• sequences
  • A trend towards minimal PS was observed for almost all complete sequences of bacterial chromosomes and plasmids, however, PS was substantially higher in separate genomic loci and several types of plasmids and phages characterized by long stretches of non-coding DNA and/or asymmetric gene distribution on the two DNA strands. (biomedcentral.com)
  • However, with more and more complete bacterial genome sequences at hand, the AT and GC composition are meanwhile known to be skewed between leading and lagging strand [ 15 , 16 ] and the extrapolation of the first-order parity rule to higher orders of oligonucleotide composition has yet not been investigated in sufficient depth to draw any valid conclusions. (biomedcentral.com)
  • Once amplified, the sequence can be cut at each end with nucleases and inserted into one of many small circular DNA sequences known as expression vectors. (wikipedia.org)
  • Building on this, and to accommodate Leonard Hayflick's idea of limited somatic cell division, Olovnikov suggested that DNA sequences are lost every time a cell/DNA replicates until the loss reaches a critical level, at which point cell division ends. (wikipedia.org)
  • In 1975-1977, Elizabeth Blackburn, working as a postdoctoral fellow at Yale University with Joseph G. Gall, discovered the unusual nature of telomeres, with their simple repeated DNA sequences composing chromosome ends. (wikipedia.org)
  • This is the reason telomeres are so important in context of successful cell division: They "cap" the end-sequences and themselves get lost in the process of DNA replication. (wikipedia.org)
  • In theory, there are two types of palindromic sequences that can be possible in DNA. (wikipedia.org)
  • The inverted repeat palindrome is also a sequence that reads the same forward and backward, but the forward and backward sequences are found in complementary DNA strands (i.e., of double-stranded DNA), as in GTATAC (GTATAC being complementary to CATATG). (wikipedia.org)
  • EcoRI digestion produces "sticky" ends, whereas SmaI restriction enzyme cleavage produces "blunt" ends: Recognition sequences in DNA differ for each restriction enzyme, producing differences in the length, sequence and strand orientation (5' end or 3' end) of a sticky-end "overhang" of an enzyme restriction. (wikipedia.org)
  • Restriction endonucleases and DNA ligase are then used to clone the sequences into bacterial plasmids. (wikipedia.org)
  • On August 16, 2012, the Federal Circuit reaffirmed Myriad's right to patent the genes although they denied rights to patent comparisons of DNA sequences. (wikipedia.org)
  • Multivariate statistical analysis of codon use within genomes with unequal quantities of coding sequences on the two strands has shown that codon use in the third position depends on the strand on which the gene is located. (wikipedia.org)
  • Because of the asymmetry in pyrimidine and purine use in coding sequences, the strand with the greater coding content will tend to have the greater number of purine bases (Szybalski's rule). (wikipedia.org)
  • and (2) that this pressure is proportional to the mismatch in the length of the coding sequences between the two strands. (wikipedia.org)
  • A DNA transcription unit encoding for a protein may contain both a coding sequence, which will be translated into the protein, and regulatory sequences, which direct and regulate the synthesis of that protein. (wikipedia.org)
  • molecule
  • A restriction enzyme or restriction endonuclease is an enzyme that cleaves DNA into fragments at or near specific recognition sites within the molecule known as restriction sites. (wikipedia.org)
  • Following "sticky end" ligation of the insert into the vector the resulting recombinant DNA molecule is transferred into E. coli host cell for cloning. (wikipedia.org)
  • The first rule holds that a double-stranded DNA molecule globally has percentage base pair equality: %A = %T and %G = %C. The rigorous validation of the rule constitutes the basis of Watson-Crick pairs in the DNA double helix model. (wikipedia.org)
  • The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. (wikipedia.org)
  • Contents: Top 0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z deletion deoxyribose diploid DNA An acronym for deoxyribonucleic acid, a polymeric molecule made of deoxyribonucleotides. (wikipedia.org)
  • enzymes
  • During chromosome replication, the enzymes that duplicate DNA cannot continue their duplication all the way to the end of a chromosome, so in each duplication the end of the chromosome is shortened (this is because the synthesis of Okazaki fragments requires RNA primers attaching ahead on the lagging strand). (wikipedia.org)
  • Ribonuclease H (abbreviated RNase H or RNH) is a family of non-sequence-specific endonuclease enzymes that catalyze the cleavage of RNA in an RNA/DNA substrate via a hydrolytic mechanism. (wikipedia.org)
  • Ribonuclease H is a family of endonuclease enzymes with a shared substrate specificity for the RNA strand of RNA-DNA duplexes. (wikipedia.org)
  • RNases H have been proposed as members of an evolutionarily related superfamily encompassing other nucleases and nucleic acid processing enzymes such as retroviral integrases, DNA transposases, Holliday junction resolvases, Piwi and Argonaute proteins, various exonucleases, and the spliceosomal protein Prp8. (wikipedia.org)
  • Ribonuclease H enzymes cleave the phosphodiester bonds of RNA in a double-stranded RNA:DNA hybrid, leaving a 3' hydroxyl and a 5' phosphate group on either end of the cut site. (wikipedia.org)
  • Ribonuclease H1 enzymes require at least four ribonucleotide-containing base pairs in a substrate and cannot remove a single ribonucleotide from a strand that is otherwise composed of deoxyribonucleotides. (wikipedia.org)
  • For this reason, it is considered unlikely that RNase H1 enzymes are involved in the processing of RNA primers from Okazaki fragments during DNA replication. (wikipedia.org)
  • Restriction enzymes are commonly classified into four types, which differ in their structure and whether they cut their DNA substrate at their recognition site, or if the recognition and cleavage sites are separate from one another. (wikipedia.org)
  • To cut DNA, all restriction enzymes make two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix. (wikipedia.org)
  • These enzymes are routinely used for DNA modification in laboratories, and they are a vital tool in molecular cloning. (wikipedia.org)
  • The restriction enzymes studied by Arber and Meselson were type I restriction enzymes, which cleave DNA randomly away from the recognition site. (wikipedia.org)
  • Restriction enzymes of this type are more useful for laboratory work as they cleave DNA at the site of their recognition sequence. (wikipedia.org)
  • Later, Daniel Nathans and Kathleen Danna showed that cleavage of simian virus 40 (SV40) DNA by restriction enzymes yields specific fragments that can be separated using polyacrylamide gel electrophoresis, thus showing that restriction enzymes can also be used for mapping DNA. (wikipedia.org)
  • The discovery of restriction enzymes allows DNA to be manipulated, leading to the development of recombinant DNA technology that has many applications, for example, allowing the large scale production of proteins such as human insulin used by diabetics. (wikipedia.org)
  • Prokaryotes do not have introns in their DNA and therefore do not possess any enzymes that can cut it out during transcription process. (wikipedia.org)
  • Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes. (wikipedia.org)
  • The cell avoids this problem by allowing its DNA-melting enzymes (helicases) to work concurrently with topoisomerases, which can chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other. (wikipedia.org)
  • Photolyases (EC 4.1.99.3) are DNA repair enzymes that repair damage caused by exposure to ultraviolet light. (wikipedia.org)
  • RNaseH enzymes are the primary proteins responsible for the dissolution of R-loops, acting to degrade the RNA moiety in order to allow the two complementary DNA strands to anneal. (wikipedia.org)
  • Exposed single-stranded DNA can come under attack by endogenous mutagens, including DNA-modifying enzymes such as activation-induced cytidine deaminase, and can block replication forks to induce fork collapse and subsequent double-strand breaks. (wikipedia.org)
  • eukaryotic
  • some prokaryotic and most eukaryotic members of the H1 group have an additional small domain at the N-terminus known as the "hybrid binding domain", which facilitates binding to RNA:DNA hybrid duplexes and sometimes confers increased processivity. (wikipedia.org)
  • The HMM architecture of eukaryotic GeneMark.hmm includes hidden states for initial, internal, and terminal exons, introns, intergenic regions and single exon genes located in both DNA strands. (wikipedia.org)
  • Gene prediction in eukaryotic transcripts can be done by the new algorithm GeneMarkS-T (2015) GeneMark GeneMarkS GeneMarkS+ MetaGeneMark GeneMark GeneMark.hmm GeneMark-ES GeneMark-ET Heuristic models GeneMarkS-T List of gene prediction software Gene prediction Borodovsky M. and McIninch J. "GeneMark: parallel gene recognition for both DNA strands. (wikipedia.org)
  • specifically it applies to the eukaryotic chromosomes, the bacterial chromosomes, the double stranded DNA viral genomes, and the archaeal chromosomes. (wikipedia.org)
  • After their discovery in adenovirus, introns were found in a number of eukaryotic genes such as the eukaryotic ovalbumin gene (first by the O'Malley laboratory, then confirmed by other groups), hexon DNA, and extrachromosomal rRNA genes of Tetrahymena thermophila. (wikipedia.org)
  • ssDNA
  • After digestion of the RNA, a single stranded DNA (ssDNA) is left and because single stranded nucleic acids are hydrophobic, it tends to loop around itself. (wikipedia.org)
  • The structure of DNAFETs is similar to that of MOSFETs with the exception of the gate structure which, in DNAFETs, is replaced by a layer of immobilized ssDNA (single-stranded DNA) molecules which act as surface receptors. (wikipedia.org)
  • In mice and humans, however, BRCA2 primarily mediates orderly assembly of RAD51 on ssDNA, the form that is active for homologous pairing and strand invasion. (wikipedia.org)
  • However, in the presence of a BRCA2 mutation, human RAD52 can mediate RAD51 assembly on ssDNA and substitute for BRCA2 in homologous recombinational DNA repair, though with lower efficiency than BRCA2. (wikipedia.org)
  • genomes
  • Strand symmetry as indicated by minimal PS is a universally conserved feature of complete bacterial genomes that results from the matching mutual compensation of local OU biases on both replichors while OUV is more a taxon specific feature. (biomedcentral.com)
  • First, we wanted to know whether an association exists between structural features of DNA and the frequency of particular tetranucleotide words in bacterial genomes. (biomedcentral.com)
  • The NASBA technique has been used to develop rapid diagnostic tests for several pathogenic viruses with single-stranded RNA genomes, e.g. influenza A, foot-and-mouth disease virus, severe acute respiratory syndrome (SARS)-associated coronavirus, human bocavirus (HBoV) and also parasites like Trypanosoma brucei. (wikipedia.org)
  • In most bacterial genomes (which are generally 80-90% coding) genes are arranged in such a fashion that approximately 50% of the coding sequence lies on either strand. (wikipedia.org)
  • genes
  • Consistent with the phenotypes observed, transcriptome analyses of kdm5 null mutant wing imaginal discs revealed the dysregulation of genes involved in several cellular processes, including cell cycle progression and DNA repair. (genetics.org)
  • Introns reduce R-loop formation and DNA damage in highly expressed yeast genes. (wikipedia.org)
  • chromatin chromosomal crossover chromosomal duplication chromosome a molecular "package" for carrying DNA in cells, organized as two double-helical DNA molecules that encode many genes. (wikipedia.org)
  • chromosomes
  • The known structures of bacterial telomeres take the form of proteins bound to the ends of linear chromosomes, or hairpin loops of single-stranded DNA at the ends of the linear chromosomes. (wikipedia.org)
  • Some simple organisms have only one chromosome made of circular DNA, while most eukaryotes have multiple chromosomes made of linear DNA. (wikipedia.org)
  • synthesize
  • To synthesize an additional DNA strand, traditionally one would digest the RNA of the hybrid strand, using an enzyme like RNase H, or through alkali digestion method. (wikipedia.org)
  • Although RNA can also be amplified by PCR using a reverse transcriptase (in order to synthesize a complementary DNA strand as a template), NASBA's main advantage is that it works at isothermic conditions - usually at a constant temperature of 41 °C. NASBA can be used in medical diagnostics as an alternative to PCR that is quicker and more sensitive in some circumstances. (wikipedia.org)
  • protein
  • A protein complex known as shelterin serves to protect the ends of telomeres from being recognised as double-strand breaks by inhibiting homologous recombination (HR) and non-homologous end joining (NHEJ). (wikipedia.org)
  • The major non-structural protein, NS1, is a site- and strand-specific endonuclease belonging to the HuH protein superfamily, and also carries a AAA+ SF3 helicase domain. (wikipedia.org)
  • Such evidence of molecular diversity, which had been presumed absent from DNA, made DNA a more credible candidate for the genetic material than protein. (wikipedia.org)
  • It was also found to interact with DNA recombination protein RAD51, which suggested its role in RAD51-related DNA recombination and repair. (wikipedia.org)
  • In S. cerevisae, Rad52 protein, acting alone, facilitates the loading of Rad51 protein onto single-stranded DNA pre-coated with replication protein A in the presynaptic phase of recombination. (wikipedia.org)
  • The Cockayne Syndrome B protein (CSB) (coded for by ERCC6) localizes at double-strand breaks at sites of active transcription, followed by RAD51, RAD51C and RAD52 to carry out homologous recombinational repair using the newly synthesized RNA as a template. (wikipedia.org)
  • This protein is located in the cell nucleus and must dimerize with another bHLH protein in order to bind DNA. (wikipedia.org)
  • produces
  • The bond length of this dimerization is shorter than the bond length of normal B-DNA structure which produces an incorrect template for replication and transcription. (wikipedia.org)
  • single
  • The nitrogenous bases present in DNA can be made of a two-ring structure, purine, or a single-ring structure, pyramidine. (reference.com)
  • RNAse H destroys the RNA template from the DNA-RNA compound (RNAse H only destroys RNA in RNA-DNA hybrids, but not single-stranded RNA). (wikipedia.org)
  • RHR is a unidirectional mechanism that displaces a single, continuous DNA strand, which rapidly folds and refolds to generate a series of concatemeric duplex replication intermediates. (wikipedia.org)
  • The mirror-like palindrome is similar to those found in ordinary text, in which a sequence reads the same forward and backward on a single strand of DNA, as in GTAATG. (wikipedia.org)
  • This describes only a global feature of the base composition in a single DNA strand. (wikipedia.org)
  • For reasons that are not yet clear the strands tend to exist longer in single form in mitochondria than in chromsomal DNA. (wikipedia.org)
  • In addition, human RAD52, in combination with ERCC1, promotes the error-prone homologous DNA repair pathway of single-strand annealing. (wikipedia.org)
  • The secondary structures of biological DNA's and RNA's tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar. (wikipedia.org)
  • A study by A. Sancar and P. Selby provided evidence to suggest this branch of cryptochromes have photolyase activity with a high degree of specificity for cyclobutane pyrimidine dimers in single-stranded DNA. (wikipedia.org)
  • In the "open complex" the promoter DNA is partly unwound and single-stranded. (wikipedia.org)
  • The exposed, single-stranded DNA is referred to as the "transcription bubble. (wikipedia.org)
  • An R-loop is a three-stranded nucleic acid structure, composed of a DNA:RNA hybrid and the associated non-template single-stranded DNA. (wikipedia.org)
  • hydrogen bonds
  • DNA with high GC-content is more stable than DNA with low GC-content, but contrary to popular belief, the hydrogen bonds do not stabilize the DNA significantly and stabilization is mainly due to stacking interactions. (wikipedia.org)
  • Hydrogen bonds of the RNA-DNA helix break, freeing the newly synthesized RNA strand. (wikipedia.org)
  • enzyme
  • meanwhile, host DNA is protected by a modification enzyme (a methyltransferase) that modifies the prokaryotic DNA and blocks cleavage. (wikipedia.org)
  • In the 1960s, it was shown in work done in the laboratories of Werner Arber and Matthew Meselson that the restriction is caused by an enzymatic cleavage of the phage DNA, and the enzyme involved was therefore termed a restriction enzyme. (wikipedia.org)
  • mechanism
  • Changes to chromatin, the structure that includes DNA and its associated histone proteins, is one key mechanism by which transcription is regulated ( Swygert and Peterson 2014 ). (genetics.org)
  • Repair of these double-strand breaks appears to use an RNA template-based recombination mechanism dependent on RAD52. (wikipedia.org)
  • The DNA repair mechanism involving photolyases is called photoreactivation. (wikipedia.org)
  • Viruses
  • The Parvoviridae are a family of small, rugged, genetically-compact DNA viruses, known collectively as parvoviruses. (wikipedia.org)
  • Homotelomeric viruses package DNA strands of both senses (into separate capsids) whereas heterotelomeric viruses generally package predominantly negative-sense DNA (discussed in references 5 and 6). (wikipedia.org)
  • promoter
  • Explained briefly, NASBA works as follows: RNA template is given to the reaction mixture, the first primer, with the T7 promoter region on it's 5' end, attaches to its complementary site at the 3' end of the template. (wikipedia.org)
  • loops
  • These R-loops are visualized by electron microscopy and reveal intron regions of DNA by creating unbound loops at these regions. (wikipedia.org)
  • Actively transcribed regions of DNA often form R-loops that are vulnerable to DNA damage. (wikipedia.org)