaller in molecular size than the protein-DNA complexes, leading to a less effective steric stabilization of the nanoparticles. (nanotech-now.com)
- The amount of the circular relaxed DNA in the samples was separated from undamaged molecules and quantified using agarose gel electrophoresis. (sigmaaldrich.com)
- Photodynamic lesions in φX174 DNA caused intracellular formation of defective double-stranded replicative form molecules which ultimately reverted to the single-stranded configuration. (asm.org)
- Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. (umassmed.edu)
- They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA. (umassmed.edu)
- Megamer fragments are 201-2000 bases in length and are generated from with clonally purified DNA, which offers the greatest purity available. (idtdna.com)
- These DNA fragments are further processed for sequencing. (futurelearn.com)
- DNA ligase 1 (LIG1) is present in all eukaryotes where it is required for joining DNA fragments produced during DNA replication. (biomedcentral.com)
- Base lesions and DNA single-strand breaks (SSBs) are very common types of DNA damage. (dissertations.se)
- Further experiments showed that SSBs can slide along DNA without having to change their binding mode. (elifesciences.org)
- Comet assay analysis of isolated nuclei showed atlig1 - RNAi lines displayed slower repair of single strand breaks (SSBs) and also double strand breaks (DSBs), implicating AtLIG1 in repair of both these lesions. (biomedcentral.com)
- The resultant DNA/RNA chimera possesses two stem-loops joined by a branch similar to the branches found in RNA splicing intermediates. (wikipedia.org)
- By studying the properties of DNA under the conditions of deformation imposed by RecA, we propose a model for recognition and strand exchange at the atomic level, via unusual triple-helical intermediates. (jbsdonline.com)
- The roles of RPA include stabilising and protecting single- stranded DNA from nuclease degradation during DNA replication and repair. (nottingham.ac.uk)
- DNA ligase enzymes catalyse the joining of adjacent polynucleotides and as such play important roles in DNA replication and repair pathways. (biomedcentral.com)
- Eukaryotes possess multiple DNA ligases with distinct roles in DNA metabolism, with clear differences in the functions of DNA ligase orthologues between animals, yeast and plants. (biomedcentral.com)
- DNA ligase 1, present in all eukaryotes, plays critical roles in both DNA repair and replication and is indispensable for cell viability. (biomedcentral.com)
- Therefore, RNAi lines with reduced levels of AtLIG1 were generated to allow the roles and importance of Arabidopsis DNA ligase 1 in DNA metabolism to be elucidated. (biomedcentral.com)
- Reduced levels of Arabidopsis DNA ligase 1 in the silenced lines are sufficient to support plant development but result in retarded growth and reduced cell size, which may reflect roles for AtLIG1 in both replication and repair. (biomedcentral.com)
- DNA ligases play essential roles in all organisms by maintaining the physical structure of DNA. (biomedcentral.com)
- Eukaryotes have evolved multiple DNA ligase isoforms, with both specific and overlapping roles in the replication and repair of the nuclear and organellar genomes. (biomedcentral.com)
- DNA ligase 1 also plays important roles in DNA single strand break (SSB) repair pathways in mammals and yeast. (biomedcentral.com)
- Deletion analysis is used to demonstrate important roles for individual OB folds in RpaC and to show that conserved N- and C-terminal domains are required for efficient repair of DNA damage. (st-andrews.ac.uk)
- Repair of damage to a single strand by base excision repair or nucleotide excision repair, for example, depends on just the two copies of genetic information contained in the two strands of the DNA double helix. (coursehero.com)
- NER is initiated by the recognition of a distorted region containing the DNA adducts followed by a 5′ and 3′ incision on either side of the lesion to create a 27-29 nucleotide gap. (radioterapiaitalia.it)
- The aim of the present study was to follow up mitochondrial nucleoid behavior under natural conditions of living cells transfected with mitochondrial single‑strand DNA‑binding protein (mtSSB) conjugated with EosFP. (spandidos-publications.com)
- HEPG2 and SH‑SY5Y cells were subjected to lentiviral transfection and subsequently immunostained with anti‑DNA, anti‑transcription factor A, mitochondrial (TFAM) or anti‑translocase of the inner membrane 23 antibodies. (spandidos-publications.com)
- Transcription and replication is then performed by specific mitochondrial RNA or DNA polymerases ( 15 , 16 ). (spandidos-publications.com)
- Generally single-stranded DNAs are not cut by restriction enzymes. (neb.com)
- The capability of RecQ helicases to process complex DNA structures is associated with a conserved domain architecture shared by Ec RecQ, human BLM and WRN enzymes, as well as at least one RecQ homolog in almost all investigated organisms ( Fig. 1 ) 10 . (nature.com)
- If DNA repair enzymes recognized such defects only on newly synthesized DNA strands, half of the defects would go uncorrected. (coursehero.com)
- Human cells possess a family of seven DNA-modification enzymes, termed APOBEC3, that function as part of our innate immune system. (prolekare.cz)
- The enzymes modify cytosine in DNA which induces mutations. (prolekare.cz)
- There has been little biochemical analysis of APOBEC3 enzymes other than APOBEC3G in terms of the mechanism by which these enzymes search DNA for target cytosines to deaminate. (prolekare.cz)
- These enzymes seal gaps in the sugar-phosphate backbone of DNA that arise during DNA replication, DNA damage and repair. (biomedcentral.com)
- Enzymes NEIL1 and NEIL2, mammalian DNA glycosylases with β,δ-lyase activity, remove an extensive amount of mutagenic and cytotoxic oxidative pyrimidien lesions and purine-derived formamidopyrimidines. (wikibooks.org)
- Despite recent efforts to elucidate the transformation mechanisms of C. jejuni , the process of DNA binding and uptake in this organism is still not well understood. (iastate.edu)
- Various mechanisms that cause strand breaks include: cleavage by physical and chemicals means such as ionizing radiation (IR) and ROS, and enzymatic processes. (wikibooks.org)
- As a rule of thumb, single-stranded DNA binds to silica with approximately half the affinity of a double-stranded DNA fragment of the same length under the buffer conditions used in the QIAquick and MinElute Kits . (qiagen.com)
- We found that mutation of the two RRM motifs of Gbp1p to match the highly conserved region of hnRNP RRMs did not alter the affinity of Gbp1p for either RNA or DNA. (asm.org)
- Binding of single-stranded DNA to the tetramer can occur in different "modes", with SSB occupying different numbers of DNA bases depending on a number of factors, including salt concentration. (wikipedia.org)
- DNA-binding protein Single-stranded binding protein Comparison of nucleic acid simulation software Oakley, A.J. (2014). (wikipedia.org)
- These activities, driven by two tandem RecA-like core domains, are thought to be controlled by accessory DNA-binding elements including the helicase-and-RnaseD-C-terminal (HRDC) domain. (nature.com)
- RPA is a single stranded DNA binding protein, whose DNA binding activity is believed to reside entirely in the 70 kDa subunit. (cellsignal.com)
- Purified Rad59 possesses DNA binding properties and strand annealing activity. (brandeis.edu)
- Another DNA binding factor, the RPA complex, is required for SSA. (brandeis.edu)
- Here, we constructed a panel of APOBEC3G amino acid substitution mutants and performed a series of biochemical, genetic, and structural assays to distinguish between "Brim" and "Kink" models for single-strand DNA binding. (mdpi.com)
- The overall data set is most consistent with the Brim model for single-stranded DNA binding by APOBEC3G. (mdpi.com)
- The Single-Strand Binding Protein has been discontinued. (epibio.com)
- Bacillus subtilis single-stranded DNA-binding protein SsbA is phosphorylated at threonine 38 by the serine/threonine. (srce.hr)
- While tyrosine phosphorylation was shown to enhance the DNA-binding properties of SsbA, arginine phosphorylation was not functionally characterized. (srce.hr)
- Phylogenetic and complementation analysis of a single-stranded DNA binding protein family from lactococcal phages indicates a non-bacterial origin. (sigmaaldrich.com)
- The researchers used the optical properties of gold nanoparticles to probe the mechanism of protein-DNA binding. (nanotech-now.com)
- Tan and co-workers discovered that when single-stranded DNA and its binding protein were both present in the solution, coupled with a salt that stimulates nanoparticle aggregation, the DNA remained red in color, indicating that the DNA-protein complexes had bound with the nanoparticles through electrosteric stabilization forces. (nanotech-now.com)
- The greatest challenge in this work was to determine the optimum conditions for single-stranded DNA to bind with its binding protein to form complexes that confer the highest stability to gold nanoparticles from salt-induced aggregation," says Tan. (nanotech-now.com)
- The researchers attribute binding of the nanoparticles and the DNA-protein complexes to the presence of sulphur-containing groups in the protein, which are known to create strong bonds with gold. (nanotech-now.com)
- The binding protein can thus attach to the dissociated single-stranded DNA to form protein-DNA complexes, offering sites to which gold nanoparticles can adhere. (nanotech-now.com)
- Development of a single-stranded DNA-binding protein fluorescent fusio" by Katarzyna Dubiel, Camille Henry et al. (edu.au)
- These modes can reversibly interconvert, with the transitions influenced primarily by salt concentration and type as well as protein binding density on the DNA ( Bujalowski and Lohman, 1986 ). (elifesciences.org)
- Mutation of RLF6 alters the subnuclear localization of the double-stranded (ds) telomere-binding protein Rap1p but does not change other telomere-associated phenotypes ( 24 ). (asm.org)
- Here we show that loss of the single-stranded DNA-binding protein replication protein A (RPA) in human ALT cells, but not in telomerase-positive cells, causes increased exposure of single-stranded G-rich telomeric DNA, cell cycle arrest in G2/M phase, accumulation of single-stranded telomeric DNA within ALT-associated PML bodies (APBs), and formation of telomeric aggregates at the ends of metaphase chromosomes. (uib.no)
- SSBP2 has several biochemical functions, for example, single-stranded DNA binding. (creativebiomart.net)
- The SOSS1 single-stranded DNA binding complex promotes DNA end resection in concert with Exo1. (semanticscholar.org)
- Replication protein A (RPA) is a single-stranded DNA-binding protein that is present in all three domains of life. (nottingham.ac.uk)
- To achieve this, RPA uses an oligosaccharide-binding fold (OB fold) to bind single- stranded DNA. (nottingham.ac.uk)
- In this study, we report a previously unrecognized DNA-binding protein (Cj0011c) in C. jejuni that contributes to natural transformation. (iastate.edu)
- PYBP is a DNA-binding protein, purified as a 58 kDa doublet which binds only to single strand pyrimidine-rich DNA present for example in PRI and DRI. (pasteur.fr)
- Even longer G-strand overhangs (200 ± 75 nucleotides) have been detected in humans ( 51 ). (asm.org)
- 3. What are the four different bases found in DNA nucleotides? (jiskha.com)
- After the termini of these strands break, they require processing before missing nucleotides can be replaced by DNA polymerase and its strands rejoined by DNA ligases. (wikibooks.org)
- The K(act) (K(m) for DNA) for Dda ATPase activity was reduced in the presence of a streptavidin block on the 3' end, whereas a streptavidin block on the 5' end had only a small effect on the steady-state ATPase parameters. (elsevier.com)
- We propose that the Cas3 ATPase/helicase domain acts as a motor protein, which assists delivery of the nuclease activity to Cascade-crRNA complex targeting foreign DNA. (embopress.org)
- Double diffusion experiments with antibodies to single-stranded (s-s) DNA confirmed physicochemical data that adeno-associated satellite virions contain s-s DNA but the DNA extracted from such virions is double-stranded. (jimmunol.org)
- Single-stranded DNA-specific cytidine deaminase. (uniprot.org)
- APOBEC3G is the best known of several DNA cytosine deaminases that function to inhibit the replication of parasitic genetic elements including the lentivirus HIV. (mdpi.com)
- APOBEC3F (A3F) and APOBEC3G (A3G) are members of a family of seven single-stranded (ss)DNA cytosine deaminases (A3A, A3B, A3C, A3D, A3F, A3G, and A3H)  and play a role in restriction of the retrovirus HIV-1 (referred to as HIV)  . (prolekare.cz)
- Double-stranded breaks are generated through CRISPR/Cas9 editing , then repaired by the endogenous cellular pathways of non-homologous end joining (NHEJ) and HDR. (genewiz.com)
- A chart of common DNA damaging agents, examples of lesions they cause in DNA, and pathways used to repair these lesions. (radioterapiaitalia.it)
- Because the efficiency of the DNA cleavage reaction is dependent on the addition of both Fe(II) and reducing agent (dithiothreitol), the initiation of the cleavage reaction can be controlled. (caltech.edu)
Role in DNA replication2
- Although 'CsCl-prepped' DNA is obviously the best, for preparing multiple templates, we DNA prepared with the normal alkaline-lysis miniprep procedure and PEG precipitate (as described, for example, in the Molecular Cloning manual). (bio.net)
- Molecular basis of BACH1/FANCJ recognition by TopBP1 in DNA replication checkpoint control. (semanticscholar.org)
- Maintenance of telomeres requires both DNA replication and telomere 'capping' by shelterin. (nih.gov)
- Early sequencing of ciliate telomeres indicated that the G strand extends beyond the C strand, creating a single-stranded (ss) 3′ overhang of 12 to 16 bases which persists throughout the vegetative life cycle of the organism ( 18 , 22 ). (asm.org)
- In contrast, in S. cerevisiae , longer G-strand overhangs that are more variable in length have been detected during late S phase, the cell cycle phase during which telomeres replicate ( 50 ). (asm.org)
- Antibody staining and 3D immunocytochemistry confirmed that nucleoid components such as TFAM and DNA were co‑localized with these aggregates. (spandidos-publications.com)
- As a unique property the ( L )-aTNAs exclusively form triplex structures with DNA and RNA and no duplex structures are observed by gel electrophoresis. (rsc.org)
- By contrast, precise repair of damage to both strands of a duplex-a double-strand break, for example-requires information from a second duplex, either a sister chromatid or a homolog. (coursehero.com)
- In this model, association takes place within a stretched and unwound triple helix of a new type, where the invading single strand occupies the minor groove of the duplex in a parallel orientation. (jbsdonline.com)
- During meiosis, two rounds of chromosome segregation occur after a single round of DNA replication, producing haploid progeny from diploid progenitors. (ebscohost.com)
- They do not arise from replication errors and are therefore equally likely to occur on either strand. (coursehero.com)
- These counter mutational and cytotoxic consequences that occur due to DNA damage. (wikibooks.org)
- Several high-resolution structures of the APOBEC3G catalytic domain have been generated, but none reveal how this enzyme binds to substrate single-stranded DNA. (mdpi.com)
- Guide RNA forms a complex with Cas9 directing enzyme to cleave target DNA resulting in a double-stranded break (DSB). (genewiz.com)
- Though this question sucks, which enzyme elongates the new DNA strand starting at an RNA primer? (jiskha.com)
- The enzyme polynucleotide kinase/phosphatase plays an important role in repairing DNA strand breaks by catalyzing the restoration of DNA's termini. (wikibooks.org)
- The enzyme PNKP carries 5'-kinase and 3'phosphatase activities that are essential for processing of single and double strand breaks at termini. (wikibooks.org)
- The enzyme topoisomerase 1 creates a DNA cut with a 5'-OH terminus and a covalent 3'-phosphate-enzyme intermediate in order to relieve torsional strain. (wikibooks.org)
- Using topoisomerase, camptothecin prevents resultant strand rejoining, leaving a DNA-enzyme 'dead-end' complex. (wikibooks.org)
- Since many DNA glycosylases have this enzyme activity, the pentenal moiety can then be eliminated by an AP endonuclease to give 3'-OH or by an AP lyase to give 3'-phosphate. (wikibooks.org)
- DNA double-strand breaks (DSBs) are the most toxic type of DNA damage. (dissertations.se)
- Multiple competition reactions for RPA order the assembly of the DNA polymerase delta holoenzyme. (semanticscholar.org)
- We describe a protocol in which libraries are constructed from single DNA strands in a three-step procedure: single-stranded ligation of the first adapter with T4 DNA ligase in the presence of a splinter oligonucleotide, copying of the DNA strand with a proofreading polymerase, and blunt-end ligation of the second double-stranded adapter with T4 DNA ligase. (springer.com)
- Marie-Theres Gansauge TG, Glocke I, Korlević P, Lippik L, Sarah Nagel LR, Schmidt A, Meyer M (2016) Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. (springer.com)
- DNA polymerase β (Pol β) removes the 5′-dRP and replicates DNA from the 3′ OH, generating a nick ready for subsequent ligation by DNA ligase (LIG). (radioterapiaitalia.it)
- The finding that DNA ligase 1 plays an important role in DSB repair in addition to its known function in SSB repair, demonstrates the existence of a previously uncharacterised novel pathway, independent of the conserved NHEJ. (biomedcentral.com)
- Protoplast infections using an A. tumefaciens virE mutant result in a low level of accumulation of T-strands in the plant cells. (pnas.org)
- Nature has evolved strategies to encode information within a single biopolymer to program biomolecular interactions with characteristic stoichiometry, orthogonality and reconfigurability. (nature.com)
- The WHD mediates protein-DNA and protein-protein interactions and has been shown to facilitate DNA unwinding and contribute to substrate recognition 10 . (nature.com)
- Hyperphosphorylation may alter RPA-DNA and RPA-protein interactions. (cellsignal.com)
- Each model predicts distinct sets of interactions between surface arginines and negatively charged phosphates in the DNA backbone. (mdpi.com)
- Unfortunately, detailed studies of these DNA-protein interactions have been hindered by the need for expensive instrumentation and time-consuming labelling techniques. (nanotech-now.com)
- RNase sensitivity of the DNA-protein interactions was tested to investigate whether an RNA component mediates the telomeric DNA-protein interaction. (deepdyve.com)