Interruptions in one of the strands of the sugar-phosphate backbone of double-stranded DNA.
A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
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 direct-acting oxidative stress-inducing agent used to examine the effects of oxidant stress on Ca(2+)-dependent signal transduction in vascular endothelial cells. It is also used as a catalyst in polymerization reactions and to introduce peroxy groups into organic molecules.
Cytosine nucleotides which contain deoxyribose as the sugar moiety.
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.
Enzymes that catalyze the transfer of multiple ADP-RIBOSE groups from nicotinamide-adenine dinucleotide (NAD) onto protein targets, thus building up a linear or branched homopolymer of repeating ADP-ribose units i.e., POLY ADENOSINE DIPHOSPHATE RIBOSE.
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.
The span of viability of a cell characterized by the capacity to perform certain functions such as metabolism, growth, reproduction, some form of responsiveness, and adaptability.
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).

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)

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 ...
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
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 Conference Paper ...
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.
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
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.. 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 [1], [2], [3]. 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 ...
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. ...
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 ...
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.
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. ...
(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.
(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 [1] (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 [2]: ...
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 ...
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, ...
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 ...
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 ...
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. ...
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, 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 , , +--------------------------------------------+ 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. ...
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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 ...
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
Imetajatest on mitokondriaalsed nukleoidid kõige paremini kirjeldatud inimeses. Samuti on nukleoidid leitud roti, rohepärdiku ja potoroo maksarakkude mitokondritest[6][7]. Imetajate mtDNA paiknemine diskreetsete üksustena oli esmakordselt näidatud 1991. aastal inimrakkude mtDNA värvimisel DAPI-ga[8] ning see oli hiljem kinnitatud ka immunofluorestsentsi katsetes, kus kasutati anti-DNA antikehi[9][10]. mtDNA kompleksid valkudega olid imetajates kirjeldatud siis, kui näidati mtDNA seondumist DNA helikaasiga Twinkle inimrakkudes[11]. 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 ...
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 ...
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.
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.
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.
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.
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 can synthesize a complementary DNA strand initiating from a primer using RNA (cDNA synthesis) or single-stranded DNA as a template.
S1 nuclease (EC, ~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). ...
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 ...
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[4][5] [6]. 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[1]. 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 ...
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 ...
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 …. ...
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 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 ...
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.
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
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 ...
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. ...
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.. ...
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 ...
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 ...
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 ...
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
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 ...
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 ...
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 ...
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.
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
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.
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.
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
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 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 ...
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 [1]. 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 [5]. 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 ...
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 ...
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.. ...
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 ...
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 ...
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 ...
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.. ...
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: 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.
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 ...
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 ...
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 …
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 ...
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 ...
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
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™ 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.. [^] ...
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 ...
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.
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 are the known short, single-stranded, labelled DNA sequences used to detect the presence or absence of nucleic acid in a sample.
... (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, ...
... 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 ...
Strand-seq (single-cell and single-strand sequencing) was one of the first single-cell sequencing protocols described in 2012. ... Single-cell DNA template strand sequencing, or Strand-seq, is a technique for the selective sequencing of a daughter cell's ... Unlike single cell sequencing protocols, Strand-seq does not utilize multiple displacement amplification or MALBAC for DNA ... By aligning Strand-seq reads from a single cell to the reference genome, the inherited template strands can be determined. If ...
The single stranded DNA (ssDNA) and complementary double stranded DNA (dsDNA) will form a D-loop structure. Another possible ... the strand would undergo a conformational change to form a triple stranded DNA helix. The triple-stranded DNA (H-DNA) was ... Triple-stranded DNA (also known as H-DNA or Triplex-DNA) is a DNA structure in which three oligonucleotides wind around each ... H-DNA formation involves the formation of single-stranded DNA (ssDNA), which is more susceptible to attack by nucleases. ...
The difference in shape between two single-stranded DNA strands with different sequences can cause them to migrate differently ... Single-strand conformation polymorphism (SSCP), or single-strand chain polymorphism, is defined as a conformational difference ... the physical properties of the double strands are almost identical for both alleles. After denaturation, single-stranded DNA ... A single nucleotide change in a particular sequence, as seen in a double-stranded DNA, cannot be distinguished by gel ...
This enzyme is not active on DNA containing a T/G mispair or single-stranded DNA. Barrett TE, Schärer OD, Savva R, Brown T, ... Double-stranded uracil-DNA glycosylase (EC, Mug, double-strand uracil-DNA glycosylase, Dug, dsUDG, double-stranded DNA ... Sung JS, Mosbaugh DW (August 2000). "Escherichia coli double-strand uracil-DNA glycosylase: involvement in uracil-mediated DNA ... Double-stranded+uracil-DNA+glycosylase at the US National Library of Medicine Medical Subject Headings (MeSH) Portal: Biology v ...
... 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 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, ...
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 ... Positive single-stranded RNA families: three non-enveloped (Astroviridae, Caliciviridae and Picornaviridae) and four enveloped ... Negative single-stranded RNA families: Arenaviridae, Bunyaviridae, Filoviridae, Orthomyxoviridae, ...
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 ...
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 ...
... es (+ssRNA viruses) are a group of related viruses that have positive-sense, single-stranded genomes ... Smith EC, Denison MR (5 December 2013). "Coronaviruses as DNA wannabes: a new model for the regulation of RNA virus replication ... Modrow S, Falke D, Truyen U, Schätzl H (2013). "Viruses with Single-Stranded, Positive-Sense RNA Genomes". Molecular virology. ... Double-stranded RNA virus Negative-strand RNA virus Sense (molecular biology) Baltimore D (September 1971). "Expression of ...
Formation of the RNA-DNA hybrid would protect the invading single-stranded DNA from degradation. After the transient RNA-DNA ... Thus DNA synthesis fills in gaps left over from annealing, and extends both ends of the still present single stranded DNA break ... ended single DNA strand that in the next step invades a homologous DNA duplex. RNA polymerase III is reported to catalyze ... Kaur H, De Muyt A, Lichten M (February 2015). "Top3-Rmi1 DNA single-strand decatenase is integral to the formation and ...
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 ...
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 ...
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". Viruses. 3 (9): 1699-1738. doi:10.3390/v3091699. PMC 3187698. PMID ... 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 two 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 ...
The sense strand is the strand of DNA that has the same sequence as the mRNA, which takes the antisense strand as its template ... An array can correspond to either strand; however, a single array will be made entirely of "sense" or "antisense" strands. ... In genetics, a sense strand, or coding strand, is the segment within double-stranded DNA that carries the translatable code in ... The "antisense" strand of DNA is complementary to the "sense" strand and is the actual template for mRNA synthesis. Knowing the ...
Krupovic M, Ghabrial SA, Jiang D, Varsani A (September 2016). "Genomoviridae: a new family of widespread single-stranded DNA ... Sclerotinia gemycircularvirus 1 is a single stranded DNA virus with a circular genome that infects the fungus Sclerotinia ... Articles with 'species' microformats, Single-stranded DNA viruses). ... The genes are encoded on complementary strands. This virus appears to be related to but distinct from members of the ...
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 ...
C. J. Chetsanga; V. Boyd; L. Peterson; K. Rushlow (1 January 1975). "Single-stranded regions in DNA of old mice". Nature. 253 ( ... Chetsanga has discovered two enzymes involved in the repair of damaged DNA: firstly, formamidopyrimidine DNA glycosylase, which ... "Release of 7-methylguanine residues whose imidazole rings have been opened from damaged DNA by a DNA glycosylase from ... "Release of 7-methylguanine residues whose imidazole rings have been opened from damaged DNA by a DNA glycosylase from ...
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 ...
It is a single stranded DNA virus (ssDNA). There are 49 species in this genus. Some members of this genus cause disease: PCV-1 ... DNA templated transcription, with some alternative splicing mechanism is the method of transcription. The virus exits the host ...
The genome of BBTV is made up of at least six circular, single-stranded DNA components, each about 1 kilo-base pair in length. ... Banana bunchy top is a viral disease caused by a single-stranded DNA virus called the banana bunchy top virus (BBTV). It was ... Banana bunchy top disease affects the banana fruit and foliage, and is caused by a single-strand DNA virus, the banana bunchy ... 1-4. Wang, Xiao-Wei; Blanc, Stéphane (2021-01-07). "Insect Transmission of Plant Single-Stranded DNA Viruses". Annual Review of ...
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 (Articles with short description, Short ...
Some include: DNA sequencing; capillary electrophoresis; mass spectrometry; single-strand conformation polymorphism (SSCP); ... A single-nucleotide variant (SNV) is a general term for single nucleotide change in DNA sequence. So a SNV can be a common SNP ... Haplotype mapping: sets of alleles or DNA sequences can be clustered so that a single SNP can identify many linked SNPs. ... In genetics, a single-nucleotide polymorphism (SNP /snɪp/; plural SNPs /snɪps/) is a germline substitution of a single ...
Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V (April 2011). "Cas3 is a single-stranded DNA nuclease and ... Class 2 systems use a single large Cas protein for the same purpose. Class 1 is divided into types I, III, and IV; class 2 is ... Brown, Kristen V. (February 24, 2017). "Scientists Are Creating a Genetic Chainsaw to Hack Superbug DNA to Bits". Gizmodo. G/O ... As of January 2022, the company and all employees were contained in a single 25,000 square foot research and manufacturing ...
The DnaC helicase loader then interacts with the DnaA bound to the single-stranded DNA to recruit the DnaB helicase, which will ... of either parent DNA or newly formed DNA and thereafter the ligating activity ligates that broken DNA strand and so the two DNA ... DNA replication initially produces two catenated or linked circular DNA duplexes, each comprising one parental strand and one ... The nicked strand, or T-strand, is then unwound from the unbroken strand and transferred to the recipient cell in a 5'-terminus ...
... a mammalian-type single-stranded DNA-binding protein, in a halophilic archaeon". Applied Microbiology and Biotechnology. 98 (4 ... and DNA repair systems. DasSarma's recent research (2010's) on an Antarctic halophilic microorganism, Halorubrum lacusprofundi ...
Regeneration occurs by a process involving DNA single-stranded binding protein and is likely a form of homologous ... "Extremely radiation-resistant mutants of a halophilic archaeon with increased single-stranded DNA-binding protein (RPA) gene ... H. salinarum is polyploid and highly resistant to ionizing radiation and desiccation, conditions that induce DNA double-strand ... To compensate, they have evolved a sophisticated DNA repair mechanism. The genome encodes DNA repair enzymes homologous to ...
... and is known as a strand-reversal/propeller, connecting adjacent parallel strands. If one or more of the DNA strands run in ... In beta sheets, sections of a single polypeptide may run side-by-side and antiparallel to each other, to allow for hydrogen ... During DNA replication, the leading strand is replicated continuously whereas the lagging strand is replicated in segments ... "Re: Why are the two strands of a DNA molecule antiparallel?". Retrieved 2017-04-06. "why is DNA antiparallel? ...
... that the tapered channel is large enough to accommodate double-stranded DNA at the wide end but only single-stranded DNA at the ... DNA exonucleases have roles to play in DNA metabolism, such as: replication, repair, and recombination. YqaJ is one of three ... The function of this protein domain is to digest DNA. Most viruses, inject their host with linear DNA, and this gets ... an enzyme that digests double-stranded DNA. It is a reaction which is dependent on Magnesium. It has a preference for 5'- ...
The key to cloning a DNA fragment is to link it to a vector DNA molecule that can replicate within a host cell. After a single ... For this reason, most restriction enzymes used in DNA cloning make staggered cuts in the DNA strands to create sticky ends. ... 2. DNA ligase During normal DNA replication, DNA ligase catalyzes end-to-end joining (ligation) of short fragments of DNA, ... Recombinant DNA ↓ Replication of recombinant DNA within host cell ↓ Isolation, sequencing, and manipulation of purified DNA ...
Some viruses can encode proteins that bind to double-stranded RNA (dsRNA) to prevent the activity of RNA-dependent protein ... Moiseeva O, Mallette FA, Mukhopadhyay UK, Moores A, Ferbeyre G (April 2006). "DNA Damage Signaling and p53-dependent Senescence ... has resistance to interferon and other anti-viral cytokines that is attributed to a single amino acid change in its Non- ... Toll Like Receptor 3 (TLR3) is important for inducing interferons in response to the presence of double-stranded RNA viruses; ...
Rao, Venigalla B.; Feiss, Michael (2015-11-09). "Mechanisms of DNA Packaging by Large Double-Stranded DNA Viruses". Annual ... Ultimately, single isomorphous replacement with anomalous scattering (SIRAS) crystallography was used to determine that the in ... Bacillus virus Φ29 (bacteriophage Φ29) is a double-stranded DNA (dsDNA) bacteriophage with a prolate icosahedral head and a ... When pRNA is in this tetramer ring form, it works as a part of the DNA packaging motor to transport DNA molecules to their ...
The ability to repair DNA double-strand breaks declines with aging in mice and humans. A set of rare hereditary (genetics) ... A single gene may affect multiple traits. Some traits that increase fitness early in life may also have negative effects later ... "Impaired DNA double-strand break repair contributes to the age-associated rise of genomic instability in humans". Cell Death ... Horvath S (2013). "DNA methylation age of human tissues and cell types". Genome Biology. 14 (10): R115. doi:10.1186/gb-2013-14- ...
... a promoter is a sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA ... Enhancers, when active, are generally transcribed from both strands of DNA with RNA polymerases acting in two different ... a large proportion of carcinogenic gene silencing is a result of altered DNA methylation (see DNA methylation in cancer). DNA ... RNA polymerase must attach to DNA near a gene for transcription to occur. Promoter DNA sequences provide an enzyme binding site ...
Inhibitors can escape removal during the DNA purification procedure by binding directly to single or double-stranded DNA. ... PCR inhibitors usually affect PCR through interaction with DNA or interference with the DNA polymerase. ... some DNA polymerases offer varying resistance to different inhibitors and increasing the concentration of the chosen DNA ... Techniques exist and kits are commercially available to enable extraction of DNA to the exclusion of some inhibitors. As well ...
The two strands of the human mitochondrial DNA are distinguished as the heavy strand and the light strand. The heavy strand is ... Whatever the mechanism, this single parent (uniparental inheritance) pattern of mtDNA inheritance is found in most animals, ... Mitochondrial DNA is replicated by the DNA polymerase gamma complex which is composed of a 140 kDa catalytic DNA polymerase ... Mitochondrial DNA is only a small portion of the DNA in a eukaryotic cell; most of the DNA can be found in the cell nucleus and ...
... upon DNA replication cause the insertion of a mis-matched base in the opposing strand. Up to 44% of hepatocellular carcinomas ... For instance, biological decontamination involving the use of a single bacterial species, Flavobacterium aurantiacum has been ... This active form then intercalates between DNA base residues and forms adducts with guanine residues, most commonly aflatoxin ... 8-hydroxyguanine lesions and DNA damage. Carcinogenicity The carcinogenicity of aflatoxin B1, which is characterized by the ...
RAD51 maintains genome integrity by repairing DNA double-strand breaks through homologous recombination. RAD51 heterozygous ... single gene test or multi-gene panel) CMM has clear severe impacts on a patient's ability to carry out daily manual tasks. It ...
... of single-strand DNA damages are converted to about 50 endogenous DNA double-strand breaks per cell per cell cycle. Although ... If the DNA is damaged, p53 will either repair the DNA or trigger the apoptosis of the cell. If p53 is dysfunctional or mutated ... Homologous recombination (HR) is an accurate process for repairing DNA double-strand breaks. HR is nearly absent in G1 phase, ... DNA replication occurs during the C period. The D period refers to the stage between the end of DNA replication and the ...
This result was not supported by molecular phylogenetic studies based on DNA sequences of nuclear and chloroplast DNA regions. ... Its small, pale yellow flowers hang in long, rope-like strands. The inflorescence is racemose in form, with up to 250 flowers. ... William R. Philipson said that Munroidendron "comprises a single species with such a distinct inflorescence and corolla that it ... Using cladistic methods, phylogenetic studies of DNA have shown that the closest relative of Munroidendron racemosum is ...
When it comes to the justification of science in the sense of general public participation by single practitioners, science ... One can trace this continental strand of thought through the phenomenology of Edmund Husserl (1859-1938), the late works of ... DNA) in 1953 to more recent advances in genetic engineering. Other key ideas such as the reduction of all life processes to ... Gauch 2002, p. 154, "Expressed as a single grand statement, science presupposes that the physical world is orderly and ...
The genus Stahlia is represented by a single species, S. monosperma (Tul.) Urb., known to occur only in Puerto Rico and the ... Well-known examples of polymers include plastics, DNA and proteins. According to the abstract released by the U.S. Patent & ... He is the founder of the international conservation organization Red Caribeña de Varamientos (Caribbean Stranding Network) ... Recently, the results of recent DNA studies have proved him right. Victor Manuel Blanco is an astronomer who, in 1959, ...
Later a single male Guardian becomes the Pale Bishop and founds The Paling, an anti-emotion faith. The females, however, see no ... The energy of Willpower was thus infused into the singular DNA of the Keepers and provided them an amazingly potent force of ... However, while doing so, Sinestro uses his Qwardian ring to force Jordan to Rayner's time portal, stranding Jordan in Rayner's ... With no Corps Kyle Rayner tries to single-handedly bring peace to the Vega System then after being kidnapped he joins the Omega ...
Kim HK, Park SJ, Nguyen VG, Song DS, Moon HJ, Kang BK, Park BK (2011) Identification of a novel single stranded circular DNA ... The genome is a single stranded circular DNA molecule 2600 bases in length. It has two open reading frames encoding a replicase ... Bovine stool associated circular virus is a single stranded DNA virus with a circular genome that was isolated from bovine ... Single-stranded DNA viruses, Unaccepted virus taxa, All stub articles, Virus stubs). ...
Other families exhibit diversification in some lineages; a single member of the SUMO family is found in the yeast genome, but ... DNA repair, and the cellular stress response. NEDD8 is best known for its role in regulating cullin proteins, which in turn ... protein fold consisting of a five-strand antiparallel beta sheet surrounding an alpha helix. The beta-grasp fold is widely ... and DNA repair. Most other UBLs have similar roles in regulating cellular processes, usually with a more restricted known range ...
This drug would be effective for ~10% of patients with DMD who have a single mutation in the DMD gene causing a stop codon to ... Small molecules may present a better way to target RNA and subsequently DNA because they can be designed to be more "drug-like ... The drug stabilizes the transient double-stranded RNA (dsRNA) structure formed between the SMN2 pre-mRNA and U1 snRNP complex, ... In 2009, the Zimmerman group discovered a compound to target the trinucleotide repeat expanded RNA and DNA that cause DM1. ...
... a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera)". The Journal of General Virology. 92 (Pt 6 ...
Double-stranded, repetitive DNA is separated from single-stranded, low-copy DNA by hydroxyapatite chromatography or other means ... at which the majority of repetitive elements have reassociated but single and low-copy elements remain single stranded. ... In CF, genomic DNA is heat-denatured and allowed to renature to a Cot value (Cot = DNA concentration x time x a factor based on ... and the two strands of each double-helix dissociate or 'denature.' If the denatured DNA is then slowly returned to a cooler ...
... the temperature at which a DNA double helix dissociates into single strands (see Nucleic acid thermodynamics) This ...
... is required for the non-homologous end joining (NHEJ) pathway of DNA repair, which rejoins double-strand breaks. It is ... The DNA-Pkcs protein is a serine/threonine protein kinase comprising a single polypeptide chain of 4,128 amino acids. DNA-PKcs ... HMGA2 protein could also have an effect on DNA-PKcs. HMGA2 delays the release of DNA-PKcs from sites of double-strand breaks, ... MicroRNA-101 targets DNA-PKcs via binding to the 3'- UTR of DNA-PKcs mRNA and efficiently reduces protein levels of DNA-PKcs. ...
Nicking endonuclease: These enzymes cut only one DNA strand, leaving the other strand untouched. **: Unknown cutting site: ... "The single group-I intron in the chloroplast rrnL gene of Chlamydomonas humicola encodes a site-specific DNA endonuclease (I- ... Yang J, Zimmerly S, Perlman PS, Lambowitz AM (May 1996). "Efficient integration of an intron RNA into double-stranded DNA by ... They act on the cellular DNA of the cell that synthesizes them; to be precise, in the opposite allele of the gene that encode ...
This is a potent enzyme inhibitor, in this case preventing the RNA polymerase II enzyme from transcribing DNA. The algal toxin ... Since ricin is a catalytic irreversible inhibitor, this allows just a single molecule of ricin to kill a cell. Methotrexate ... Many antibiotics such as penicillin and vancomycin inhibit the enzymes that produce and then cross-link the strands of this ... Satz AL, Kuai L, Peng X (May 2021). "Selections and screenings of DNA-encoded chemical libraries against enzyme and cellular ...
The process consists of multiple steps: The sample DNA is denatured, resulting in single-stranded sample DNA. Pairs of probes ... combining probe pairs that are hybridized immediately next to each other into a single strand of DNA that can be amplified by ... MLPA has a variety of applications including detection of mutations and single nucleotide polymorphisms, analysis of DNA ... Single Strand Conformation Analysis) effectively identify SNPs and small insertions and deletions. MLPA, however, is one of the ...
New "Prime Editing" Method Makes Only Single-Stranded DNA Cuts. In demonstrations in cell lines, the technique has a similar ... Once the new genetic material is incorporated into the cut strand of DNA, the prime editor nicks the unedited strand, signaling ... rewrites DNA by only cutting a single strand to add, remove, or replace base pairs. The method may allow researchers to edit ... A. Anzalone et al., "Search-and-replace genome editing without double-strand breaks or donor DNA," Nature, doi:10.1038/s41586- ...
Single-stranded DNA (ssDNA) ligation is a crucial step in many biochemical assays. Efficient ways of carrying out this reaction ... Single-stranded DNA (ssDNA) ligation is a crucial step in many biochemical assays. Efficient ways of carrying out this reaction ... A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation Anal Biochem. 2013 Apr 15;435(2):181- ... Our method uses a hairpin DNA to hybridize to any incoming acceptor ssDNA with low bias, with ligation of these strands ...
Nanotechnologists are using DNA, the genetic material present… ... Single-stranded DNA and RNA origami go live on Wyss Institute ... Single-stranded origami technology is based on design rules that can be used to cross DNA strands in and out of single stranded ... This schematic shows how a single strand of DNA can be programmed to self-fold into a large nanostructure, like, for example, ... To first enable the production of single-stranded and stable DNA-based origami with distinct folding patterns, the team had to ...
... reactions that combine two complementary single-stranded DNA molecules) ... DNA molecule used in hybridization reactions to detect the presence of a particular gene in an assortment of DNA fragments.( ... A _____ is a single-stranded DNA molecule used in hybridization reactions to detect the presence of a particular gene in an ... assortment of DNA fragments.. (Hybridization Reactions: reactions that combine two complementary single-stranded DNA molecules) ...
N2 - Unlabelled single- and double-stranded DNA (ssDNA and dsDNA, respectively) has been detected at concentrations =10-9?M by ... AB - Unlabelled single- and double-stranded DNA (ssDNA and dsDNA, respectively) has been detected at concentrations =10-9?M by ... Unlabelled single- and double-stranded DNA (ssDNA and dsDNA, respectively) has been detected at concentrations =10-9?M by ... Papadopoulou, E., & Bell, S. E. J. (2012). Label-free detection of nanomolar unmodified single- and double-stranded dna by ...
Here we show that parental Watson and Crick DNA template strands can be identified in sister chromatids of murine metaphase ... All chromosomes were found to have a uniform orientation with the 5′ end of the short arm on the same strand as T-rich major ... They find that sister chromatids can be distinguished by virtue of the organization of repetitive DNA relative to major ... Our results establish that DNA template sequences can be used to distinguish sister chromatids and follow their mitotic ...
Liu, Z., & Martin, L. J. (2001). Motor neurons rapidly accumulate DNA single-strand breaks after in vitro exposure to nitric ... Liu, Zhiping ; Martin, Lee J. / Motor neurons rapidly accumulate DNA single-strand breaks after in vitro exposure to nitric ... We tested the hypothesis that oxidative stress in vitro and axotomy in vivo induce single-strand breaks (SSB) in DNA, a form of ... Liu, Z & Martin, LJ 2001, Motor neurons rapidly accumulate DNA single-strand breaks after in vitro exposure to nitric oxide ...
DNA lesions formed by alkylating agents trigger double-strand breaks, in the absence of replication, by the action of MMR and ... Estimation of the N-alkyl adduct level is achieved by converting these adducts to single-stranded DNA (ssDNA) breaks by a ... 2008) DNA mismatch repair-induced double-strand breaks DNA Repair 7:48-56. ... allowing single-stranded nicks present in DNA to be revealed. The number below each lane indicates the amount of signals per ...
"Soft" CRISPR May Offer New Fix for Genetic Defects; Targeted Repairs With "Nicks" of Single DNA Strands Provide Foundation for ... Their strategy, which makes use of natural DNA repair machinery, provides a foundation for novel gene therapy strategies with ...
Physical and functional interaction between yeast Pif1 helicase and Rim1 single-stranded DNA binding protein. Nucleic Acids Res ... Physical and functional interaction between yeast Pif1 helicase and Rim1 single-stranded DNA binding protein.. ...
The best defined role of ADP-ribosylation in the DNA damage response is in repair of single strand breaks (SSBs). Recently, we ... Adprt1a signals MMS-induced DNA lesions to promote resistance of cells to DNA damage. As a consequence of defective signalling ... Taken together, these data indicate overlapping functions of different ARTs in signalling DNA damage, and illustrate a critical ... results in accumulation of DNA damage throughout the cell cycle following exposure to agents that induce base damage and DNA ...
Does single-stranded DNA pass through the inner channel of the protein hexamer in the complex with the Escherichia coli DnaB ... Does single-stranded DNA pass through the inner channel of the protein hexamer in the complex with the Escherichia coli DnaB ... Does single-stranded DNA pass through the inner channel of the protein hexamer in the complex with the Escherichia coli DnaB ... T1 - Does single-stranded DNA pass through the inner channel of the protein hexamer in the complex with the Escherichia coli ...
M13 mp18 single-stranded virion DNA can be used as a size marker for gel electrophoresis or as a control template for DNA ... M13 mp18 Single Strand DNA (Virion DNA). 25 ug. USD $120.00 M13mp18 DNA single-stranded virion DNA (7,249 bases) may be used as ... M13mp18 single-stranded virion DNA. M13mp18 DNA Single-Stranded Virion DNA (7,249 bases) may be used as a control template for ... M13mp18 DNA may also be used as a semi-quantitative marker to verify helper phage-enabled single-stranded DNA generation. ...
single-stranded DNA binding. id: GO:0003697. name: single-stranded DNA binding. namespace: molecular_function. type: go. ...
"Molecular crossmatching" for allogeneic bone marrow transplants by DNA single-strand polymorphism analysis. / Young, Neil ... title = "{"}Molecular crossmatching{"} for allogeneic bone marrow transplants by DNA single-strand polymorphism analysis", ... "Molecular crossmatching" for allogeneic bone marrow transplants by DNA single-strand polymorphism analysis. ... T1 - "Molecular crossmatching" for allogeneic bone marrow transplants by DNA single-strand polymorphism analysis ...
The presence of many single-stranded antibodies that bind to DNA often result from autoimmune reactions or viral infections. ... Hepatitis B is a single-stranded DNA virus, meaning the genetic information that it carries is in the form of a single-strand ... Research has shown that people who are infected with hepatitis B produce antibodies against the single-stranded DNA of this ... The presence of many single-stranded antibodies that bind to DNA often result from autoimmune reactions or viral infections. ...
To counteract the deleterious effects exerted by DNA lesions, eukaryotic cells have evolved a network of cellular pathways, ... termed DNA damage response (DDR). The DDR comprises both mechanisms devoted to re … ... DNA is exposed to both endogenous and exogenous DNA damaging agents that chemically modify it. ... Keywords: ATM; ATR; DNA damage response; DNA recombination; DNA repair; single-stranded DNA. ...
NEB offers a vast selection DNA plasmids for use in cloning, protein expression, gene expression, and cellular analysis. ... DNA Plasmids & Substrates. Close Lambda DNA Close Lambda DNA (dam-) Close M13mp18 RF I DNA Close M13mp18 Single-stranded DNA ... ΦX174 RF I DNA Close ΦX174 RF II DNA Close ΦX174 Virion DNA ... DNA Plasmids & Substrates. NEB offers a selection of common and ... Home Reagents and Molecular Biology Products DNA Plasmid & Substrates Products ...
Consisting of only eight strands, our DNA nanostructure spontaneously inserts into biological membranes by forming a toroidal ... Here, we employ DNA nanotechnology to design a synthetic enzyme that substantially outperforms its biological archetypes. ... Here the authors design a DNA nanostructure that catalyzes the transport of lipids between bilayers at a rate three orders of ... Furthermore, we show that our DNA-based enzyme can control the composition of human cell membranes, which opens new avenues for ...
A divergent clade of circular single-stranded DNA viruses from pig feces - (Peer Reviewed Journal) ... A divergent clade of circular single-stranded DNA viruses from pig feces. Archives of Virology. 158(10):2157-2162. ... DNA MICROARRAYS: GENE EXPRESSION APPLICATIONS - (Other) Bayles, D.O. 2003. Dna microarrays: gene expression applications. ... DNA sequence and analysis of a 90.1 kb virulence plasmid in shiga toxin-producing Escherichia coli (STEC) O145:NM 83-75 - (Peer ...
Chromatography of rNA polymerase from escherichia coli on single stranded DNA-agarose columns. scientific article published on ... Chromatography of rNA polymerase from escherichia coli on single stranded DNA-agarose columns (English) ...
... Export. ... or by hybridization of total DNA using universal cytoplasmic probes. In this study, we demonstrate that single-stranded ... Plant somatic hybrid cytoplasmic DNA characterization by single-strand conformation polymorphism. Tree physiology, 27(6), 785- ... Cytoplasmic DNA composition in somatic hybrids is commonly elucidated either by length polymorphism analysis of restricted ...
Order Human anti-single stranded DNA Antibody ssDNA IgM ELISA Kit 01012358012 at Gentaur single stranded DNA ,ssDNA ...
... this work should make it possible to study the dynamics of DNA processes involving DNA-SSB complexes as intermediates by AFM. ... The studies of SSB-binding mode transition and cooperativity are therefore critical to many cellular processes like DNA repair ... DNA in living cells is generally processed via the generation and the protection of single-stranded DNA involving the binding ... High-resolution AFM imaging of single-stranded DNA-binding (SSB) protein--DNA complexes L. Hamon 1, 2 D. Pastré 1, 2 P. ...
In 2012, Churchs team of Harvard scientists fit a single book with photographs into a DNA strand. ... and artwork in DNA strands. Imagine storing hundreds of books, videos, and works of art in strands of DNA no larger than the ... Share: Why Microsoft stored 200MB of data in DNA strands, and whats next By Alison DeNisco Rayome ... Why Microsoft stored 200MB of data in DNA strands, and whats next * ...
Once the DNA damage is repaired or bypassed using polymerases or through recombination, the amount of single-stranded DNA in ... Another type of DNA double-strand breaks originates from the DNA heat-sensitive or heat-labile sites. These DNA sites are not ... Reduced expression of DNA repair genes causes deficient DNA repair. When DNA repair is deficient DNA damages remain in cells at ... Single-strand damageEdit. Structure of the base-excision repair enzyme uracil-DNA glycosylase excising a hydrolytically- ...
  • Single-stranded DNA (ssDNA) ligation is a crucial step in many biochemical assays. (
  • Our method uses a hairpin DNA to hybridize to any incoming acceptor ssDNA with low bias, with ligation of these strands mediated by T4 DNA ligase. (
  • This technique potentially can be applied in protocols that require ligation of ssDNA, including ligation-mediated polymerase chain reaction (LMPCR) and complementary DNA (cDNA) library construction. (
  • Unlabelled single- and double-stranded DNA (ssDNA and dsDNA, respectively) has been detected at concentrations =10-9?M by surface-enhanced Raman spectroscopy. (
  • These data indicate that both ssDNA and the 5' arm of the fork bind in the same manner to the DNA binding site. (
  • Moreover, in the complex with the helicase, the length of the ssDNA is similar to the length of the ssDNA strand in the double-stranded DNA conformation. (
  • DNA in living cells is generally processed via the generation and the protection of single-stranded DNA involving the binding of ssDNA-binding proteins (SSBs). (
  • The presence of the RB69 DNA polymerase at the primer terminus results in a 57-fold increase in gp32 (SSB) affinity for ssDNA as a result of DNA polymerase:SSB cooperativity. (
  • With the establishment of the technology for providing of the SWCNTs for water through wrapping in single-stranded DNA (ssDNA), their potential applications have tremendously increased. (
  • Despite numerous studies about the mechanical and vibration characteristics of single-walled carbon nanotubes, these characteristics have not been fully explored in ssDNA and SWCNT composites. (
  • Proteins that bind to single stranded DNA (ssDNA) destabilize melting, provided that the rate of association is comparable to the pulling rate of the experiment. (
  • A _____ is a single-stranded DNA molecule used in hybridization r. (
  • A _____ is a single-stranded DNA molecule used in hybridization reactions to detect the presence of a particular gene in an assortment of DNA fragments. (
  • Each antibody only recognizes a specific type of foreign particle, whether it's a protein molecule, sugar molecule, fat molecule or DNA molecule. (
  • Cells on the glomerulus have a sugar molecule called heparin-sulfate, which happens to attract anti-DNA antibodies. (
  • [2] Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. (
  • We implement this approach to work with two next-generation sequencing (NGS) platforms: (1) a 3rd generation single molecule sequencing (SMS) platform (Helicos/SeqLL) whose unique capabilities obviate the need for lengthy sample preparation and PCR amplification, and (2) the more commonly used Illumina platform. (
  • Current theories say life on Earth started in an " RNA world ," in which the RNA molecule guided the formation of life, only later taking a backseat to DNA, which could more efficiently achieve the same end result. (
  • Like DNA, RNA is a helix-shaped molecule that can store or pass on information. (
  • RNA is most typically single-stranded, which means it is inherently less stable than DNA , the double-stranded molecule that encodes the human genome, and it's more prone to mutations. (
  • RNA is a single-stranded molecule composed of nucleobases. (
  • It's more prone to mutations than DNA, in which nucleobases pair up to create a double-stranded molecule. (
  • Each person's overall blueprint is basically the same, made up of about 3 billion "letters" of code, each letter corresponding to a chemical subunit of the DNA molecule. (
  • A new study has found this extra layer of encoded information in our DNA, in that the way the molecule itself is folded acts as yet another layer of information that can be used by the host organism's cells. (
  • because each molecule is amplified in isolation from other molecules it also precludes template competition, which frequently occurs when large numbers of different DNA fragments are amplified together. (
  • because each sequenced product stems from just one original single-stranded template molecule of known orientation, the DNA strand from which the sequence is derived is known. (
  • This kit gives students a chance to "handle" a molecule of DNA by first constructing 24 nucleotides from sugars, bases, and phosphates. (
  • Deoxyribonucleic Acid or DNA is a complex molecule that consists of many components. (
  • A nucleoside is the combination of these atoms into two structures, a five- carbon sugar molecule called deoxyribose, which is responsible for the name of DNA, and a phosphate group. (
  • Physical and functional interaction between yeast Pif1 helicase and Rim1 single-stranded DNA binding protein. (
  • Does single-stranded DNA pass through the inner channel of the protein hexamer in the complex with the Escherichia coli DnaB helicase? (
  • The structure of the complex of the Escherichia coli primary replicative helicase DnaB protein with single-stranded (ss) DNA and replication fork substrates has been examined using the fluorescence energy transfer method. (
  • The initiating events in the DDR entail both DNA lesion recognition and assembly of protein complexes at the damaged DNA sites. (
  • NEB offers a selection of common and specialized DNA plasmids for use in cloning experiments and applications such as protein expression, gene expression, and cellular analysis. (
  • The PURA gene provides instructions for making a protein called Pur-alpha (Purα), which is able to attach (bind) to DNA and RNA (a molecular cousin of DNA). (
  • This protein has multiple roles in cells, including controlling the activity of genes (gene transcription) and aiding in the copying (replication) of DNA. (
  • Others change single building blocks (amino acids) in the Purα protein or lead to production of an abnormally short protein. (
  • Reference: Biochemical characterization of interactions between DNA polymerase and single-stranded DNA-binding protein in bacteriophage RB69. (
  • To examine protein-protein interactions at the DNA replication fork, we have established solution conditions for the formation of a discrete and homogeneous complex of RB69 DNA polymerase (gp43), primer-template DNA, and RB69 single-stranded DNA-binding protein (gp32) using equilibrium fluorescence and light scattering. (
  • We have characterized the interaction between DNA polymerase and single-stranded DNA-binding protein and measured a 60-fold increase in the overall affinity of RB69 single-stranded DNA-binding protein (SSB) for template strand DNA in the presence of DNA polymerase that is the result of specific protein-protein interactions. (
  • We have also shown that a functional domain of RB69 single-stranded DNA-binding protein suggested previously to be the site of RB69 DNA polymerase-SSB interactions is dispensable. (
  • The protein encoded by this gene contains a RING finger, a motif present in a variety of functionally distinct proteins and known to be involved in protein-DNA and protein-protein interactions. (
  • The structural features for the biologically active genomic DNA were observed all living cells including the organelle- and the viralgenome, the potentiality of a new analytical method of the genome structure based on the appearance frequency, Sequence Spectrum Method (SSM) could be analyzed DNA, RNA and protein on genome and the structural features of genome might be related the biological complexity. (
  • DNA binding assays confirmed that the purified SsbB protein had single-stranded DNA binding activity. (
  • We exploit our discovery of lesion segregation to reveal how strand-asymmetric processes such as replication, transcription, and protein interactions shape DNA damage and repair. (
  • The cell consists of a permeable cell membrane, DNA, protein factories called ribosomes, and a protective outer cell wall. (
  • We describe experiments upon DNA + HMGB2 (box A), a nuclear protein that is believed to facilitate transcription. (
  • Which of the following structures is composed of DNA and protein? (
  • We have shown that in this system, MMR proteins are enriched on MNU-treated DNA and we observed robust, MMR-dependent, repair synthesis. (
  • ADP-ribosylation of proteins at DNA lesions by ADP-ribosyltransferases (ARTs) is an early response to DNA damage. (
  • Unlike proteins and RNA , DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. (
  • DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable to the effects of DNA damage. (
  • The organization and proper assembly of proteins to the primer-template junction during DNA replication is essential for accurate and processive DNA synthesis. (
  • Our data further suggest that the cooperative binding of the RB69 DNA polymerase and SSB to the primer-template junction is a simple but functionally important means of regulatory assembly of replication proteins at the site of action. (
  • The Gram positive bacterium, Streptococcus pneumoniae, has two genes, designated ssbA and ssbB, which are predicted to encode single-stranded DNA binding proteins (SSB proteins). (
  • FA is the result of a genetic defect in a cluster of proteins responsible for DNA repair via homologous recombination . (
  • A gene is a strand of chemical code, a sort of blueprint for proteins and other substances necessary for life. (
  • Bacterial rep proteins, a single-stranded DNA-dependent ATPase involved in DNA replication which can initiate unwinding at a nick in the DNA. (
  • Fungal srs2 proteins, an ATP-dependent DNA helicase involved in DNA repair. (
  • Proteins that bind to the double strand will tend to stabilize dsDNA, and melting will occur at higher forces. (
  • Because phosphorus is an essential element for DNA, RNA, several ubiquitous cofactors, and phosphorylated proteins, Pi-limitation has major affects on cellular metabolism and physiology. (
  • The data from these studies have been used to model the RB69 DNA polymerase-SSB interaction at the primer-template junction. (
  • The procedure relies on the 3'OH group of an SSB to prime a DNA polymerase I nick-translation reaction that labels downstream DNA with a biotinylated nucleotide 12 . (
  • Purpose: The principal aims of this study were as follows: 1) to validate the utility of detecting p53 gene mutations by means of polymerase chain reaction-single-strand conformation polymorphism (PCR- SSCP) analysis of complementary DNA (cDNA) (synthesized from prostate tissue RNA and 2) to study the concordance of RNA- and DNA-based PCR-SSCP assays in detecting p53 mutations in individual tumor fragments. (
  • Our Bst DNA/RNA Polymerase is at the core of this platform, which is a mixture of Bst polymerase and extremely thermostable reverse transcriptase. (
  • Polymerase chain reaction (PCR) is a widely used method in molecular biology, which can rapidly replicate millions to billions of specific DNA samples, enabling scientists to extract only a small amount of DNA samples for detailed research. (
  • A single-tube DNA identification process, Loop-mediated Isothermal Amplification recognises a total of six distinct sequences on the target DNA through the DNA polymerase and a set of four to six primers. (
  • Using assay primers and strand-displacing polymerase allows speedy amplification at a consistent temperature without the need for thermal cycling. (
  • SGR occurs when a gene sequence is cut and recombined within a single cell's genomic DNA, generally independent of DNA replication and the cell cycle. (
  • The base sequences of the genomic DNA including the genomic-RNA might be universal in all genomes, and the relationship between the structural features of the genome and the biological complexity was discussed. (
  • It is concluded that the contribution of the widespread stem-loop potential of single-stranded genomic DNA to the formation and maintenance of strand symmetry would be very limited, at least for higher-order oligonucleotides. (
  • Methods: RNA and genomic DNA were isolated by means of standard techniques from specimens of 19 carcinomas of the prostate, selected on the basis of p53 data obtained in a previous analysis of cDNA (indicating that 14 were mutant and five were wild-type). (
  • Genomic DNA was examined by means of SSCP analysis of isotopically labeled ( 32 PO 4 ) PCR products (DNA-PCR- SSCP analysis). (
  • For comprehensive analysis of p53 mutations in carcinomas of the prostate, and perhaps in other tumor tissues, SSCP analysis of cDNA should be used in combination with SSCP analysis of genomic DNA. (
  • The ssbB gene was amplified from genomic S. pneumoniae DNA and cloned into the E. coli expression vector, pET21a. (
  • Footprint competition assays are utilized to study the binding of Xenopus transcription factor A to a variety of single-stranded nucleic acids. (
  • Hanas, JS, Bogenhagen, DF & Wu, C-W 1984, ' Binding of Xenopus transcription factor a to 5S RNA and to single stranded DNA ', Nucleic acids research , 卷 12, 編號 6, 頁 2745-2758. (
  • Dual - beam optical tweezers experiments subject single molecules of DNA to high forces (∼ 300 pN) with 0.1 pN accuracy, probing the energy and specificity of nucleic acid - ligand structures. (
  • Most recently, GeneXpert MTB/RIF (Cepheid) advanced nucleic acid-based detection by integrating PCR and a highly sensitive molecular-beacon assay into a single, automated system. (
  • We herein report on the development of a nucleic acid platform designed to provide fast and portable detection, and demonstrated the utility by detecting MTB DNA from mechanically processed TB patient sputum samples. (
  • DNA Software, Inc . combines science and software to enable industrial genomics through advances in technologies based on nucleic acids. (
  • The company's first software platform, OMP™ (Oligonucleotide Modeling Platform™), models in silico the folding and hybridization of single-stranded nucleic acids with great accuracy. (
  • When nucleotides form chains they are referred to as nucleic acids, thus DNA is a type of nucleic acid. (
  • HuCaT uses an algorithm based on number of matching queries, k-mers are used to calculate the actual matching nucleic acid k-mers (short substrings of DNA [n 9 nt in number of nucleotide sequence matches for type assignment using the HuCaT]) to build alignments between query and reference sequences. (
  • The mutations were changed back to healthy DNA sequences with 35-55 percent efficiency, similar to rates that would likely be achieved with CRISPR-Cas9 editing. (
  • Like genetic DNA (and RNA) in nature, these engineered nanotechnological devices are also made up of strands that are comprised of the four bases known in shorthand as A, C, T, and G. Regions within those strands can spontaneously fold and bind to each other via short complementary base sequences in which As from one sequence specifically bind to Ts from another sequence, and Cs to Gs. (
  • In addition, they self-assemble from hundreds to thousands of individual DNA sequences that each need to be verified and tested for high-precision applications, and whose expensive synthesis often produces undesired side products. (
  • In a large DNA strand that goes through a complex folding process, many sequences need to accurately pair up with sequences that are far away from each other. (
  • Our results establish that DNA template sequences can be used to distinguish sister chromatids and follow their mitotic segregation in vivo . (
  • Meyne, J. & Goodwin, E. H. Strand-specific fluorescence in situ hybridization for determining orientation and direction of DNA sequences. (
  • Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. (
  • The article represents a new class of hidden symmetries in long sequences of oligonucleotides of single stranded DNA from their representative set that are associated with the common ability of all living organisms to grow and develop on the basis of incorporation into their body of new and new molecules of nutrients becoming new quantum-mechanic subsystems of the united quantum- mechanic organism. (
  • Nucleotide sequences in DNA. (
  • DNA) sequences of interest in organisms present in a clinical specimen. (
  • Web-based to query sequences using a k-mer (DNA substring) based algorithm. (
  • This normally shouldn't happen, so the presence of high levels of antibody against single-stranded DNA may indicate an autoimmune disease. (
  • In single antibody ELISAs the antigen is coated and only a detector antibody is used. (
  • Another type of gene editing that doesn't rely on DNA breaks and was thought to minimize inaccuracy is base editing , in which an enzyme can trade one DNA nuclease for another, but this strategy offers limited options as it can only make four of the 12 possible base pair changes, and some recent work has suggested it's not as precise as scientists first thought. (
  • When postdoc and lead author of the study Andrew Anzalone joined David Liu 's lab at the Broad Institute, which previously developed the technique for base editing, he was especially excited by the possibility of editing genes without using DNA breaks. (
  • We tested the hypothesis that oxidative stress in vitro and axotomy in vivo induce single-strand breaks (SSB) in DNA, a form of early DNA damage, in adult motor neurons early during their degeneration. (
  • Liu, Z & Martin, LJ 2001, ' Motor neurons rapidly accumulate DNA single-strand breaks after in vitro exposure to nitric oxide and peroxynitrite and in vivo axotomy ', Journal of Comparative Neurology , vol. 432, no. 1, pp. 35-60. (
  • Current models propose that during DNA replication, thymine is incorporated across from O 6 mG, promoting a futile cycle of mismatch repair (MMR) that leads to DNA double-strand breaks (DSBs). (
  • Nonhomologous end-joining promotes resistance to DNA damage in the absence of an ADP-ribosyltransferase that signals DNA single strand breaks. (
  • The best defined role of ADP-ribosylation in the DNA damage response is in repair of single strand breaks (SSBs). (
  • When normal repair processes fail, and when cellular apoptosis does not occur, irreparable DNA damage may occur, including double-strand breaks and DNA crosslinkages (interstrand crosslinks or ICLs). (
  • The Ubiquitin Ligase RNF138 Cooperates with CtIP to Stimulate Resection of Complex DNA Double-Strand Breaks in Human G1-Phase Cells. (
  • Single strand breaks (SSBs) represent the major form of DNA damage, yet no technique exists to map these lesions genome-wide with nucleotide-level precision. (
  • SSBs can further deteriorate into highly toxic double-strand breaks (DSBs) by stalling or collapsing replication fork 4 . (
  • Using a physiologically relevant exposure model (long-term/low-dose) with system validation using a human carcinogen, asbestos , we demonstrated that single-walled carbon nanotubes, multi-walled carbon nanotubes, ultrafine carbon black, and crocidolite asbestos induced particle-specific anchorage-independent colony formation, DNA-strand breaks, and p53 downregulation, indicating the genotoxicity and carcinogenic potential of CNMs. (
  • Several evidences suggested that majority of non-allelic homologous deletions are non-meiotic (non-classical) i.e. originate during homology directed repair of spontaneous DNA double-stranded breaks. (
  • Anti-DNA antibodies not only bind to the DNA that is on the surface of the cells lining the glomerulus, but they also bind to sugar molecules on this surface. (
  • Through a combination of microscopic simulations and fluorescence microscopy we find the lipid transport rate catalyzed by the DNA nanostructure exceeds 10 7 molecules per second, which is three orders of magnitude higher than the rate of lipid transport catalyzed by biological enzymes. (
  • After the translation is complete, researchers must manufacture the DNA molecules to encode the sequence. (
  • DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome . (
  • Instead, the new Duke device performs calculations in an analog fashion by measuring the varying concentrations of specific DNA molecules directly, without requiring special circuitry to convert them to zeroes and ones first. (
  • The newly released strand can in turn pair up with other complementary DNA molecules downstream in the circuit, creating a domino effect. (
  • While life was once thought to just be a happy accident by mainstream science, the building blocks of DNA and RNA are proving to be not only tenacious, these organic molecules also appear to be able to form in the most unlikely of places, including in deep space on the surface of comets. (
  • Many genes that were initially shown to influence life span have turned out to be involved in DNA damage repair and protection. (
  • The 46 chromosomes humans have contain approximately 35,000 genes We have approximately three billion base pairs (6 billion bases total) of DNA in most of our cells. (
  • Arguments that purine loading is specific for the loops of RNA-synonymous strands of genes whose transcripts function by virtue of their secondary structure need to take into account, as controls, the loop regions of mRNA- synonymous strands. (
  • After seeing the exploding need for synthetic genes and developing an industry-leading platform for creating short, single-stranded DNA (oligonucleotides), the company made a $21 million investment in DNA synthesis start-up Gen9 that combined each company's sequencing library in return for an equity stake and a position on the board. (
  • These genes are involved in DNA repair. (
  • Human DNA contains more than 20,000 genes, all of which are stored in our cells' nuclei. (
  • Viruses are tinier still, and are mostly just made up of a few genes on a strip of DNA. (
  • Cytoplasmic DNA composition in somatic hybrids is commonly elucidated either by length polymorphism analysis of restricted genome regions amplified with universal primers (PCR-RF) or by hybridization of total DNA using universal cytoplasmic probes. (
  • The DNA repair ability of a cell is vital to the integrity of its genome and thus to the normal functionality of that organism. (
  • Strikingly, we show that patterns of SSBs in the genome are non-random, specific to different biological states, enriched in regulatory elements, exons, introns, specific types of repeats and exhibit differential preference for the template strand between exons and introns. (
  • Thus, all this leads to a total dearth of knowledge of nucleotide-level genome-wide patterns for this critical type of DNA lesion. (
  • Here, we develop and validate an approach, SSiNGLe (single-strand break mapping at nucleotide genome level, Fig.1 ) that can provide nucleotide level maps of native SSBs genome-wide. (
  • One classification criterion is the virus's genetic material-for example, is the virus genome made of DNA or RNA? (
  • DNA viruses comprise a wide array of genome structures and infect diverse host species. (
  • These results provide insight into how strand asymmetric mechanisms underlie the formation, tolerance, and repair of DNA damage and thus shape cancer genome evolution. (
  • Since the current B. subtilis plasmids in the iGEM registry are single copy plasmids that integrate into the genome, our team designed a high copy number backbone compatible with B. subtilis based on pUB110 (9). (
  • During this talk, I will tell two such stories: 1) Structural variations in the human genome originate from different mechanisms related to DNA repair, replication, and retro-transposition. (
  • 3 ng/��l as measured by using Quant-it Picogreen kit (Invitrogen) on the Genios Tecan fluorometer Genome sequencing and assembly DNA (5 ��g) was mechanically fragmented for the paired-end sequencing, using a Covaris device (Covaris Inc., Woburn, MA,USA) with an enrichment size of 3-4 kb. (
  • Agrobacterium tumefaciens Competent Cells Market growth to be driven by the increasing Mutagenesis, Single-Stranded Dna Production, Bacmid creation, Cre-lox recombination (PIR1/PIR2) activities across the globe at a very fast speed. (
  • The product Assay kit for Monkey anti-double stranded DNA,dsDNA IgG (ELISA) should be kept between two and eight degrees Celsius to ensure the retention of the stability and reactivity of the reagents included in the kit. (
  • The product Assay kit for Monkey anti-double stranded DNA,dsDNA IgG (ELISA) is intended to be used for research purposes only. (
  • In this region, base pairing and stacking are disrupted as double stranded DNA (dsDNA) is melted. (
  • Factor A binds preferentially to non-specific single stranded (M13) DNA versus double stranded (pBR322) DNA. (
  • Factor A binds equally well to single stranded DNA fragments containing either the coding or non-coding strands of the 5S RNA gene. (
  • When a single strand encounters a perfect match at the end of one of the partially double-stranded ones, it latches on and binds, displacing the previously bound strand and causing it to detach, like someone cutting in on a dancing couple. (
  • It binds to the single-stranded DNA and acts in a progressive fashion along the DNA in the 3' to 5' direction. (
  • The nitrogen bases protruding from the existing strand bind to bases of the strand being synthesized according to the base pairing rules: Adenine binds to Thymine, and Cytosine binds to Guanine. (
  • For instance, the width of a strand of human hair is about 90,000 nanometers, bacteria are between 300-5,000 nanometers, viruses are 5-300 nanometers, the diameter of deoxyribonucleic acid (DNA) is 2.5 nanometers, and a single atom is 0.1-0.5 nanometers. (
  • Whereas current popular cloning approaches use in vitro assembly of DNA fragments, in vivo cloning offers potential for greater simplification. (
  • We also demonstrated that DNA fragments down to 400 base pairs have tryptase-stabilizing effects equal to that of intact DNA. (
  • Thus, DNA is digested with one rare andone frequently cutting restriction enzyme, and suitable adapters are ligated to theresulting restriction fragments. (
  • Although ADP-ribosylation is evident in adprt2(-) cells exposed to methylmethanesulfonate (MMS), disruption of adprt1a and adprt2 in combination abolishes this response and further sensitises cells to this agent, indicating that in the absence of Adprt2, Adprt1a signals MMS-induced DNA lesions to promote resistance of cells to DNA damage. (
  • How do cells sense DNA lesions? (
  • To counteract the deleterious effects exerted by DNA lesions, eukaryotic cells have evolved a network of cellular pathways, termed DNA damage response (DDR). (
  • The DDR comprises both mechanisms devoted to repair DNA lesions and signal transduction pathways that sense DNA damage and transduce this information to specific cellular targets. (
  • [1] In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA damage, resulting in tens of thousands of individual molecular lesions per cell per day. (
  • DNA damage, due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 10,000 to 1,000,000 molecular lesions per cell per day. (
  • While multiple types of DNA lesions exist, SSBs are considered the most common type of DNA damage 3 . (
  • These lesions can represent sites of oxygen radical DNA damage, intermediates in excision DNA repair pathway and products of unresolved intermediates of enzymes such as topoisomerases 3 . (
  • Some studies have detected Borrelia DNA within morphea lesions from a subset of European and Japanese patients (representing Borrelia afzelii and Borrelia garinii rather than B burgdorferi sensu stricto, the predominant subtype in the United States). (
  • Here we reveal that most mutagenic DNA lesions are not resolved into a mutated DNA base pair within a single cell cycle. (
  • Instead, DNA lesions segregate, unrepaired, into daughter cells for multiple cell generations, resulting in the chromosome-scale phasing of subsequent mutations. (
  • Furthermore, DNA replication across these persisting lesions can produce multiple alternative alleles in successive cell divisions, thereby generating both multiallelic and combinatorial genetic diversity. (
  • We demonstrate that replication over lesions produces almost identical collateral mutagenesis on the leading and lagging strands. (
  • In contrast to the synthesis of multi-stranded nanostructures, these entirely new types of origami are folded from one single strand, which can be replicated in living cells, allowing their potential low-cost production at large scales and with high purities, opening entirely new opportunities for diverse applications such as drug delivery and nanofabrication. (
  • DNA synthesis is a technology that links deoxynucleic acids (adenine, thymine, cytosine, and guanine) together to form DNA. (
  • As the cornerstone of modern molecular biology, DNA synthesis plays a pivotal role in the field of synthetic biology. (
  • Besides, we have been providing high-quality DNA synthesis products (phosphoramidites, controlled pore glass, molecular sieves, etc), and the products have been successfully applied in various fields of molecular biology. (
  • We use unique gene synthesis design software, which includes a full set of tools to design ideal structural units, thus enabling rapid and efficient gene construction and synthesis in a single reaction. (
  • Methotrexate is an antimetabolite that inhibits dihydrofolate reductase, thereby hindering DNA and RNA synthesis in lymphocytes and other immune cells. (
  • Termination of DNA synthesis by novel 3'-modified-deoxyribonucleoside 5'-riphosphates. (
  • IMSEAR at SEARO: Clinical relevance of the estimation of antibodies to single stranded DNA in systemic lupus erythematosus. (
  • DNAtranscription Is The Process By Which A Single Strand Of DNA Is Used As A Template To Generate A Strand Of MRNA. (
  • In genetics, complementary DNA (cDNA) is DNA synthesized from a single stranded RNA (e.g., messenger RNA (mRNA) or microRNA) template in a reaction catalyzed by the enzyme reverse transcriptase. (
  • To date, most studies of DNA viruses have focused on those with the strongest disease associations. (
  • Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. (
  • A single liter of seawater has about one billion bacteria and 10 billion viruses. (
  • This transmission electron micrographic (TEM) image reveals the presence of numerous linear, non-segmented single-stranded DNA, parvovirus H1 virions of the Parvoviridae family of viruses. (
  • The family Caliciviridae consists of a genetically diverse group of typing of norovirus, short nucleotide regions at the 5'-end of the capsid single-stranded RNA viruses that can be divided into 10 genera [ 1 ]. (
  • Here we show that parental 'Watson' and 'Crick' DNA template strands can be identified in sister chromatids of murine metaphase chromosomes using CO-FISH (chromosome orientation fluorescence in situ hybridization 4 ) with unidirectional probes specific for centromeric and telomeric repeats. (
  • Highly conserved orientation of telomeric and major satellite DNA in murine chromosomes revealed by four-colour CO-FISH. (
  • This, together with the ability to basically clone and multiply the single component strand in bacteria, presents a game-changing advance in DNA nanotechnology that greatly enhances single-stranded origami's potential for real-world applications. (
  • They are also extremely abundant-in just a single drop of water there can be over 100 species of bacteria. (
  • Unlike more complex organisms, such as eukaryotes, bacteria lack an enclosed nucleus and instead the DNA floats in a bunched tangle called the nucleoid. (
  • Bacteria occasionally carry DNA in smaller rings known as plasmids. (
  • Micro-organisms inhabiting teeth surfaces grow on biofilms where a specific and complex succession of bacteria has been described by co-aggregation tests and DNA-based studies. (
  • Previous studies had shown that when CRISPR-Cas9 targeted these same mutations, it caused off-target DNA changes in 16 predictable locations. (
  • Daughter cells that inherit these wrong bases carry mutations from which the original DNA sequence is unrecoverable (except in the rare case of a back mutation , for example, through gene conversion ). (
  • Scientists currently believe that single gene mutations cause approx. (
  • Conclusions and Implications: PCR-SSCP analysis of both RNA and DNA allows the detection of more mutations than the analysis of either alone. (
  • Prime editing requires this first step, but also includes two more components, a part of the guide RNA called the primer must also bind to the target site and the newly introduced DNA must bind to the original site. (
  • The presence of many single-stranded antibodies that bind to DNA often result from autoimmune reactions or viral infections. (
  • The B cells then produce antibodies that bind to this DNA. (
  • Antibodies cannot pass through the cell's outer membrane, so they cannot bind to the DNA that is inside the nucleus. (
  • Anti-DNA antibodies have been found to bind the wall of the glomerulus, which is the filtration bulb at the beginning of the filtration tube in the kidney. (
  • Just like Velcro and magnets have complementary hooks or poles, the nucleotide bases of DNA pair up and bind in a predictable way. (
  • Among the available nanomaterials, single-walled carbon nanotubes (SWCNTs) have specifically attracted significant research attention owing to their lightweight and excellent mechanical and optical properties. (
  • The feasibility of the method in practical applications was validated by designing an appropriate length of single-walled carbon nanotubes concerning the absorption stiffness between the single-stranded DNA and single-walled carbon nanotubes. (
  • Comparative proteomics and pulmonary toxicity of instilled single-walled carbon nanotubes, crocidolite asbestos , and ultrafine carbon black in mice. (
  • M13mp18 DNA Single-Stranded Virion DNA (7,249 bases) may be used as a control template for DNA sequencing and as a molecular size marker in agarose gel electrophoresis. (
  • Young, NT & Darke, C 1993, ' "Molecular crossmatching" for allogeneic bone marrow transplants by DNA single-strand polymorphism analysis ', The Lancet , vol. 341, no. 8838, pp. 183-184. (
  • The 2015 Nobel Prize in Chemistry was awarded to Tomas Lindahl , Paul Modrich , and Aziz Sancar for their work on the molecular mechanisms of DNA repair processes. (
  • Reif's lab is also beginning to work on DNA-based devices that could detect molecular signatures of particular types of cancer cells, and release substances that spur the immune system to fight back. (
  • 2001. Molecular dynamics studies of sequence-directed curvature in bending locus of Trypanosome kinetoplast DNA . (
  • 2001. Molecular dynamics of minimal B-DNA . (
  • Bailey, S. M., Goodwin, E. H. & Cornforth, M. N. Strand-specific fluorescence in situ hybridization: the CO-FISH family. (
  • Cleavage of DNA by Nuclease micrococcal is greater at the 5′ sides of A or T nucleotides than at G or C. (
  • The data is translated from zeros and ones into the letters of the four nucleotide bases of a DNA strand-(A)denine, (C)ytosine, (G)uanine, and (T)hymine. (
  • The replication of damaged DNA before cell division can lead to the incorporation of wrong bases opposite damaged ones. (
  • mismatch of bases, due to errors in DNA replication , in which the wrong DNA base is stitched into place in a newly forming DNA strand, or a DNA base is skipped over or mistakenly inserted. (
  • The relative quantities of bases in DNA were determined chemically many years before sequencing technologies permitted direct counting of bases. (
  • However, this approach maps a region of DNA, quite possibly extending thousands of bases from the original SSB, thus precluding identification of the lesion with nucleotide precision. (
  • The DNA sequence of kerA is 1458 bases long and codes for a serine protease. (
  • This provides an advantage over traditional PCR from double-stranded templates, in which the template strand is not known, because the frequency of different nucleotide misincorporations can be deduced … damage that affects different bases differently. (
  • It unwinds DNA duplexes with 3'-5' polarity with respect to the bound strand and initiates unwinding most effectively when a single-stranded region is present. (
  • To revisit the mechanism of O 6 mG processing, we reacted plasmid DNA with N-methyl-N-nitrosourea (MNU), a temozolomide mimic, and incubated it in Xenopus egg-derived extracts. (
  • Often a single plasmid is transmitted from one bacterium to another in a sex-like interaction called conjugation. (
  • Measurements of Watson and Crick DNA template strand fluorescence in post-mitotic cells. (
  • In this study, we demonstrate that single-stranded conformational polymorphism (SSCP) analysis is a powerful, quick and easy alternative method for cytoplasmic DNA characterization of somatic hybrids, especially for mitochondrial DNA. (
  • Once the new genetic material is incorporated into the cut strand of DNA, the prime editor nicks the unedited strand, signaling to the cell to rebuild it to match the edited strand. (
  • BOSTON) - Nanotechnologists are using DNA, the genetic material present in living organisms, as well as its multifunctional cousin RNA, as the raw material in efforts to build miniscule devices that could potentially function as drug delivery vehicles, tiny nanofactories for the production of pharmaceuticals and chemicals, or highly sensitive elements of electric and optical technologies. (
  • While the sheer amount of information that can be stored in genetic code is well known - a single gram of DNA is estimated to be able to hold 700 terabytes of information - it turns out that there is yet another layer of information that is mechanically encoded into our genetic material. (
  • They're nothing but naked RNA, single-stranded genetic material all folded in on itself. (
  • We used single-cell gel electrophoresis (comet assay) to detect DNA-SSB in motor neurons. (
  • The line probe assay, for instance, colorimetrically detects multi-drug resistant (MDR) strains from PCR-amplified products MTB DNA. (
  • These targets, in turn, impact a wide range of cellular processes including DNA replication, DNA repair and cell cycle transitions. (
  • The studies of SSB-binding mode transition and cooperativity are therefore critical to many cellular processes like DNA repair and replication. (
  • In an in vivo model of motor neuron apoptosis, DNA-SSB accumulate slowly in avulsed motor neurons before apoptotic nuclear features emerge, and the comet fingerprint is similar to NO toxicity. (
  • RecBCD is a multi-functional enzyme complex that processes DNA ends resulting from a double-strand break. (
  • The cysteine residues have been modified with a fluorescent marker which serves as a donor or an acceptor to another fluorescence label placed in different locations on the DNA substrates. (
  • It emits green fluorescence when bound to DNA or RNA. (
  • The Fluorescence emission of GoodView bound to DNA is centered at 530 nm. (
  • DNA Software will collaborate with Dr. Nils Walters at the University of Michigan to perform a systematic study of the kinetics (time course) of PCR using the advanced fluorescence spectroscopy and stopped-flow kinetics equipment available in Dr. Walters lab. (
  • Fluorescence detection in automated DNA sequence analysis. (
  • DNA sequencing by capillary electrophoresis with replaceable linear polyacrylamide and laser-induced fluorescence detection. (
  • Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. (
  • We came to an epiphany in 2012 when we realized we had the right things in place to encode, copy, and decode something in DNA," Church said. (
  • DNA is exposed to both endogenous and exogenous DNA damaging agents that chemically modify it. (
  • Implications of these results for the mechanism of a hexameric helicase binding to DNA are discussed. (
  • Gram-positive bacterial pcrA helicase, an essential enzyme involved in DNA repair and rolling circle replication. (
  • How do anti-DNA antibodies affect normal cells in MS? (
  • The anti-DNA antibodies produced by B cells attack healthy cells by attaching to this surface DNA. (
  • Research has shown that people who are infected with hepatitis B produce antibodies against the single-stranded DNA of this virus. (
  • The DNA damage profiles (shown by the comet morphology and moment) of NO donors, NO donor plus H 2 O 2 , and peroxynitrite are similar. (
  • Here we report that disruption of adprt2 results in accumulation of DNA damage throughout the cell cycle following exposure to agents that induce base damage and DNA SSBs. (
  • Taken together, these data indicate overlapping functions of different ARTs in signalling DNA damage, and illustrate a critical requirement for NHEJ in maintaining cell viability in the absence of an effective SSB response. (
  • As a consequence, the DNA repair process is constantly active as it responds to damage in the DNA structure. (
  • Active caspase-3 was subsequently increased, and 85% of the hippocampal CA1 neurons showed apoptotic DNA damage 3 d after ischemia. (
  • Subsequent active caspase-3 expression was not evident, and only 45% of the neurons showed apoptotic DNA damage. (
  • DNA damage is now widely recognized as a major reason behind cancer and many other aging-associated diseases and as such represents a very important issue for human health 1 , 2 . (
  • Fanconi anaemia ( FA ) is a rare genetic disease resulting in impaired response to DNA damage. (
  • But scientists have been able to sequence DNA from fossils that are 700,000 years old, so its storage potential could be much larger, Strauss added. (
  • Scientists were quick to sequence the novel coronavirus's genetic code, revealing it to be a single strand of RNA that is folded and twisted inside the virus's lipid envelope. (
  • Similarly, a strand of RNA is made up of a sequence of nucleotides, and on top of that sequence, there's the secondary structure of how the strand is folded up. (
  • But most DNA circuits are digital, where information is encoded as a sequence of zeroes and ones. (
  • We purchased two gBlocks from IDT to assemble the kerA DNA sequence, which included the signal peptide. (
  • The technology of DNA fingerprinting is based on the assumption that no two people have the same DNA sequence. (
  • Does not show good practice through the repeating sequence of acetic acid, dna fingerprinting and its application of core loci and this introductory video superimposition technique that eventually identified. (
  • but unlike DNA, RNA exists in nature in the form of single-stranded folds rather than paired double strands. (
  • Consisting of only eight strands, our DNA nanostructure spontaneously inserts into biological membranes by forming a toroidal pore that connects the membrane's inner and outer leaflets. (
  • Here, we employ DNA nanotechnology to design a synthetic enzyme that substantially outperforms its biological archetypes. (
  • Furthermore, we show that our DNA-based enzyme can control the composition of human cell membranes, which opens new avenues for applications of membrane-interacting DNA systems in medicine. (
  • Further, we showed that DNA-stabilized tryptase was more efficient in degrading nuclear core histones than heparin-stabilized enzyme. (
  • All chromosomes were found to have a uniform orientation with the 5′ end of the short arm on the same strand as T-rich major satellite repeats. (
  • Researchers at the Wyss Institute of Biologically Inspired Engineering and elsewhere have used these features to design self-assembling nanostructures such as scaffolded DNA origami and DNA bricks with ever-growing sizes and complexities that are becoming useful for diverse applications. (
  • Single-stranded origami technology is based on design rules that can be used to cross DNA strands in and out of single stranded regions to build large nanostructures. (
  • In contrast to traditional scaffolded origamis, which are assembled from hundreds of components, our new approach allows us to reliably design and synthesize stable single-stranded and self-folding origami," said Wyss Institute Core Faculty member and corresponding author Peng Yin, Ph.D. "Our fundamentally new approach relies on single-strand folding, rather than multi-component assembly, to produce large nanostructures. (
  • 2016. Homologous Pairing between Long DNA Double Helices . (
  • Interruptions in one of the strands of the sugar-phosphate backbone of double-stranded DNA. (
  • Results: RT-PCR-SSCP and DNA-PCR-SSCP identified p53 gene abnormalities in 15 of the 19 selected carcinomas, including one previously reported to be wild- type for p53. (
  • Six (33%) of the 18 abnormalities were detected by both RT-PCR-SSCP and DNA-PCR-SSCP, 10 (56%) were detected by RT-PCR-SSCP alone, and two (11%) were detected by DNA- PCR-SSCP alone. (
  • A new gene editing technique called prime editing, tested in human and mouse cells, rewrites DNA by only cutting a single strand to add, remove, or replace base pairs. (
  • Klar, A. J. Differentiated parental DNA strands confer developmental asymmetry on daughter cells in fission yeast. (
  • Recently, we initiated a study of how ADP-ribosylation regulates DNA repair in Dictyostelium and found that two ARTs (Adprt1b and Adprt2) are required for tolerance of cells to SSBs, and a third ART (Adprt1a) promotes nonhomologous end-joining (NHEJ). (
  • In autoimmune diseases, a person's healthy cells are attacked, and the DNA inside those cells is released. (
  • B cells find this DNA and think that it belongs to a foreign invader. (
  • Normal cells store their DNA inside their nucleus, which is deep inside a cell. (
  • However, cells have some DNA that is attached to its outer surface in the form of what is called DNA-histone complexes. (
  • [2] Because of the genetic defect in DNA repair, cells from people with FA are sensitive to drugs that treat cancer by DNA crosslinking , such as mitomycin C . The typical age of death was 30 years in 2000. (
  • Simple staining: Simple staining is a basic staining technique that uses a single dye to color all the cells in a sample. (