Dna single stranded. Medical search. Web

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 breaks (SSBs) refer to a type of DNA damage in which one strand of the double-helix structure is cleaved or broken. This kind of damage can occur spontaneously due to cellular metabolism or can be induced by various genotoxic agents, such as ionizing radiation and certain chemicals.

SSBs are typically repaired rapidly and efficiently by enzymes known as DNA repair proteins. However, if left unrepaired or misrepaired, they can lead to mutations, genomic instability, and increased risk of diseases, including cancer. In some cases, single-stranded breaks may also precede the formation of more severe double-stranded DNA breaks (DSBs).

It is important to note that while SSBs are less catastrophic than DSBs, they still play a significant role in genome maintenance and cellular health.

Single-stranded DNA (ssDNA) is a form of DNA that consists of a single polynucleotide chain. In contrast, double-stranded DNA (dsDNA) consists of two complementary polynucleotide chains that are held together by hydrogen bonds.

In the double-helix structure of dsDNA, each nucleotide base on one strand pairs with a specific base on the other strand through hydrogen bonding: adenine (A) with thymine (T), and guanine (G) with cytosine (C). This base pairing provides stability to the double-stranded structure.

Single-stranded DNA, on the other hand, lacks this complementary base pairing and is therefore less stable than dsDNA. However, ssDNA can still form secondary structures through intrastrand base pairing, such as hairpin loops or cruciform structures.

Single-stranded DNA is found in various biological contexts, including viral genomes, transcription bubbles during gene expression, and in certain types of genetic recombination. It also plays a critical role in some laboratory techniques, such as polymerase chain reaction (PCR) and DNA sequencing.

DNA damage refers to any alteration in the structure or composition of deoxyribonucleic acid (DNA), which is the genetic material present in cells. DNA damage can result from various internal and external factors, including environmental exposures such as ultraviolet radiation, tobacco smoke, and certain chemicals, as well as normal cellular processes such as replication and oxidative metabolism.

Examples of DNA damage include base modifications, base deletions or insertions, single-strand breaks, double-strand breaks, and crosslinks between the two strands of the DNA helix. These types of damage can lead to mutations, genomic instability, and chromosomal aberrations, which can contribute to the development of diseases such as cancer, neurodegenerative disorders, and aging-related conditions.

The body has several mechanisms for repairing DNA damage, including base excision repair, nucleotide excision repair, mismatch repair, and double-strand break repair. However, if the damage is too extensive or the repair mechanisms are impaired, the cell may undergo apoptosis (programmed cell death) to prevent the propagation of potentially harmful mutations.

Tert-butylhydroperoxide (t-BuOOH) is not typically considered a medical term, but rather a chemical compound. It is used in some medical and laboratory contexts. Here's a definition:

Tert-butylhydroperoxide (t-BuOOH) is an organic peroxide with the formula (CH3)3COOH. It is a colorless liquid, commercially available in concentrations up to 70%. It is used as an initiator in chemical reactions, a source of hydroxyl radicals in free-radical chemistry, and as a reagent in organic synthesis. Its use in medical contexts is typically limited to laboratory research and not as a therapeutic agent.

Handling tert-butylhydroperoxide requires caution due to its potential to cause fires and explosions when it comes into contact with certain substances, especially reducing agents and strong acids. Always follow safety guidelines and use appropriate personal protective equipment when handling this compound.

Deoxycytosine nucleotides are chemical compounds that are the building blocks of DNA, one of the two nucleic acids found in cells. Specifically, deoxycytosine nucleotides consist of a deoxyribose sugar, a phosphate group, and the nitrogenous base cytosine.

In DNA, deoxycytosine nucleotides pair with deoxyguanosine nucleotides through hydrogen bonding between the bases to form a stable structure that stores genetic information. The synthesis of deoxycytosine nucleotides is tightly regulated in cells to ensure proper replication and repair of DNA.

Disruptions in the regulation of deoxycytosine nucleotide metabolism can lead to various genetic disorders, including mitochondrial DNA depletion syndromes and cancer. Therefore, understanding the biochemistry and regulation of deoxycytosine nucleotides is crucial for developing effective therapies for these conditions.

The Comet Assay, also known as single-cell gel electrophoresis (SCGE), is a sensitive method used to detect and measure DNA damage at the level of individual cells. The assay gets its name from the comet-like shape that formed DNA fragments migrate towards the anode during electrophoresis, creating a "tail" that represents the damaged DNA.

In this assay, cells are embedded in low melting point agarose on a microscope slide and then lysed to remove the cell membranes and histones, leaving the DNA intact. The slides are then subjected to electrophoresis under neutral or alkaline conditions, which causes the negatively charged DNA fragments to migrate out of the nucleus towards the anode. After staining with a DNA-binding dye, the slides are visualized under a fluorescence microscope and the degree of DNA damage is quantified by measuring the length and intensity of the comet "tail."

The Comet Assay is widely used in genetic toxicology to assess the genotoxic potential of chemicals, drugs, and environmental pollutants. It can also be used to measure DNA repair capacity and oxidative DNA damage.

DNA repair is the process by which cells identify and correct damage to the DNA molecules that encode their genome. DNA can be damaged by a variety of internal and external factors, such as radiation, chemicals, and metabolic byproducts. If left unrepaired, this damage can lead to mutations, which may in turn lead to cancer and other diseases.

There are several different mechanisms for repairing DNA damage, including:

1. Base excision repair (BER): This process repairs damage to a single base in the DNA molecule. An enzyme called a glycosylase removes the damaged base, leaving a gap that is then filled in by other enzymes.
2. Nucleotide excision repair (NER): This process repairs more severe damage, such as bulky adducts or crosslinks between the two strands of the DNA molecule. An enzyme cuts out a section of the damaged DNA, and the gap is then filled in by other enzymes.
3. Mismatch repair (MMR): This process repairs errors that occur during DNA replication, such as mismatched bases or small insertions or deletions. Specialized enzymes recognize the error and remove a section of the newly synthesized strand, which is then replaced by new nucleotides.
4. Double-strand break repair (DSBR): This process repairs breaks in both strands of the DNA molecule. There are two main pathways for DSBR: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ directly rejoins the broken ends, while HR uses a template from a sister chromatid to repair the break.

Overall, DNA repair is a crucial process that helps maintain genome stability and prevent the development of diseases caused by genetic mutations.

Cell survival refers to the ability of a cell to continue living and functioning normally, despite being exposed to potentially harmful conditions or treatments. This can include exposure to toxins, radiation, chemotherapeutic drugs, or other stressors that can damage cells or interfere with their normal processes.

In scientific research, measures of cell survival are often used to evaluate the effectiveness of various therapies or treatments. For example, researchers may expose cells to a particular drug or treatment and then measure the percentage of cells that survive to assess its potential therapeutic value. Similarly, in toxicology studies, measures of cell survival can help to determine the safety of various chemicals or substances.

It's important to note that cell survival is not the same as cell proliferation, which refers to the ability of cells to divide and multiply. While some treatments may promote cell survival, they may also inhibit cell proliferation, making them useful for treating diseases such as cancer. Conversely, other treatments may be designed to specifically target and kill cancer cells, even if it means sacrificing some healthy cells in the process.

Deoxyribonucleic acid (DNA) is the genetic material present in the cells of organisms where it is responsible for the storage and transmission of hereditary information. DNA is a long molecule that consists of two strands coiled together to form a double helix. Each strand is made up of a series of four nucleotide bases - adenine (A), guanine (G), cytosine (C), and thymine (T) - that are linked together by phosphate and sugar groups. The sequence of these bases along the length of the molecule encodes genetic information, with A always pairing with T and C always pairing with G. This base-pairing allows for the replication and transcription of DNA, which are essential processes in the functioning and reproduction of all living organisms.

... (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, ...

https://en.wikipedia.org/wiki/Multicopy_single-stranded_DNA

... 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 ...

https://en.wikipedia.org/wiki/Single-strand_DNA-binding_protein

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 ...

https://en.wikipedia.org/wiki/Single-cell_DNA_template_strand_sequencing

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. ...

https://en.wikipedia.org/wiki/Triple-stranded_DNA

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 3.2.2.28, 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 U.S. National Library of Medicine Medical Subject Headings (MeSH) Portal: Biology ...

https://en.wikipedia.org/wiki/Double-stranded_uracil-DNA_glycosylase

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 ...

https://en.wikipedia.org/wiki/Single-strand_conformation_polymorphism

... 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 ...

https://en.wikipedia.org/wiki/Filamentous_bacteriophage

Reineck P, Wienken CJ, Braun D (January 2010). "Thermophoresis of single stranded DNA". Electrophoresis. 31 (2): 279-286. doi: ... A short introduction to thermophoresis, including helpful animated graphics, is at aerosols.wustl.edu Thermophoresis of DNA in ... Thamdrup LH, Larsen NB, Kristensen A (February 2010). "Light-Induced Local Heating for Thermophoretic Manipulation of DNA in ... Furthermore, thermophoresis has been demonstrated as a versatile technique for manipulating single biological macromolecules, ...

https://en.wikipedia.org/wiki/Thermophoresis

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 ...

https://en.wikipedia.org/wiki/Begomovirus

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: ...

https://en.wikipedia.org/wiki/Microscale_thermophoresis

... 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 ...

https://en.wikipedia.org/wiki/Bat_virome

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, ...

https://en.wikipedia.org/wiki/Viral_disease

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 ...

https://en.wikipedia.org/wiki/Phage_monographs

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 ...

https://en.wikipedia.org/wiki/TectoRNA

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 ...

https://en.wikipedia.org/wiki/Parvoviridae

... 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 ...

https://en.wikipedia.org/wiki/Veterinary_virology

... 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) "Current ICTV Taxonomy Release , ICTV". ictv. ...

https://en.wikipedia.org/wiki/Positive-strand_RNA_virus

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 ...

https://en.wikipedia.org/wiki/Sclerotinia_gemycircularvirus_1

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. ...

https://en.wikipedia.org/wiki/PAGEV_RNA_motif

... 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 ( ...

https://en.wikipedia.org/wiki/Iotatorquevirus

"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 ...

https://en.wikipedia.org/wiki/Nina_Papavasiliou

DNA helicases, DNA clamps and DNA topoisomerases, and replication proteins; e.g. single-stranded DNA binding proteins (SSB). In ... single stranded viruses) or one of the DNA strands (plasmids). The 5′ end of the nicked strand is transferred to a tyrosine ... including DNA gyrase) achieve this by adding negative supercoils to the DNA helix. Bare single-stranded DNA tends to fold back ... each one made up of a single strand of DNA. These two strands serve as the template for the leading and lagging strands, which ...

https://en.wikipedia.org/wiki/DNA_replication

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 ...

https://en.wikipedia.org/wiki/Reduced_representation_bisulfite_sequencing

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 ...

https://en.wikipedia.org/wiki/Circovirus

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 ...

https://en.wikipedia.org/wiki/Banana_bunchy_top_virus

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 ...

https://en.wikipedia.org/wiki/RTF1

Some include: DNA sequencing; capillary electrophoresis; mass spectrometry; single-strand conformation polymorphism (SSCP); ... Haplotype mapping: sets of alleles or DNA sequences can be clustered so that a single SNP can identify many linked SNPs. ... Single nucleotide substitutions with an allele frequency of less than 1% are sometimes called single-nucleotide variants (SNVs ... An intronic SNP in DNA mismatch repair gene PMS2 (rs1059060, Ser775Asn) is associated with increased sperm DNA damage and risk ...

https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism

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 ...

https://en.wikipedia.org/wiki/Synthesis-dependent_strand_annealing

... and Single-Stranded DNA Polymers". Physical Review Letters. American Physical Society (APS). 92 (4): 048303. Bibcode:2004PhRvL ... Tang, Jau; Marcus, R. A. (2005-11-22). "Single particle versus ensemble average: From power-law intermittency of a single ... "Counting statistics of single molecule reaction events and reaction dynamics of a single molecule". Chemical Physics Letters. ... Colquhoun, D.; Hawkes, A. G. (1982-12-24). "On the Stochastic Properties of Bursts of Single Ion Channel Openings and of ...

https://en.wikipedia.org/wiki/Reduced_dimensions_form

Kikuchi M, Ohnishi K, Harayama S (2000-02-08). "An effective family shuffling method using single-stranded DNA". Gene. 243 (1 ... Ogiwara H, Kohno T (2011-12-14). "Essential factors for incompatible DNA end joining at chromosomal DNA double strand breaks in ... First, DNase I is used to fragment a set of parent genes into segments of double stranded DNA ranging from 10-50 bp to more ... In RACHITT, fragments of single stranded (ss) parent genes are annealed onto a ss template resulting in decreased mismatching ...

https://en.wikipedia.org/wiki/DNA_shuffling

... sequences that melt become single-stranded and wash off. The temperatures at which labelled DNA comes off reflects the amount ... The mixture is incubated to allow DNA strands to dissociate and then cooled to form renewed hybrid double-stranded DNA. ... "DNA melting". To assess the melting profile of the hybridized DNA, the double-stranded DNA is bound to a column or filter and ... One method was introduced for hybridizing large numbers of DNA samples against large numbers of DNA probes on a single membrane ...

https://en.wikipedia.org/wiki/DNA–DNA_hybridization

Multicopy single-stranded DNA (msDNA) is a type of extrachromosomal satellite DNA that consists of a single-stranded DNA ... further extension of the DNA strand presents a problem: as DNA synthesis progresses, the bulky RNA strand extending from the 3 ... Hsu MY, Inouye M, Inouye S (December 1990). "Retron for the 67-base multicopy single-stranded DNA from Escherichia coli: a ... Yee T, Furuichi T, Inouye S, Inouye M (August 1984). "Multicopy single-stranded DNA isolated from a gram-negative bacterium, ...

https://en.wikipedia.org/wiki/Multicopy_single-stranded_DNA

Title:Sugar-Pucker Force-Induced Transition in Single-Stranded~DNA. Authors:X. Viader-Godoy, M. Manosas, F. Ritort ... Download a PDF of the paper titled Sugar-Pucker Force-Induced Transition in Single-Stranded~DNA, by X. Viader-Godoy and 2 other ... Download a PDF of the paper titled Sugar-Pucker Force-Induced Transition in Single-Stranded~DNA, by X. Viader-Godoy and 2 other ... Abstract:The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the ...

https://aps.arxiv.org/abs/2110.09370

... Genes Dev. 2008 Jan 1;22(1):8-13. doi ... Here, we report that the miRNA iab-4 locus in the Drosophila Hox cluster is transcribed convergently from both DNA strands, ...

https://pubmed.ncbi.nlm.nih.gov/18172160/

Topology- and linking number-controlled synthesis of a closed 3 link chain of single-stranded DNA Q. Li, G. Wu, Y. Yang, R. An ... Topology- and linking number-controlled synthesis of a closed 3 link chain of single-stranded DNA† ...

https://pubs.rsc.org/en/Content/ArticleLanding/2018/CC/C8CC04965C

... such as proteins and DNA, can be monitored in situ to understand their sensitivity to ch ... Bio-SAXS of single-stranded DNA-binding proteins: radiation protection by the compatible solute ectoine D. C. Hallier, G. J. ... Bio-SAXS of single-stranded DNA-binding proteins: radiation protection by the compatible solute ectoine† ... as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). In this ...

https://pubs.rsc.org/en/content/articlelanding/2023/CP/D2CP05053F

... single-stranded DNA overhangs, which are rapidly bound by the single-stranded DNA binding protein RPA. Next, Rad51 replaces RPA ... The most deleterious DNA damages are double-strand breaks (DSBs), and a single unrepaired DSB can lead to cell death. In human ... Ku encircles the DNA ends and recruits other factors, such the kinase DNA-PKcs, to bluntly ligate the ends back together. In ... Then, once it reaches the end, MRN removes DNA-PK and recruits Exo1 and BLM in order to promote long-range digestion of the DNA ...

https://repositories.lib.utexas.edu/items/01c6b0e4-83dc-4af1-a87c-e1be9d543797

Half-time of DNA repair of single-strand breaks (SSB) and double-strand breaks (DSB). Range. SSB a few minutes: DSB ,1 hour ... Estimated numbers of single-strand breaks and spontaneous base losses in nuclear DNA. ... This damage takes the form of single-strand breaks (SSB), much less abundant double-strand breaks (DSB), alkali-labile sites, ... Number of ATP molecules that may be required for repair of a single double-strand break (used in signaling, the generation of ...

https://bionumbers.hms.harvard.edu/bionumber.aspx?s=n&v=2&id=112195

A movie, an operating system and an Amazon gift card stored in a single strand of DNA. juin 11, 2021. par vqm7w ... in a single strand of DNA by reaching a record theoretical density of 215 petabytes per gram. ... Recall that DNA data storage is not only an amazing space saver, but also that the technique could allow us to preserve ... The new Fountain DNA technique makes it possible here to generate additional data for the information transmitted by packets. ...

https://www.speclab.com/a-movie-an-operating-system-and-an-amazon-gift-card-stored-in-a-single-strand-of-dna/

Study of the secondary nature of a single-stranded DNA fragment by the use of a self-modification reaction. / Bichenkova, EV; ... Study of the secondary nature of a single-stranded DNA fragment by the use of a self-modification reaction. In: Bioorgan. Khim ... Study of the secondary nature of a single-stranded DNA fragment by the use of a self-modification reaction. Bioorgan. Khim ( ... Bichenkova, EV, Adeenah-Zadah, A, Fedorova, OS & Knorre, DG 1997, Study of the secondary nature of a single-stranded DNA ...

https://research.manchester.ac.uk/en/publications/study-of-the-secondary-nature-of-a-single-stranded-dna-fragment-b

... without requiring double-strand breaks or donor DNA templates. We used prime editing in human cells to correct, efficiently and ... A new DNA-editing technique called prime editing offers improved versatility and efficiency with reduced byproducts ... a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a ... g, An in vitro primer extension reaction using a 3′-pegRNA generates a single apparent product by denaturing urea PAGE. The RT ...

https://www.nature.com/articles/s41586-019-1711-4?error=cookies_not_supported&code=a50b137c-f8da-4731-82d3-22a1f197e8d4

DNA Replication / physiology* * DNA, Single-Stranded / genetics * Membrane Proteins / genetics * Membrane Proteins / metabolism ... Asymmetric division and cosegregation of template DNA strands in adult muscle satellite cells Nat Cell Biol. 2006 Jul;8(7):677- ... Strikingly, some of these cells display selective template-DNA strand segregation during mitosis in the muscle fibre in vivo, ... The cosegregation of immortal template DNA strands and their link with the asymmetry apparatus has important implications for ...

https://pubmed.ncbi.nlm.nih.gov/16799552/?dopt=Abstract

DNA binding proteins can be classified into double-stranded DNA binding proteins (DSBs) and single-stranded DNA binding ... The evaluation results on both bound (DNA-bound) and non-bound (DNA-free) proteins have shown the satisfactory performance of ... Understanding the binding specificity of a DNA binding protein is helpful for the research of protein functions. In this paper ... Experimental results on 10-fold cross validation indicate that the new feature set are effective to describe DNA binding ...

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-S12-S4

... measurements in cryogenic conditions and computer simulations to characterize the structure and mechanics of single-strand DNA ... Lifting of a single-strand DNA at low temperature (Image from Scixel). The ssDNA molecules were adsorbed onto the substrate ... Stretching a single-strand DNA in cryogenic conditions. Cryo-electron microscopy can determine the structure of biological ... Stretching a single-strand DNA in cryogenic conditions. Cryo-electron microscopy can determine the structure of biological ...

https://chemistrycommunity.nature.com/posts/43322-stretching-single-strand-dna-by-cryo-force-spectroscopy

Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous ... "Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous ... Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous ... "Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous ...

https://scholars.duke.edu/publication/801235

A 60 base long DNA aptamer specific for BT tied to the 5 end of a 16 base cytosine rich DNA oligonucleotide is chosen as the ... UV/Vis absorption and fluorescence spectroscopic studies confirmed the formation of the fluorescent Ag NC on the DNA templates ... template for growing the Ag NC Two DNA aptamers specific for PA and part of their sequences were chosen as templates for ... Functional Fluorescent Silver Nanoclusters on Single Stranded DNA Scaffolds. Stephen F Austin State University, Baker Pattillo ...

https://scholarworks.sfasu.edu/urc/2023/Posters/29/

Genetically encoding DNA nanostructures provides a route for their production as well as applications in living cells. DNA ... Here the authors combine RNA hairpins and reverse transcription to generate and assemble a complex DNA structure inside the ... which nucleates DNA synthesis and is aided in elongation by murine leukemia reverse transcriptase. Purified ssDNA that is ... The field of DNA nanotechnology has harnessed the programmability of DNA base pairing to direct single-stranded DNAs (ssDNAs) ...

https://www.nature.com/articles/ncomms11179?error=cookies_not_supported&code=a09cc963-5006-412d-8db6-ce44557f6e30

One is called a "catalytic DNA hairpin mediator", which is a single-stranded DNA molecule that partially pairs up with itself ... Published in Nature Chemistry (Programmable autonomous synthesis of single-stranded DNA), research by Peng Yin at Harvards ... Autonomously growing synthetic DNA strands. (Nanowerk News) Synthetic biologists and nanobiologists are re-purposing DNA, the ... However, so far, researchers do not have tools at their disposal that would allow larger single-stranded sequences to ...

https://www.nanowerk.com/nanotechnology-news/newsid=48547.php

The Tom Schneider DNA Single Strand Shelving Unit is a dramatic piece of furniture perfect for a modern home. The winding ... Tom Schneider DNA Single Strand Shelving Unit. Give your living space a dramatic edge with the Tom Schneider DNA Single Strand ... The DNA Single Strand Shelves are available with either glass or wooden shelves. There is also a range of wood colours to ... Tom Schneider DNA Single Strand Shelving Unit Add to Wish List *View Product Information ...

https://www.taskers.com/brands/tom-schneider/tom-schneider-dna/tom-schneider-dna-single-strand-shelving-unit-tsk112492

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 ... Our high quality reagents are available for every workflow, including popular DNA assembly methods such as NEBuilder® HiFi DNA ...

https://www.neb.com/en-us/products/dna-plasmids-and-substrates

keywords = "optical tweezer, single-stranded DNA, single-stranded DNA binding protein",. author = "Lee, {Kyung Suk} and Marciel ... N2 - Single-stranded DNA binding proteins (SSBs) selectively bind single-stranded DNA (ssDNA) and facilitate recruitment of ... AB - Single-stranded DNA binding proteins (SSBs) selectively bind single-stranded DNA (ssDNA) and facilitate recruitment of ... Single-stranded DNA binding proteins (SSBs) selectively bind single-stranded DNA (ssDNA) and facilitate recruitment of ...

https://profiles.wustl.edu/en/publications/ultrafast-redistribution-of-e-coli-ssb-along-long-single-stranded

SS/RG/BK/Necklace DNA Spring Polvere/Single Strand with Floating Center/Rose gold plated and Black ... Necklace - Collar - DNA Spring - Single Strand Floating Polve BLACK - SS-RG WDNAG179 ... SS/RG/BK/Necklace DNA Spring Polvere/Single Strand with Floating Center/Rose gold plated and Black ... ":"Necklace - Collar - DNA Spring - Single Strand Floating Polve BLACK - SS-RG","public_title":null,"options":["Default Title ...

https://www.zfolio.com/collections/necklaces/products/necklace-collar-dna-spring-single-strand-floating-polve-black-ss-rg

Contrast from a single strand of DNA. This image, taken with equipment in the MIST lab at UM-StL with specimens developed by ... single DNA strands as well as the obscuring effect of a 10nm thick carbon support film (the curved material at the right of ... scattering cross-section for 300 kV electrons by DNA strands, the carbon support film, and the "known thickness" single walled ... Barns] [Yoctograms] [DNA] [Nuclei] [More] [Credits] Cross-sections and mean free paths. Although lights wavelength is too ...

https://www.umsl.edu/~fraundorfp/contrast.html

DNA is the result of a complex Know H ... Description In the DNA Pearl collection introduces a new ... DNA Perla Pink Single Strand and Black Dust Necklace. Regular Price $270.00 Sale Price $270.00 Regular Price Save -Infinity ... DNA is the result of a complex Know How, thanks to which it is possible to create a spiral-shaped and surprisingly elastic 925 ... In the DNA Pearl collection introduces a new materiality: a silver thread is the sole element of this collection. Wrought and ...

https://pesavento.ca/products/dna-perla-pink-single-strand-and-black-dust-necklace

Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1 ... Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1. Protein crystallography data. The structure of Single ... A full contact list of Zinc with other atoms in the Zn binding site number 1 of Single Stranded Dna-Binding Protein(ICP8) From ... A full contact list of Zinc with other atoms in the Zn binding site number 2 of Single Stranded Dna-Binding Protein(ICP8) From ...

http://zinc.atomistry.com/pdb1urj.html

... natures medium for engineering of single-stranded DNA-binding proteins",. abstract = "The architecture of single-stranded DNA- ... The architecture of single-stranded DNA-binding proteins, which play key roles in DNA metabolism, is based on different ... N2 - The architecture of single-stranded DNA-binding proteins, which play key roles in DNA metabolism, is based on different ... AB - The architecture of single-stranded DNA-binding proteins, which play key roles in DNA metabolism, is based on different ...

https://pure.johnshopkins.edu/en/publications/the-euryarchaeota-natures-medium-for-engineering-of-single-strand

Dive into the research topics of In Vivo Binding of Single-Stranded DNA-Binding Protein to Stalled Replication Fork Helicases ... In Vivo Binding of Single-Stranded DNA-Binding Protein to Stalled Replication Fork Helicases. ...

https://experts.nebraska.edu/en/publications/in-vivo-binding-of-single-stranded-dna-binding-protein-to-stalled/fingerprints/

Wakamatsu, T. et al., Structure of RecJ exonuclease defines its specificity for single-stranded DNA. J.Biol.Chem. (2010) ...

https://swissmodel.expasy.org/templates/2zxr

In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). (rsc.org)
In human cells, there exist two canonical pathways of DSB repair: Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR). Two protein complexes that rapidly bind DNA ends coordinate these separate pathways: the Ku70-Ku80 heterodimer (Ku) and the Mre11-Rad50-Nbs1 complex (MRN), respectively. (utexas.edu)
In contrast, MRN along with the long-range nuclease Exo1 and helicase BLM digests the DNA to create long 3' single-stranded DNA overhangs, which are rapidly bound by the single-stranded DNA binding protein RPA. (utexas.edu)
Protein-DNA interactions are essential for many biological processes. (biomedcentral.com)
Understanding the binding specificity of a DNA binding protein is helpful for the research of protein functions. (biomedcentral.com)
Therefore, a computational method is required to annotate the DNA binding protein as DSB or SSB automatically. (biomedcentral.com)
The protein products of this gene cluster play an important role in the transport of large molecules such as the E colicins and filamentous phage DNA into the bacterium. (duke.edu)
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. (neb.com)
The apparent diffusion coefficient of E. coli SSB thus determined ranged from 70,000 to 170,000 nt 2 /s, which is at least 600 times higher than that determined from SSB diffusion on short ssDNA oligomers, and is within the range of values reported for protein diffusion on double-stranded DNA. (wustl.edu)
The Crystal Structure of the Herpes Simplex Virus 1 Ssdna-Binding Protein Suggests the Structural Basis For Flexible, Cooperative Single-Stranded Dna Binding. (atomistry.com)
We created several deletion mutants of this protein based on its conserved motifs, and from these structures functional chimeras were synthesized, supporting the hypothesis that gene duplication and recombination could lead to novel functional forms of single-stranded DNA-binding proteins. (johnshopkins.edu)
Biophysical studies showed that the orthologs of the two OB fold/one zinc finger replication protein A in Hethanosarcina acetivorans and Methanopyrus kandleri exhibit two binding modes, wrapping and stretching of DNA. (johnshopkins.edu)
Most interestingly, a second single-stranded DNA-binding protein, FacRPA2, in this archaeon exhibited the wrapping mode. (johnshopkins.edu)
Domain analysis of this protein, which contains a single OB fold, showed that its architecture is similar to the functional homologs thought to be unique to the Crenarckaeotes. (johnshopkins.edu)
Catalyzed by primosome proteins such as PriA, PriB, PriC, DnaT, and DnaG, DNA replication restart pathways facilitate origin-independent reloading of the replicative helicase onto a repaired DNA replication fork in a process that involves coordinated protein and nucleic acid binding within a nucleoprotein complex called the DNA replication restart primosome [ 2 ]. (biomedcentral.com)
Bound or free: interaction of the C-terminal domain of E. coli single-stranded DNA binding protein (SSB) with the tetrameric core of SSB. (cipps.org.au)
This progression from DNA to RNA to protein is called the " central dogma " of molecular biology. (khanacademy.org)
Researchers find that temporary double-stranded DNA breaks commonly result from normal neuron activation-but expression of an Alzheimer's-linked protein increases the damage. (the-scientist.com)
Download DNA or protein sequence, view genomic context and coordinates. (yeastgenome.org)
Single-stranded binding protein Pot1, initially up-regulated at 12 wk in the WF+REG group, was later down-regulated in liver tissue at 24 wk along with the WF+HF group. (cdc.gov)
A protein interacting with an A-T-rich region that is a positive control element within the SP6 κ promoter was purified and identified as CArG-box binding factor-A. The purified protein was shown to interact specifically with the coding strand of single-stranded DNA and, with lower affinity, with double-stranded DNA. (lu.se)
Two Ets proteins, PU.1 and elf-1, that have previously been shown to bind to an adjacent DNA element were shown to physically interact with CArG- box binding factor.A. An antiserum raised against the protein recognized two different forms indicating either that different splice-forms of. (lu.se)
Some viruses have an outer envelope consisting of protein and lipid, surrounding a protein capsid complex with genomic RNA or DNA and sometimes enzymes needed for the first steps of viral replication. (msdmanuals.com)

This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. (rsc.org)
DNA binding proteins can be classified into double-stranded DNA binding proteins (DSBs) and single-stranded DNA binding proteins (SSBs), and they take part in different biological functions. (biomedcentral.com)
Experimental results on 10-fold cross validation indicate that the new feature set are effective to describe DNA binding proteins. (biomedcentral.com)
The evaluation results on both bound (DNA-bound) and non-bound (DNA-free) proteins have shown the satisfactory performance of our method. (biomedcentral.com)
Accordingly, the DNA binding proteins usually consist of single-stranded DNA-binding proteins (SSBs) and double-stranded DNA-binding proteins (DSBs). (biomedcentral.com)
Single-stranded DNA binding proteins (SSBs) selectively bind single-stranded DNA (ssDNA) and facilitate recruitment of additional proteins and enzymes to their sites of action on DNA. (wustl.edu)
The architecture of single-stranded DNA-binding proteins, which play key roles in DNA metabolism, is based on different combinations of the oligonucleotide/oligosaccharide binding (OB) fold. (johnshopkins.edu)
Here we show that unlike these groups of organisms, the Euryarchaeota has exploited the potential in the OB fold to re-invent single-stranded DNA-binding proteins many times. (johnshopkins.edu)
Although the diversity shown by archaeal single-stranded DNA-binding proteins is unparalleled, the presence of their simplest form in many organisms across all domains of life is of greater evolutionary consequence. (johnshopkins.edu)
We find that this type of non-canonical fork convergence in fission yeast is prone to trigger deletions between repetitive DNA sequences via a mechanism we call Inter-Fork Strand Annealing (IFSA) that depends on the recombination proteins Rad52, Exo1 and Mus81, and is countered by the FANCM-related DNA helicase Fml1. (elifesciences.org)
In Neisseria gonorrhoeae , the primosome proteins that catalyze DNA replication restart differ from the well-studied primosome proteins of E. coli with respect to the number of proteins involved and the affinities of their physical interactions: the PriA:PriB interaction is weak in E. coli , but strong in N. gonorrhoeae , and the PriB:DNA interaction is strong in E. coli , but weak in N. gonorrhoeae . (biomedcentral.com)
PriA is thought to recognize and bind to repaired DNA replication forks and D-loop recombination intermediates, facilitate assembly of the primosome complex by recruiting other primosome proteins, and catalyze duplex DNA unwinding using energy furnished by hydrolysis of ATP [ 4 , 5 ]. (biomedcentral.com)
DNA bears the hereditary information that's passed on from parents to children, providing instructions for how (and when) to make the many proteins needed to build and maintain functioning cells, tissues, and organisms. (khanacademy.org)
This type of RNA is called a messenger RNA ( mRNA ), as it serves as a messenger between DNA and the ribosomes, molecular machines that read mRNA sequences and use them to build proteins. (khanacademy.org)
Glass or quartz nanopipettes have found increasing use as tools for studying the biophysical properties of DNA and proteins, and as sensor devices. (imperial.ac.uk)
and proteins from the same stretch of DNA, plays an important role in molecular biology. (news-medical.net)
Telomeric DNA and shelterin proteins prevent loss of essential genetic information during cell division. (cdc.gov)
Double- and single-stranded telomere DNA-binding proteins Trf1/Trf2 and Pot1, as well as telomeric DNA damage foci LambdaH2AX and 53BP1, were influenced at 12 wk and 24 wk by both diet and exposure. (cdc.gov)
Once the provirus is integrated into the host cell DNA, it is transcribed using typical cellular mechanisms to produce viral proteins and genetic material. (msdmanuals.com)

The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. (arxiv.org)
There are two kinds of DNAs, single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). (biomedcentral.com)
SSB binds with ssDNA with high affinity and low specificity, and is mainly involved in DNA replication, recombination and repair. (biomedcentral.com)
In our study published in Nature Communications , we used a low temperature AFM to image individual 20-Cytosine single-strand DNA (ssDNA) adsorbed on a gold surface down to the sub-molecular level. (nature.com)
Comparing theoretical and experimental force curves, we estimated that the pulling stretched the lifted ssDNA segment with an average tension of about 2 nN, value 10 to 100 times higher than hitherto applied in most single-molecule force spectroscopy studies under ambient conditions. (nature.com)
In this work, we used a hybrid instrument that combines single-molecule fluorescence and force spectroscopy to directly visualize the movement of Escherichia coli SSB on long polymeric ssDNA. (wustl.edu)
The function of DnaT is not well understood, but it has been proposed that DnaT binding leads to dissociation of single-stranded DNA (ssDNA) from PriB through a competition mechanism, possibly exposing the ssDNA on the lagging strand template for reloading the replicative helicase, which ultimately leads to fork reactivation [ 8 ]. (biomedcentral.com)

Fig. 2: Prime editing of genomic DNA in human cells by PE1 and PE2. (nature.com)
Strikingly, some of these cells display selective template-DNA strand segregation during mitosis in the muscle fibre in vivo, as well as in culture independent of their niche, indicating that genomic DNA strands are nonequivalent. (nih.gov)
Problems that arise during DNA replication can drive genomic alterations that are instrumental in the development of cancers and many human genetic disorders. (elifesciences.org)
Accurate DNA replication is essential for genomic stability. (rcsb.org)
Negative-sense RNA viruses possess a single-stranded negative-sense genome that first must synthesize a complementary positive-sense antigenome, which is then used to make genomic negative-sense RNA. (msdmanuals.com)

Based on the nucleotides, the researchers then obtain a large quantity of small packets which are then coded into DNA sequences. (speclab.com)
They themselves inserted errors or even randomly deleted DNA sequences, but the information could still be restored each time. (speclab.com)
While DSBs involve in binding to particular dsDNA sequences, to modulate the process of transcription, to cleave DNA molecules, or to be involved in chromosome packaging and transcription in the cell nucleus, etc. (biomedcentral.com)
The number of errors in synthetic DNA increases with oligonucleotide length, and the resulting diversity of sequences can be a problem. (scilifelab.se)
These nanoscale applications often involve the synthesis of large sequences comprising thousands of the building blocks that DNA is made of, known as the A, T, C and G nucleotide bases, which can be further folded and structured due to the specific base-pairing abilities between As and Ts, and Cs and Gs, respectively. (nanowerk.com)
However, so far, researchers do not have tools at their disposal that would allow larger single-stranded sequences to autonomously grow and then join each other end-to-end following a molecular design plan, a capability that could generate structures and devices with diverse capabilities. (nanowerk.com)
Yin and his team have developed a method that allows pre-designed sequences of DNA to autonomously grow and concatenate along specific assembly routes, hence providing the basis for a new generation of programmable molecular devices. (nanowerk.com)
The approach gives us tremendous creative freedom: we can not only synthesize the same piece of DNA again and again as new additions of a growing sequence, but we can also vary the types of DNA sequences to be appended simply by changing the composition of catalytic hairpin DNAs and primers in the mix while the assembly is ongoing. (nanowerk.com)
Oligonucleotides are short sequences of nucleotides (RNA or DNA), typically with twenty or fewer bases. (news-medical.net)

Multicopy single-stranded DNA (msDNA) is a type of extrachromosomal satellite DNA that consists of a single-stranded DNA molecule covalently linked via a 2'-5'phosphodiester bond to an internal guanosine of an RNA molecule. (wikipedia.org)
Here, I use a combination of ensemble biochemical assays as well as high-throughput single-molecule microscopy to visualize the repair process. (utexas.edu)
We presented our works from the group of Prof. E. Meyer on single-molecule manipulation experiments over surfaces at low temperature (5 K) using an atomic force microscope (AFM). (nature.com)
The AFM apex is approached to the end of a single oligomer until a tip-molecule bound is formed. (nature.com)
One is called a "catalytic DNA hairpin mediator", which is a single-stranded DNA molecule that partially pairs up with itself to form a hairpin structure with a short overhanging single strand. (nanowerk.com)
Theranostics are emerging as a pillar of cancer therapy that enable the use of single molecule constructs for diagnostic and therapeutic application. (osti.gov)
The stochastic nature of single-molecule charge transport measurements requires collection of large data sets to capture the full complexity of a molecular system. (imperial.ac.uk)
Here we present such an approach based on multivariate pattern analysis and apply it to simulated and experimental single-molecule charge transport data. (imperial.ac.uk)
Thus researchers can predict, with reasonably good success, the shapes into which a DNA molecule of a given sequence will fold. (thebulletin.org)

The field of DNA nanotechnology has harnessed the programmability of DNA base pairing to direct single-stranded DNAs (ssDNAs) to assemble into desired 3D structures. (nature.com)
Primer Exchange Reaction (PER) cascades enable the autonomous growth of single-stranded DNAs. (nanowerk.com)

abstract = "Plasma cell-free DNA is being widely explored as a biomarker for clinical screening. (ncku.edu.tw)

Some viruses use RNA, not DNA, as their genetic material, but aren't technically considered to be alive (since they cannot reproduce without help from a host). (khanacademy.org)
Viruses that have RNA as genetic material, such as SARS-CoV-2 (the virus that causes COVID-19) and influenza, mutate much faster than viruses with DNA. (cdc.gov)
Rather than designing a single-strand DNA from scratch, he turned to naturally occurring, ready-made pieces of DNA: viruses. (thebulletin.org)
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. (cdc.gov)
either DNA or RNA viruses may have single or double strands of genetic material. (msdmanuals.com)
Single-strand RNA viruses are further divided into those with (+) sense and (-) sense RNA. (msdmanuals.com)
Positive-sense RNA viruses possess a single-stranded RNA genome that can serve as messenger RNA (mRNA) that can be directly translated to produce an amino acid sequence. (msdmanuals.com)
DNA viruses typically replicate in the host cell nucleus, and RNA viruses typically replicate in the cytoplasm. (msdmanuals.com)
Certain single-strand, (+) sense RNA viruses termed retroviruses use a very different method of replication. (msdmanuals.com)
Because RNA transcription does not involve the same error-checking mechanisms as DNA transcription, RNA viruses, particularly retroviruses, are particularly prone to mutation. (msdmanuals.com)
the genome of RNA viruses ranges from 3.5 kilobases (some retroviruses) to 27 kilobases (some reoviruses), and the genome of DNA viruses ranges from 5 kilobases (some parvoviruses) to 280 kilobases (some poxviruses). (msdmanuals.com)
RNA viruses that have their genetic material encoded in the form of single-stranded, positive-sense RNA. (bvsalud.org)

Scholars@Duke publication: Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous bacteriophages into Escherichia coli. (duke.edu)
The nucleotide sequence of a 1,854-base-pair DNA fragment carrying the fii region was determined. (duke.edu)
We prepared 14-378-nucleotide MOSIC oligonucleotides either by in vitro rolling-circle amplification or by amplification of phagemid DNA in Escherichia coli. (scilifelab.se)
Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T). Adenine and guanine are purines , meaning that their structures contain two fused carbon-nitrogen rings. (khanacademy.org)
With the arrival of a new class of single-nucleotide editors, researchers can target the most common type of pathogenic SNP in humans. (the-scientist.com)

The priming of msDNA synthesis offers a fascinating challenge to our understanding of DNA synthesis. (wikipedia.org)
HTBS recruits HIV reverse transcriptase, which nucleates DNA synthesis and is aided in elongation by murine leukemia reverse transcriptase. (nature.com)
Published in Nature Chemistry ( 'Programmable autonomous synthesis of single-stranded DNA' ), research by Peng Yin at Harvard's Wyss Institute for Biologically Inspired Engineering provides a broadly applicable solution to this problem. (nanowerk.com)
The Wyss Institute's team used the new concept to design a series of such PER DNA transcripts for very diverse applications, including the autonomous synthesis of large DNA nanostructures known as DNA-origamis, and synthetic biology approaches, in which the synthesis of a DNA transcript hinges on a trigger, such as a cancer-associated small micro RNA. (nanowerk.com)
These complex synthesis pathways proceed autonomously, comparable to a molecular robot performing a given task, and at a single temperature, which makes the technology very robust. (nanowerk.com)
Regardless of its precise form, collapse renders the fork incompetent for further DNA synthesis. (elifesciences.org)

Mutations in fii or tolA of the fii-tolA-tolB gene cluster at 17 min on the Escherichia coli map render cells tolerant to high concentrations of the E colicins and do not allow the DNA of infecting single-stranded filamentous bacteriophages to enter the bacterial cytoplasm. (duke.edu)

DSBs usually act as transcriptional factors to regulate the genes' expressions, while SSBs usually play roles in DNA replication, recombination, and repair, etc. (biomedcentral.com)
This so-called recombination-dependent replication (RDR) helps ensure that DNA is fully replicated prior to sister chromatid segregation, thereby avoiding mitotic catastrophes. (elifesciences.org)

A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. (nature.com)
We amplified oligonucleotides from clonal templates derived from single bacterial colonies and then digested cutter hairpins in the products, which released pools of oligonucleotides with precisely controlled relative stoichiometric ratios. (scilifelab.se)
Bacterial DNA replication restart pathways facilitate reinitiation of DNA replication following disruptive encounters of a replisome with DNA damage, thereby allowing complete and faithful duplication of the genome. (biomedcentral.com)
DNA replication restart pathways provide bacterial cells with a mechanism to reactivate replisomes that are disrupted in this manner [ 2 ]. (biomedcentral.com)
PriA belongs to the DExH family of DNA helicases and is well-conserved among sequenced bacterial genomes [ 3 ]. (biomedcentral.com)

Structure of RecJ exonuclease defines its specificity for single-stranded DNA. (expasy.org)

After a DNA fragment coding for the production of msDNA in E. coli was discovered, it was conjectured that bacteriophages might have been responsible for the introduction of the RT gene into E. coli. (wikipedia.org)
Whether you are performing your first cloning experiment or constructing multi-fragment DNA assemblies, NEB ® has the solution for you. (neb.com)

We report that N. gonorrhoeae PriA's DNA binding and unwinding activities are similar to those of E. coli PriA, and N. gonorrhoeae PriA's helicase activity is stimulated by its cognate PriB, as it is in E. coli . (biomedcentral.com)
This finding is significant because N. gonorrhoeae PriB's single-stranded DNA binding activity is weak relative to that of E. coli PriB, and in E. coli , PriB's single-stranded DNA binding activity is important for PriB stimulation of PriA helicase. (biomedcentral.com)
Furthermore, a N. gonorrhoeae PriB variant defective for binding single-stranded DNA can stimulate PriA's helicase activity, suggesting that DNA binding by PriB might not be important for PriB stimulation of PriA helicase in N. gonorrhoeae . (biomedcentral.com)
While it remains unclear if N. gonorrhoeae PriB's weak DNA binding activity is required for PriB stimulation of PriA helicase, the ability of PriB to stimulate PriA-catalyzed ATP hydrolysis could play an important role. (biomedcentral.com)
DNA replication restart initiated by PriA helicase is a highly coordinated process and probably represents the major pathway of DNA replication restart in E. coli . (biomedcentral.com)
Recruitment of PriB to a PriA:DNA complex stabilizes PriA on the DNA [ 6 ] and enhances its helicase activity through a mechanism that involves PriB's single-stranded DNA-binding activity [ 7 ]. (biomedcentral.com)

Nucleic acids, and DNA in particular, are key macromolecules for the continuity of life. (khanacademy.org)

Rothemund designed DNA staples that would bind to specific points along the "scaffold" strand of a virus. (thebulletin.org)

Retroviruses use reverse transcription to create a double-stranded DNA copy (a provirus) of their RNA genome, which is inserted into the genome of their host cell. (msdmanuals.com)
Unlike RETROVIRUSES they do not employ DNA intermediates in their life-cycle. (bvsalud.org)

DNA is the genetic material found in living organisms, all the way from single-celled bacteria to multicellular mammals like you and me. (khanacademy.org)

Here the authors combine force spectroscopy in cryogenic conditions with computer simulations to characterize the properties of DNA simultaneously down to the sub-nm level. (nature.com)
We also think that cryo-force spectroscopy might enable single-base distinction in DNA from their mechanical response. (nature.com)

deoxyribonucleic acid ( DNA ) and ribonucleic acid ( RNA ). (khanacademy.org)

This approach depends on "bricks" rather than scaffolds-that is, small lengths of DNA are assembled into units reminiscent of Legos, which can in turn be joined together. (thebulletin.org)

Telomeric DNA mediates de novo PML body formation. (nih.gov)

We performed more than 175 edits in human cells, including targeted insertions, deletions, and all 12 types of point mutation, without requiring double-strand breaks or donor DNA templates. (nature.com)
In the present study, we used enzymatic digestion of the protruding end of a probe-target DNA duplex to avoid interference by untargeted guanine on fluorescence quenching for detection of a nucleobase mutation. (elsevierpure.com)
A mutation refers to a single change in a virus's genome (genetic code). (cdc.gov)

Genetically encoding DNA nanostructures provides a route for their production as well as applications in living cells. (nature.com)
Since the early 1980s, it has been recognized that the information storage capacity of DNA is ideal for programming the self-assembly of nanostructures 1 . (nature.com)
The ability to create nanostructures within living cells using DNA has the potential to be a powerful tool for basic biology, biomedical engineering and medicine ( Fig. 1a ). (nature.com)
Analyses of the formation of a DNA crystal and folding of DNA nanostructures confirmed the scalability, purity and stoichiometry of the produced oligonucleotides. (scilifelab.se)
Nanowerk News ) Synthetic biologists and nanobiologists are re-purposing DNA, the hereditary material present in nearly all the body's cells, as a smart and stable self-assembling material to build nanofactories, drug-delivering nanostructures and molecular devices that can sense their environment and respond in different ways by, for example, detecting inflammation in the body or toxins in the environment. (nanowerk.com)
Putting their new concept of so-called 'Primer Exchange Reaction' (PER) cascades to the test, they successfully engineered a first set of devices with diverse functions, such as self-building DNA-origami and DNA nanostructures that sense, amplify, record or logically evaluate environmental signals. (nanowerk.com)

Next, Rad51 replaces RPA and facilitates strand exchange into a homologous chromosome to resynthesize the missing information in a largely error-free way. (utexas.edu)

In eukaryotes, such as plants and animals, DNA is found in the nucleus , a specialized, membrane-bound vault in the cell, as well as in certain other types of organelles (such as mitochondria and the chloroplasts of plants). (khanacademy.org)
In eukaryotes, DNA is typically broken up into a number of very long, linear pieces called chromosomes , while in prokaryotes such as bacteria, chromosomes are much smaller and often circular (ring-shaped). (khanacademy.org)

However, the desired nucleotides must be incorporated into a long DNA with complex secondary structure from which they would need to be cleaved as a second step. (nature.com)
DNA and RNA are polymers (in the case of DNA, often very long polymers), and are made up of monomers known as nucleotides . (khanacademy.org)

In the living world, DNA is designed to store, transport and transmit information, in this case the genetic heritage (genome). (speclab.com)
Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. (nature.com)
Consequently, DNA replication forks that stall or collapse due to encounters of the replisome with DNA damage must be reactivated to allow complete replication of the genome and ensure survival of the cell. (biomedcentral.com)

Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides. (scilifelab.se)
Enzymatic digestion of the protruding end of the DNA duplex fully prevented interference by untargeted guanine, and produced a marked difference in the quenching ratios (36% for wild-type, and 0% for mutant). (elsevierpure.com)

The most deleterious DNA damages are double-strand breaks (DSBs), and a single unrepaired DSB can lead to cell death. (utexas.edu)
The kinetics of repair of oxidative DNA damage (strand breaks and oxidised pyrimidines) in human cells. (harvard.edu)
This damage takes the form of single-strand breaks (SSB), much less abundant double-strand breaks (DSB), alkali-labile sites, and various species of oxidised purines and pyrimidines (van Sonntag, 1987). (harvard.edu)
DNA breaks in living cells are fairly easily measured, and the time course of their repair has been studied. (harvard.edu)
Kosicki, M., Tomberg, K. & Bradley, A. Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. (nature.com)
Cells were exposed to ozone at levels of 0, 60, 80, and 120ppb, and then DNA single-strand breaks and 8-oxoguanine levels were measured. (tmu.edu.tw)
However, tail moment appeared to be more sensitive than the other two indicators in detecting DNA single-strand breaks. (tmu.edu.tw)

This caused the viral DNA strand to automatically fold into a predetermined, two-dimensional shape. (thebulletin.org)

DNA damage is ubiquitous to all organisms and very complex pathways have evolved to recognize and repair these lesions. (utexas.edu)

Parvovirus B19 is a small, single-stranded DNA virus that replicates in dividing cells and thus has a remarkable tropism for human erythroid progenitor cells. (medscape.com)

Bases include the pyrimidine bases (cytosine, thymine in DNA, and uracil in RNA, one ring) and the purine bases (adenine and guanine, two rings). (khanacademy.org)
The four bases that make up DNA-adenine, cytosine, guanine, and thymine-always pair up in the same way. (thebulletin.org)

On the top, a 'catalytic PER hairpin' binds a first 'primer' (shown as a short grey strand), triggers its elongation with a sequence encoded by the hairpin itself, and releases it to start another cycle with the already extended primer, and so forth, until a long transcript is generated. (nanowerk.com)

Currently, methods are optimized for the extraction and detection of double-stranded mononucleosomal cell-free DNA of ∼160bp in length. (ncku.edu.tw)
High-bandwidth detection of short DNA in nanopipettes. (imperial.ac.uk)
Recently, we have demonstrated high-bandwidth detection of double-stranded (ds) DNA with microsecond time resolution in nanopipettes, using custom-designed electronics. (imperial.ac.uk)

Treatment with single-stranded and double-stranded specific nucleases suggests that ultrashort cell-free DNA is primarily single-stranded. (ncku.edu.tw)

Frankenberg-Schwager, M. (1989) Review of repair kinetics for DNA damage induced in eukaryotic cells in vitro by ionizing radiation, Radiother. (harvard.edu)
Finally, we show that template DNA cosegregates with Numb in label-retaining cells that express the self-renewal marker Pax7. (nih.gov)
Although it may seem counterintuitive that it is difficult to make DNA in cells, the production of short ssDNAs with precisely defined length and sequence has proven challenging. (nature.com)
Depletion of SMC5/6 sensitizes male germ cells to DNA damage. (nih.gov)
How DNA carries this information, and how it is put into action by cells and organisms, is complex, fascinating, and fairly mind-blowing, and we'll explore it in more detail in the section on molecular biology . (khanacademy.org)
Here, we investigated a radioiodinated PARP inhibitor, [ 125 I]KX1, and show drug target specific DNA damage and subsequent killing of BRCA1 and non-BRCA mutant ovarian cancer cells at sub-pharmacological concentrations several orders of magnitude lower than traditional PARP inhibitors. (osti.gov)
This study used single-cell gel electrophoresis (the Comet assay) and flow cytometry to investigate DNA damage in A549 cells exposed to ozone levels below the current ambient standard. (tmu.edu.tw)

The folded lengths are bound together as ladders are bound together by their rungs-and just as with ladders and rungs, the structure becomes more rigid and stable as more staple strands are added. (thebulletin.org)

Since the discovery of the DNA double helix 65 years ago, researchers have developed a detailed understanding of this molecular-scale building material and its properties. (thebulletin.org)

The biopharmaceutical relevance of producing plasmid DNA at large scale has increased steadily over the years due to the development of a growing number of direct and indirect applications. (scoop.it)

DNA polymerases (which include RT) share highly conserved structural features, which means that their active catalytic sites vary little from species to species, or even between DNA polymerases using DNA as a template, versus DNA polymerases using RNA as a template. (wikipedia.org)
One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. (rcsb.org)

Fluorescence quenching by guanine allows DNA hybridization to be monitored and any point mutations in oligonucleotides to be detected. (elsevierpure.com)

Telomere attrition resulting in DNA damage contributes to liver pathology. (cdc.gov)

Eukaryotic DNA replication initiates at multiple origin sites along each chromosome and terminates when replication forks (RFs) from adjacent origins converge. (elifesciences.org)

Ku encircles the DNA ends and recruits other factors, such the kinase DNA-PKcs, to bluntly ligate the ends back together. (utexas.edu)
ATM kinase phosphorylation and DNA damage activation was observed in the liver at 12 wk of WF exposure. (cdc.gov)

A single string of DNA can fold into all kinds of intricate shapes-depending on the base sequence encoded in the staple strands. (thebulletin.org)

Interestingly, PER DNA transcripts can become catalytic themselves, being able to cut an arbitrary target RNA, become fluorescently labeled probes that amplify the presence of a particular molecular stimulus, or "molecular recorders" that faithfully indicate the order in which certain molecular signals appear in their environments. (nanowerk.com)

A new genetic sensor called PRISM makes use of a host cell's DNA replication machinery to trigger fluorescence in neurons with damaged DNA. (the-scientist.com)

The Taq DNA Polymerase is intended for molecular biology applications. (qiagen.com)

In conclusion, our data suggest that disruption/down-regulation of single-stranded Pot1 and double-stranded Trf1/Trf2 expression in liver might act as an anti-apoptotic mechanism in the DNA-damage response leading to multistep liver injury by involvement in the telomere response to diet changes and WF exposure. (cdc.gov)

Here we combined measurements in cryogenic conditions and computer simulations to characterize the structure and mechanics of single-strand DNA adsorbed on gold down to the sub-nm level. (nature.com)

The examination of this cfDNA species could reveal new features of cell death pathways or it can be used for cell-free DNA biomarker discovery. (ncku.edu.tw)

However, fluorescence quenching is often affected by untargeted guanine located in a protruding end (single-strand DNA) of the probe-target DNA duplex resulting in an unsatisfactory sensitivity. (elsevierpure.com)

DNA origami: Unfolding risk? (thebulletin.org)
This area of biotechnology research, known as DNA origami, folds DNA into nano-scale shapes designed to perform specific mechanical functions or biological interactions. (thebulletin.org)
DNA's strict base-pairing rule and its self-assembly principle are what make it possible to design and create DNA origami structures. (thebulletin.org)
The arrival of DNA origami was announced to the world in 2006 when Rothemund's smiley face graced the cover of Nature . (thebulletin.org)
In 2012, another version of DNA origami was introduced. (thebulletin.org)

Single-stranded oligonucleotides are important as research tools, as diagnostic probes, in gene therapy and in DNA nanotechnology. (scilifelab.se)

Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. (yeastgenome.org)

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Impaired translesion synthesis in xeroderma pigmentosum variant extracts. (1/5092)

The DNA binding activity of Translin is mediated by a basic region in the ring-shaped structure conserved in evolution. (2/5092)

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)

An allosteric synthetic DNA. (4/5092)

The binding affinity of Ff gene 5 protein depends on the nearest-neighbor composition of the ssDNA substrate. (5/5092)

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)

Nuclear foci of mammalian recombination proteins are located at single-stranded DNA regions formed after DNA damage. (7/5092)

Structure of DNA-dependent protein kinase: implications for its regulation by DNA. (8/5092)

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Impaired translesion synthesis in xeroderma pigmentosum variant extracts. (1/5092)

The DNA binding activity of Translin is mediated by a basic region in the ring-shaped structure conserved in evolution. (2/5092)

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)

An allosteric synthetic DNA. (4/5092)

The binding affinity of Ff gene 5 protein depends on the nearest-neighbor composition of the ssDNA substrate. (5/5092)

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)

Nuclear foci of mammalian recombination proteins are located at single-stranded DNA regions formed after DNA damage. (7/5092)

Structure of DNA-dependent protein kinase: implications for its regulation by DNA. (8/5092)

Multicopy single-stranded DNA

Single-strand DNA-binding protein

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Multicopy single-stranded DNA - Wikipedia

2110.09370] Sugar-Pucker Force-Induced Transition in Single-Stranded~DNA

A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands

Topology- and linking number-controlled synthesis of a closed 3 link chain of single-stranded DNA - Chemical Communications ...

Bio-SAXS of single-stranded DNA-binding proteins: radiation protection by the compatible solute ectoine - Physical Chemistry...

Single-molecule studies reveal mechanisms of human DNA double-strand break repair

Half-time of DNA repair of single-strand brea - Human Homo sapiens - BNID 112195

A movie, an operating system and an Amazon gift card stored in a single strand of DNA - Tips and science

Study of the secondary nature of a single-stranded DNA fragment by the use of a self-modification reaction<...

Search-and-replace genome editing without double-strand breaks or donor DNA | Nature

Asymmetric division and cosegregation of template DNA strands in adult muscle satellite cells

Identification of single-stranded and double-stranded dna binding proteins based on protein structure | BMC Bioinformatics |...

Stretching a single-strand DNA in cryogenic conditions | Chemistry Community

Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous...

SFA ScholarWorks - Undergraduate Research Conference: Functional Fluorescent Silver Nanoclusters on Single Stranded DNA...

Genetic encoding of DNA nanostructures and their self-assembly in living bacteria | Nature Communications

Autonomously growing synthetic DNA strands

Tom Schneider DNA Single Strand Shelving Unit

DNA Plasmids & Substrates Products | NEB

Ultrafast redistribution of E. coli SSB along Long single-stranded DNA via intersegment transfer<...

Necklace - Collar - DNA Spring - Single Strand Floating Polve BLACK - - ZFolio

Billiards with Electrons

DNA Perla Pink Single Strand and Black Dust Necklace - Pesavento Canada

Zinc in PDB 1urj: Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1

The euryarchaeota, nature's medium for engineering of single-stranded DNA-binding proteins<...

In Vivo Binding of Single-Stranded DNA-Binding Protein to Stalled Replication Fork Helicases - Fingerprint - Research...

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