AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation ScienceHealth Care
NucleotidesBase SequenceBase PairingMolecular Sequence DataPolymorphism, Single NucleotideAdenine NucleotidesAmino Acid SequenceGuanine NucleotidesPurine NucleotidesCloning, MolecularBase CompositionNucleic Acid ConformationDNASequence Homology, Nucleic AcidEscherichia coliSequence Analysis, DNASkull BaseNucleotides, CyclicGuanine Nucleotide Exchange FactorsPyrimidine NucleotidesMutationSchiff BasesTranscription, GeneticGenesBinding SitesPhylogenyAdenosine TriphosphateKineticsPlasmidsGenes, BacterialRestriction MappingCodonRNA, MessengerSequence AlignmentSequence Homology, Amino AcidGenetic VariationPolymerase Chain ReactionBase Pair MismatchDNA, BacterialGenotypeRNA, ViralAdenosine DiphosphateDNA Restriction EnzymesGuanosine TriphosphateNucleic Acid HybridizationRNAModels, MolecularOpen Reading FramesDNA PrimersDNA RepairPromoter Regions, GeneticDNA, ViralOligonucleotidesSpecies SpecificityProtein BindingThymine NucleotidesOligodeoxyribonucleotidesBacterial ProteinsSubstrate SpecificityGenes, ViralCytosine NucleotidesGenome, ViralGuanosine DiphosphateCell LineIntronsRepetitive Sequences, Nucleic AcidChromosome MappingAllelesAdenineSkull Base NeoplasmsEvolution, MolecularDeoxyadenine NucleotidesDNA, ComplementaryProtein BiosynthesisDNA-Binding ProteinsDeoxyguanine NucleotidesRNA, RibosomalHaplotypesUridine TriphosphateDeoxycytosine NucleotidesDNA Mutational AnalysisModels, GeneticPoint MutationSaccharomyces cerevisiaeAdenosine MonophosphateProtein ConformationHydrolysisRNA, TransferRNA, BacterialTemplates, GeneticViral ProteinsExonsRibonucleotidesCattleOligonucleotide ProbesMolecular WeightPolymorphism, GeneticOperonRecombinant ProteinsInosine Nucleotides
SNPsGuanineSequencesAmino acidCyclic Nucleotide PhosphodiesteraseVariationsIncorrect nucleotideSingleGenomeExcisionSubstitutionsPhosphate groupStrandsPolymeraseSynthesisPyrimidinesMismatchResiduesGeneticChromosomeMutationsMolecular basisSplicingIncorporationHydrogen bondsInhibitorsRegionsMetabolismGenomesDeletionDouble helixMoleculePhenotypeStructuralPrimerRecognitionCrystalsVariantChemicalComplementary baseBRCA1GenesDiseaseChange
SNPs9
  • Aligning the single nucleotide polymorphisms (SNPs) from the public human SNP database to the chimpanzee genome allowed inference of the direction of the mutations that created present-day SNPs. (nih.gov)
  • plural SNPs /snɪps/) is a germline substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of considered population (generally regarded as 1% or more). (wikipedia.org)
  • Variant" may also be used as a general term for any single nucleotide change in a DNA sequence, encompassing both common SNPs and rare mutations, whether germline or somatic. (wikipedia.org)
  • We compared two methods to model the combined effect of 14 prostate cancer risk-associated SNPs and family history for the estimation of absolute risk for prostate cancer in a population-based case-control study in Sweden (2,899 cases and 1,722 controls). (johnshopkins.edu)
  • The aim of this study was to identify any impact of CYP2A13 single-nucleotide polymorphisms (SNPs) on CYP2A13 expression in human lung. (aspetjournals.org)
  • To date, more than 20 single-nucleotide polymorphisms (SNPs) have been identified in CYP2A13 (Zhang et al. (aspetjournals.org)
  • Variations in toxicity and response to therapy are observed among patients despite similar clinicopathologic characteristics which are attributed to single nucleotide polymorphisms (SNPs). (researchsquare.com)
  • So, the aim of this review was to investigate the effect of single nucleotide polymorphisms (SNPs) on response rate and toxicity in HNSCCs. (researchsquare.com)
  • The $45-million project will identify and analyse single nucleotide polymorphisms (SNPs). (newscientist.com)
Guanine5
  • however, dGTPase residues at the end of the substrate-binding pocket mimic Watson Crick interactions providing Guanine base specificity, while a 7 Å cleft separates SAMHD1 residues from dNTP bases, abolishing nucleotide-type discrimination. (biorxiv.org)
  • Adenine and guanine are purine bases. (knowgenetics.org)
  • Methylation of guanine bases produces a change in the structure of DNA by forming a product that is complimentary to thymine rather than cytosine. (news-medical.net)
  • The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people. (medlineplus.gov)
  • It is known to act through protein phosphorylation via PRKA and through the activation of guanine nucleotide exchange factors like EPAC. (plos.org)
Sequences11
  • Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions(regions between genes). (wikipedia.org)
  • Promoter region sequences were extracted oil palm genome spanning from 1500 nucleotides (nt) upstream to 1000 nt downstream of every annotated transcription start sites (TSS). (bvsalud.org)
  • Homologous recombination involves the exchange of nucleotide sequences to repair damaged bases on both strands of DNA through the utilization of a sister chromatid. (news-medical.net)
  • The new features allow users to 1) add primer annotations or other data sets in batch mode, 2) export differences between sequences to other genome browsers, 3) compare multiple genomes at a single nucleotide level of detail, 4) create new alignments from subsets/subsequences of a very large master alignment and 5) allow display of summaries of deep RNA sequencing data sets on a genome sequence. (biomedcentral.com)
  • BBB-v2 significantly improves the ability of virologists to work with genome sequences and provides a platform with which they can use a multiple sequence alignment as the basis for their own editable documents. (biomedcentral.com)
  • Key distinctive features of the original BBB were its ability to read annotations (CDS positions) from GenBank files, an explicit display of differences between sequences and a tool to compare genomes, including the ability to summarize the consequences of all nucleotide changes on encoded proteins throughout a genome. (biomedcentral.com)
  • Phylogenetic tree constructed by the neighbor-joining method based on the partial sequences of HEV ORF1 gene. (scielo.br)
  • The nucleotide sequences found in the present study (9B and A1) are narrowed with diamonds. (scielo.br)
  • As a sub-objective, since PDE10A transcript variants were reported strictly through analyses of bovine genomic sequence, we also wanted to determine the nucleotide and amino acid sequences by experimental evidence. (plos.org)
  • A cohort of 80 healthy subjects of Western European descent was screened to evaluate and validate the detection of exomic sequences of the coding genes with 25 base pair exon padding. (researchgate.net)
  • This technology involves breaking the entire genome into small segments, sequencing the segments, and then reassembling the sequences using intensive computational techniques to provide the base-by-base sequence of the entire genome or more limited regions, such as the expressed portion of the genome known as the exome. (msdmanuals.com)
Amino acid4
  • What amino acid sequence does the following mRNA nucleotide sequence specify? (answersmcq.com)
  • This rule also applies to variants in single residue stretches (mono-nucleotide or amino acid) or tandem repeats. (mitomap.org)
  • indicates amino acid change that require more complex mutation than single nucleotide substitution. (lu.se)
  • indicates codon change that single nucleotide doesn't change amino acid (silent mutation). (lu.se)
Cyclic Nucleotide Phosphodiesterase1
  • Goupil S, Maréchal L, El Hajj H, Tremblay M-È, Richard FJ, Leclerc P (2016) Identification and Localization of the Cyclic Nucleotide Phosphodiesterase 10A in Bovine Testis and Mature Spermatozoa. (plos.org)
Variations6
  • The two possible nucleotide variations of this SNP - G or A - are called alleles. (wikipedia.org)
  • With the development of high throughput technologies such as tandem mass spectrometry (MS/MS) and next generation sequencing, more and more nonsynonymous single-nucleotide variations (nsSNVs) that cause variation of amino acids have been identified, some of which result in the damage of PTMs. (hindawi.com)
  • Either at genomic or at proteomic level, mutations have significant impact on normal gene or protein function, and human diseases could be associated with mutations like nonsynonymous single-nucleotide variations (nsSNVs) on amino acids. (hindawi.com)
  • NextGene analysis provided higher sensitivity, as four previously undetected single-nucleotide variations were found. (nih.gov)
  • These are variations in single DNA bases, which account for most of the genetic differences between people. (newscientist.com)
  • This process helps identify single or multiple nucleotide variations as well as areas of insertion or deletion. (msdmanuals.com)
Incorrect nucleotide2
  • Yellow crystals of CSF-labeled T7 DNA polymerase with DNA and correct nucleotide (closed complex), incorrect nucleotide (misaligned complex) or no nucleotide (open complex) were grown to good size and diffracted to 3 Å during X-ray data collection. (utexas.edu)
  • Damage to DNA is caused by the incorporation of incorrect nucleotide bases during DNA replication and the chemical changes caused by spontaneous mutation or exposure to environmental factors such as radiation. (news-medical.net)
Single14
  • Senior author Lukas Dow , PhD, an Associate Professor of Biochemistry In Medicine at Weill Cornell Medicine, and his colleagues genetically engineered mice to carry an enzyme that allows the scientists to change a single base or "letter" in the mouse's genetic code. (bioquicknews.com)
  • We demonstrate that TdT-dNTP conjugates can quantitatively extend a primer by a single nucleotide in 10-20 s, and that the scheme can be iterated to write a defined sequence. (nature.com)
  • Figure 2: TdT-dNTP conjugates can extend a DNA molecule by a single nucleotide in 10-20 s, enabling stepwise DNA synthesis. (nature.com)
  • Single nucleotide substitutions with an allele frequency of less than 1% are sometimes called single-nucleotide variants (SNVs). (wikipedia.org)
  • A single nucleotide polymorphism (abbreviated SNP, pronounced snip) is a genomic variant at a single base position in the DNA. (genome.gov)
  • Single nucleotide polymorphism, or SNP. (genome.gov)
  • Identification of oil palm cis-regulatory elements based on DNA free energy and single nucleotide polymorphism density. (bvsalud.org)
  • using the combination of DNA free energy and single nucleotide polymorphism (SNP) density approaches. (bvsalud.org)
  • A high-density single nucleotide polymorphism (HD-SNP) chip-based comparative analysis of genetic characteristics was performed for seven Shandong indigenous pig breeds in the context of five Western commercial breeds. (animbiosci.org)
  • Base-excision repair involves the recognition and removal of a single damaged base. (news-medical.net)
  • Single-stranded annealing provides end joining between interspersed nucleotide repeats within the genome leading to one copy of the repeat and the intervening sequence being deleted in the process. (news-medical.net)
  • Disease risk-associated single nucleotide polymorphisms (SNP) identified from genome-wide association studies have the potential to be used for disease risk prediction. (johnshopkins.edu)
  • Analysis of radioactive and nonradioactive purine bases, purine nucleosides and purine nucleotides by high-speed chromatography on a single column. (elsevierpure.com)
  • Multiple distinct single- and double-nucleotide substitution signatures were discernible. (lu.se)
Genome4
  • For example, a G nucleotide present at a specific location in a reference genome may be replaced by an A in a minority of individuals. (wikipedia.org)
  • Conclusions Results suggested that the NGS approach based on AmpliSeq™ libraries and Ion Personal Genome Machine (PGM) sequencing is a highly efficient mutation detection method. (researchgate.net)
  • We used the bivariate causal mixture model (MiXeR) to quantify genome-wide polygenic overlap and the conditional/conjunctional false discovery rate (pleioFDR) method to identify shared loci, based on genome-wide association study summary statistics on depression (n = 450,619), coronary artery disease (n = 502,713) and nine cardiovascular risk factors (n = 204,402-776,078). (plos.org)
  • Array comparative genomic hybridization (aCGH) is a type of microarray now routinely used to identify deleted or duplicated regions of DNA sequence in specific chromosomes on a genome-wide basis. (msdmanuals.com)
Excision4
  • Base-excision repair. (news-medical.net)
  • Nucleotide excision repair. (news-medical.net)
  • Nucleotide excision repair is a widespread mechanism for repairing damage to DNA and recognizes multiple damaged bases. (news-medical.net)
  • The third excision mechanism is called mismatch repair and occurs when mismatched bases are incorporated into the DNA strand during replication and are not removed by proofreading DNA polymerase. (news-medical.net)
Substitutions1
  • Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. (lu.se)
Phosphate group2
  • The sugar and phosphate group make up the backbone of the DNA double helix, while the bases are located in the middle. (knowgenetics.org)
  • A chemical bond between the phosphate group of one nucleotide and the sugar of a neighboring nucleotide holds the backbone together. (knowgenetics.org)
Strands2
  • Chemical bonds (hydrogen bonds) between the bases that are across from one another hold the two strands of the double helix together. (knowgenetics.org)
  • Nucleotides are arranged in two long strands that form a spiral called a double helix. (medlineplus.gov)
Polymerase2
  • An important study of T7 DNA polymerase performed by Tsai and Johnson using a conformationally sensitive fluorophore (CSF) characterized a conformational change directly and presented a new paradigm for nucleotide selectivity. (utexas.edu)
  • The enzymes remove the damaged base forming an AP site which is repaired by AP endonuclease before the nucleotide gap in the DNA strand is filled by DNA polymerase. (news-medical.net)
Synthesis1
  • The non-defective strand is used as a template with the damaged DNA on the other strand removed and replaced by the synthesis of new nucleotides. (news-medical.net)
Pyrimidines1
Mismatch1
  • In mismatch repair, the missed errors are later corrected by enzymes which recognize and excise the mismatched base to restore the original sequence. (news-medical.net)
Residues1
  • The data suggested that active site residues play important roles in maintaining a fast conformational change and an accurate alignment of the active site during correct nucleotide incorporation. (utexas.edu)
Genetic2
  • The method adds a large amount of genetic information as a basis for complete analysis of TRPV1 ion channel genetics and its functional consequences. (researchgate.net)
  • The NBDPS was a multisite, population-based, case-control study of genetic and non-genetic risk factors for major structural birth defects that included women with deliveries between 1997 and 2011. (cdc.gov)
Chromosome1
  • This identified approximately 140 chromosome loci where nucleotides deviated from the reference sequence GRCh37 hg19 comprising the three genes TRPV1, LTB4R and LTB4R2. (researchgate.net)
Mutations1
  • Based on the favorable preclinical and clinical strain (GenBank ID MZ245455), and isolates were classified into data, and the public health emergency of international concern one of nine categories, based on their risk profile and loss of key generated by ongoing endemic wild poliovirus transmission attenuating nOPV2 mutations (Figure 1). (cdc.gov)
Molecular basis1
  • This thesis describes work to further characterize the underlying molecular basis regulating the conformational change by a combination of site-directed mutagenesis, transient kinetics and crystallography. (utexas.edu)
Splicing2
  • In addition, a third conserved intronic sequence that is known to be functionally important in splicing is the so-called branch point site (BPS) which is usually located very close to the end of the intron, at most 40 nucleotides before the terminal dinucleotide. (ijbs.com)
  • There are at least two classes of pre-mRNA introns, based on the splicing machineries that catalyze the reaction. (ijbs.com)
Incorporation1
  • Quantification of the kinetics of incorporation of correct and incorrect base pairs showed the decrease of fidelity mainly was from the decreased forward rate during correct nucleotide incorporation. (utexas.edu)
Hydrogen bonds1
  • These complementary bases are bonded together via hydrogen bonds, which can be easily broken apart when the DNA needs to unzip and duplicate itself. (knowgenetics.org)
Inhibitors2
  • Receptor-interacting protein kinase 2 (RIPK2) and nucleotide-binding oligomerization domain (NOD) cell signaling inhibitors based on a 3,5-diphenyl-2-aminopyridine scaffold. (ox.ac.uk)
  • A new class of RIPK2 kinase/NOD signaling inhibitors based on a 3,5-diphenyl-2-aminopyridine scaffold was developed. (ox.ac.uk)
Regions1
  • Using our new profiles based on hydrophobicity properties we pointed out specific properties for regions surrounding splice sites. (ijbs.com)
Metabolism1
  • SE50/110, but that its metabolism is coupled to the nucleotide messenger system of c-di-GMP. (frontiersin.org)
Genomes2
  • In version 2, BBB-v2, of Base-By-Base we have added a series of new features aimed at providing the bench virologist with a better platform to view, annotate and analyze these complex genomes. (biomedcentral.com)
  • The original version of Base-By-Base (BBB) [ 1 ] was developed by the Virus Bioinformatics Resource Center primarily because of a need for a customizable, platform-independent (Java), multiple sequence alignment (MSA) editor that could be used for the comparison, annotation and analysis of viral genomes, and also integrated directly with our MySQL database. (biomedcentral.com)
Deletion1
  • The methods used in multigene panels may include sequence analysis , deletion/duplication analysis , and/or other non-sequencing-based tests. (nih.gov)
Double helix3
  • The structure of the double helix is somewhat like a ladder, with the base pairs forming the ladder's rungs and the sugar and phosphate molecules forming the vertical sidepieces of the ladder. (medlineplus.gov)
  • Each strand of DNA in the double helix can serve as a pattern for duplicating the sequence of bases. (medlineplus.gov)
  • DNA is a double helix formed by base pairs attached to a sugar-phosphate backbone. (medlineplus.gov)
Molecule1
  • Each base is also attached to a sugar molecule and a phosphate molecule. (medlineplus.gov)
Phenotype2
  • Bases are the part of DNA that stores information and gives DNA the ability to encode phenotype , a person’s visible traits. (knowgenetics.org)
  • These findings provide a basis for further studies that associate CYP2A13 haplotypes with incidences of smoking-related lung tumors and for studies on the mechanisms of the low-expression phenotype of the 7520G-containing allele. (aspetjournals.org)
Structural1
Primer1
  • Cleaving the linkage between TdT and the incorporated nucleotide releases the primer and allows subsequent extension. (nature.com)
Recognition1
  • The positions given by our method, which may be important for recognition by spliceosome, were compared to the nucleotide consensus provided by a classical method, Pictogram . (ijbs.com)
Crystals1
  • To obtain these structures, we applied UV-fluorescence microscopy, video analysis and highly automated goniometer-based instrumentation to map and rapidly position individual crystals randomly-located on fixed target holders, resulting in the highest indexing-rates observed for a serial femtosecond crystallography (SFX) experiment. (biorxiv.org)
Variant1
  • Here, we describe an approach based on this idea called VERIFY (variant elimination reinforces functionality), which can be used to assess the extent of natural selection acting on an oligonucleotide motif or set of motifs predicted to have biological activity. (nih.gov)
Chemical1
  • the direct reversal of the chemical process generating the damage and the replacement of damaged nucleotide bases. (news-medical.net)
Complementary base1
BRCA11
  • Bearing in mind that the performance and quality criteria expected from NGS in diagnostic or research settings are strikingly different, we have developed an Ion Torrent's PGM-based routine diagnostic procedure for BRCA1/2 sequencing. (nih.gov)
Genes1
  • The NGS workflow was based on a custom AmpliSeq™ panel and designed for sequencing of human genes on an Ion PGM™ Sequencer. (researchgate.net)
Disease1
  • Centers for Disease Control and Prevention, Fort Collins, Colo- nucleotide identity with ZIKV. (folkhalsomyndigheten.se)
Change1
  • Correct nucleotide binding caused an increase in fluorescence, suggesting that the conformational change of the fingers domain delivers incoming nucleotide to a misaligned status even for a correct nucleotide with each of the mutants. (utexas.edu)