AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation Science
Heteroduplex AnalysisSilverBase Pair MismatchCationsMercuryCytosineNucleic Acid HeteroduplexesTransition TemperatureThymineDNA Mismatch RepairThermodynamicsNucleic Acid DenaturationCalorimetryBase SequenceBase PairingSpectrometry, FluorescencePolymorphism, Single NucleotideMutS Homolog 2 ProteinMutS DNA Mismatch-Binding ProteinDNA RepairBase CompositionDNA Repair EnzymesMolecular Sequence DataSkull BaseDNASchiff BasesMutationDNA-Binding ProteinsColorectal Neoplasms, Hereditary NonpolyposisNucleic Acid ConformationAdaptor Proteins, Signal TransducingAdenosine TriphosphatasesMicrosatellite RepeatsEscherichia coliDNA GlycosylasesOligonucleotidesNuclear ProteinsContingent Negative VariationN-Glycosyl HydrolasesMicrosatellite InstabilityFrameshift MutationGuanineEndodeoxyribonucleasesOligodeoxyribonucleotidesEscherichia coli ProteinsSkull Base NeoplasmsAdenineRecombination, GeneticMutagenesisThymine DNA GlycosylaseCarrier ProteinsAmino Acid SequenceModels, MolecularNeoplasm Proteins2-AminopurineMethylnitronitrosoguanidineRhodiumPolymerase Chain ReactionSaccharomyces cerevisiae
SequenceWobbleMicrosatellite instabilityAdenineAlignmentsProteinsCleavageSpecificityPolymeraseTumorReplication errorsMechanismsNucleotideHydrogen bondsGeneticBindsDownstreamGenomeGenesOverlapRepairSequencesComplementaryQuantificationMechanismInteractionDetectProbesOccurProtonFragmentsSitesPresenceMutationsFindSingleMolecularHighContributionRulesLargelyLeadActiveCorrectLargeSpecificIdentify
Sequence8
  • Dictated by specific hydrogen bonding patterns, "Watson-Crick" (or "Watson-Crick-Franklin") base pairs (guanine-cytosine and adenine-thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. (wikipedia.org)
  • In addition, base-pairing between transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins via the genetic code. (wikipedia.org)
  • We demonstrate that relatively short single-stranded oligodeoxynucleotides, 25-61 bases homologous to the target sequence except for a single mismatch to the targeted base, are capable of correcting a single point mutation (G to A) in the mutant beta-galactosidase gene, in nuclear extracts, episome, and chromosome of mammalian cells, with correction rates of approximately 0.05%, 1% and 0.1%, respectively. (nih.gov)
  • The requirement for a total of 6-12 fingers, each of which binds three base pairs, provides enough specificity to address a unique sequence in a genome as complex as the three billion base pairs of human DNA. (ddw-online.com)
  • At its heart, it's also a restriction enzyme-based cloning system, but it takes advantage of type IIS restriction enzymes and these types, these enzymes, unlike the type IIP, they cut outside of the recognition sequence and so this has the advantage of one recognition sequence can be used to assemble many different fragments. (neb.com)
  • Based on relaxed sequence similarity searches, morFeus selects sequences based on the similarity of their alignments to the query, tests for orthology by iterative reciprocal BLAST searches and calculates a network score for the resulting network of orthologs that is a measure of orthology independent of the E-value. (biomedcentral.com)
  • Other orthology search methods combine sequence-based searches with phylogenetic methods or graph-clustering algorithms to circumvent computationally intense phylogenetic calculations. (biomedcentral.com)
  • We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. (cdc.gov)
Wobble3
  • The GU pairing, with two hydrogen bonds, does occur fairly often in RNA (see wobble base pair). (wikipedia.org)
  • Inosine is commonly found in tRNAs and is essential for proper translation of the genetic code in wobble base pairs . (wikidoc.org)
  • X-ray analysis reveals that a T⋅U mismatch impairs RNA extension by forming a wobble base pair at the Pol II active center that dissociates the catalytic metal ion and misaligns the RNA 3′ end. (cipsm.de)
Microsatellite instability2
Adenine5
  • This is particularly important in RNA molecules (e.g., transfer RNA), where Watson-Crick base pairs (guanine-cytosine and adenine-uracil) permit the formation of short double-stranded helices, and a wide variety of non-Watson-Crick interactions (e.g. (wikipedia.org)
  • Adenine-guanine base pairing ribosomal RNA. (wikidata.org)
  • The DNA glycosylase MutY repairs the DNA damage by removing adenine from mismatched adenine:8-oxoganine base pair. (rutgers.edu)
  • Adenine is converted to adenosine or inosine monophosphate (IMP), either of which, in turn, is converted into inosine (I), which pairs with Adenine (A), cytosine (C), and uracil (U). (wikidoc.org)
  • When designing primers for polymerase chain reaction , inosine is useful in that it can pair with adenine, thymine, or cytosine. (wikidoc.org)
Alignments2
  • Such unexpected editing was not previously reported in vitro, presumably because the common use of artificially tight mRNA:gRNA base pairing precludes alternate alignments. (tamu.edu)
  • Detect if there is a mismatch between two VERIFIED alignments. (lu.se)
Proteins3
  • Many DNA-binding proteins can recognize specific base-pairing patterns that identify particular regulatory regions of genes. (wikipedia.org)
  • DNA recognition in these proteins is provided by modules, each of which binds a single base pair, and there is a robust code to address each of the four base pairs (2,3). (ddw-online.com)
  • Two proteins that are each others best hit (also known as reciprocal best hit (RBH) or symmetrical best hit) in a pair-wise genome comparison are considered orthologous. (biomedcentral.com)
Cleavage4
  • In animals, the degree of base pairing between a miRNA and its target messenger RNA seems to determine whether the regulation occurs through cleavage or translation inhibition 1 . (nature.com)
  • Other mismatches allow for RNA extension but are inefficiently formed and efficiently proofread by RNA cleavage. (cipsm.de)
  • We wanted to determine the effect of crRNA mismatches on target cleavage in vitro. (billfryer.com)
  • Mismatched crRNAs may also provide low-level immunity through continued target cleavage. (billfryer.com)
Specificity2
  • Watson-Crick base pairing's contribution to global structural stability is minimal, but its role in the specificity underlying complementarity is, by contrast, of maximal importance as this underlies the template-dependent processes of the central dogma (e.g. (wikipedia.org)
  • While most of the issues were solved, primer template mismatches constantly tamper the overall specificity, resulting in unwanted false-positives. (researchsquare.com)
Polymerase6
  • The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and RNA polymerase transcribes DNA into RNA. (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)
  • Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. (rcsb.org)
  • Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. (rcsb.org)
  • Its principle is based on the use of DNA polymerase which is an in vitro replication of specific DNA sequences. (intechopen.com)
  • We show that RNA polymerase (Pol) II prevents erroneous transcription in vitro with different strategies that depend on the type of DNA⋅RNA base mismatch. (cipsm.de)
Tumor1
  • Twenty-three genes, which were differentially expressed between adjacent normal and tumor samples, were selected and analyzed using 24 paired lung adenocarcinoma samples by Q-RT-PCR using two internal controls, DDX5 and GAPDH . (biomedcentral.com)
Replication errors3
  • Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. (rcsb.org)
  • Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors. (rcsb.org)
  • Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. (embl-heidelberg.de)
Mechanisms2
  • In contrast, the selection of regulatory mechanisms is independent of the degree of mismatch between a plant miRNA and its target transcript 5 . (nature.com)
  • Mutations in the genes BRCA1, BRCA2 or PIK3CA have important implications in the cellular DNA repair mechanisms, and are associated with sensitivity and improved response to platinum-based chemotherapy and PAPR inhibitors. (unilabs.ch)
Nucleotide2
  • Paired DNA and RNA molecules are comparatively stable at room temperature, but the two nucleotide strands will separate above a melting point that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content. (wikipedia.org)
  • The mismatch can also stabilize a paused state of Pol II with a frayed RNA 3′ nucleotide. (cipsm.de)
Hydrogen bonds2
  • A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. (wikipedia.org)
  • The application of larger electric fields (10⁹ V/m) parallel to base pair hydrogen bonds is found to increase the lifetime of the tautomers by one order of magnitude at most. (ucl.ac.uk)
Genetic1
  • The complementary nature of this based-paired structure provides a redundant copy of the genetic information encoded within each strand of DNA. (wikipedia.org)
Binds1
  • The continuous effort to improve the overall mixture was mainly aimed to enhance reactions, diminish unnecessary primer dimers, reduce nonspecific binds due to mismatches, and block efficiency drops occurred by high G/C rates [6, 7]. (researchsquare.com)
Downstream1
  • The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. (embl-heidelberg.de)
Genome5
  • The size of an individual gene or an organism's entire genome is often measured in base pairs because DNA is usually double-stranded. (wikipedia.org)
  • The haploid human genome (23 chromosomes) is estimated to be about 3.2 billion bases long and to contain 20,000-25,000 distinct protein-coding genes. (wikipedia.org)
  • We are in the midst of a revolution in genome engineering, based on reagents that can be designed to cut chromosomal DNA at arbitrary sites. (ddw-online.com)
  • To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses. (cdc.gov)
  • Cas9-based genome editing to endogenously tag Osk with the decapping complex recruitment leads to turnover of select maternal mRNAs. (billfryer.com)
Genes1
  • They identified, for example, 23 genes responsible for excising erroneous bases, 36 genes needed for mending double-strand breaks, and 16 genes involved in mismatch repair, or the re-aligning of complementary base pairs. (damonrunyon.org)
Overlap1
  • purine-purine pairings are energetically unfavorable because the molecules are too close, leading to overlap repulsion. (wikipedia.org)
Repair1
Sequences1
  • citation needed] The following DNA sequences illustrate pair double-stranded patterns. (wikipedia.org)
Complementary1
  • To do this, the team created two groups of complementary nanoparticles: one batch containing complementary base pairs, called "seed" PAEs, and the other containing mismatched base pairs to make "growth" PAEs. (phys.org)
Quantification1
  • The short-oligonucleotide-based Affymetrix GeneChip ® arrays utilize multiple probes for each gene with an automated control for the experimental process from hybridization to quantification and thus provide reliable and comparable data [ 2 ]. (biomedcentral.com)
Mechanism1
  • The aims of this thesis are to i) reassess the viability of base pair tautomerism as a contributory mechanism towards spontaneous single point mutations in DNA and ii) predict how external electric fields (ranging from strengths of 10⁴ V/m to 10⁹ V/m) influence the thermodynamic stability of the tautomers and the kinetics of the DPT reaction. (ucl.ac.uk)
Interaction1
  • Hydrogen bonding is the chemical interaction that underlies the base-pairing rules described above. (wikipedia.org)
Detect1
  • An example of an experiment we would like to perform is to set up single-molecule tethers in an unzipping configuration and then detect whether or not a DNA-binding protein is present based on the unzipping force. (openwetware.org)
Probes1
  • Each row tells whether the affyprobe is a perfect match or mismatch, what number it has in the list of probes for this probeset (so that pm/mm pairs can be identified), and what feature defines its position. (lu.se)
Occur2
  • Intramolecular base pairs can occur within single-stranded nucleic acids. (wikipedia.org)
  • The ensemble-based methodology utilised in this study has shown that several different proton transfer reaction pathways, each with varying probabilities, occur within the same base pair. (ucl.ac.uk)
Proton1
  • Löwdin proposed that the base pair double proton transfer (DPT) tautomers, A*T* and G*C*, may cause mutations during the replication process via mismatches, e.g. the pairing of A* with C, and G* with T. This thesis uses multiscale modelling techniques to study base pair tautomerism in a realistic DNA system. (ucl.ac.uk)
Fragments1
  • In reversible terminator sequencing - pure genomic DNA is first cut into smaller fragments of 100-1000 base pairs. (jove.com)
Sites2
  • Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing. (bioconductor.org)
  • In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites. (bioconductor.org)
Presence3
  • The stability of a model substrate for topoisomerase 1-mediated DNA religation depends on the presence of mismatched base pairs. (wakehealth.edu)
  • Gmeiner WH, Salsbury F, Olsen CM, Marky LA. The stability of a model substrate for topoisomerase 1-mediated DNA religation depends on the presence of mismatched base pairs. (wakehealth.edu)
  • Familial polyposis syndromes are divided into 2 major groups based on the presence of adenomas or hamartomas. (medscape.com)
Mutations2
  • The results show that DPT between base pairs has a negligible contribution towards spontaneous mutations in DNA. (ucl.ac.uk)
  • In the context of mutations in human beings, the effect of external electric fields on base pair tautomerism is deemed insignificant. (ucl.ac.uk)
Find1
  • In 2005, curators at the Judy Garland Museum entered the actress' former home in Grand Rapids, Minnesota, to find the display case holding a pair of her iconic ruby slippers from The Wizard of Oz smashed, with only a single red sequin remaining among the broken glass. (smithsonianmag.com)
Single2
  • Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non-coding single-stranded regions of telomeres). (wikipedia.org)
  • Here, single-molecule high-resolution optical trapping measurements reveal that Mtr4p unwinds RNA duplexes by 3′-to-5′ translocation on the loading strand, that strand separation occurs in discrete steps of 6 base pairs and that a single Mtr4p molecule performs consecutive unwinding steps. (nature.com)
Molecular3
  • A kilobase (kb) is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. (wikipedia.org)
  • We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. (springer.com)
  • An ensemble of reaction coordinates and the rate coefficients of tautomerism for each base pair in aqueous DNA is calculated using quantum mechanics/molecular mechanics (QM/MM) methods. (ucl.ac.uk)
High2
  • GaN and AlGaN are the most common pairing for producing GaN-based DBRs due to their high difference in refractive index. (compoundsemiconductor.net)
  • High-resolution structure of a DNA helix containing mismatched base pairs. (wikidata.org)
Contribution1
  • 26. Hudson, G. A., Bloomingdale, R. J., and Znosko, B. M. (2013) Thermodynamic contribution and nearest neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides , RNA 19 , 1474-1482. (slu.edu)
Rules1
  • These rules generate 95 pair trading signals over 9+ years. (cxoadvisory.com)
Largely1
  • A standalone pairs trading strategy appears to require a large inventory of pairs at all times in order to keep capital largely engaged in trades. (cxoadvisory.com)
Lead1
  • Messages that lead to a "Verified mismatch" are not trusted, which is indicated with line-through styled text. (lu.se)
Active1
  • ACS's Standard Package lets you stay up to date with C&EN, stay active in ACS, and save. (acs.org)
Correct1
  • Spectra are presented which simulate scaled versions of the AM 1.5 solar reference spectrum, correct for spectral mismatch, and model attenuation from increasing air- mass. (nist.gov)
Large3
  • A standalone pairs trading strategy of any kind probably requires a large inventory of potential pairs. (cxoadvisory.com)
  • However, this combination suffers from large differences in lattice mismatch and thermal expansion coefficient, which ultimately cause epiwafer cracking. (compoundsemiconductor.net)
  • However, traditional Sanger sequencing-based DNA barcoding protocols can be prohibitively expensive and laborious when large community samples have to be processed. (springer.com)
Specific2
  • Paired-end, strand specific sequencing for total RNA was performed on Illumina HiSeq 2500 with 100 bp read lengths. (nih.gov)
  • Based on our results, we conclude that morFeus is a powerful and specific search method for detecting remotely conserved orthologs. (biomedcentral.com)
Identify2
  • After each round of dNTP addition to the growing strand, the chip is imaged, and the emission wavelength from each DNA cluster is used to identify the base. (jove.com)
  • note] It's sometimes necessary to identify plates by name, but this should be solved without requiring plate names to be unique (this was a source of problems in BASE 1). (lu.se)