• 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)