• 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)
  • If the DNA sequences don't match, the cells float on by. (healthcanal.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)
  • Long terminal repeats (LTRs) are identical sequences of DNA that repeat hundreds or thousands of times found at either end of retrotransposons or proviral DNA formed by reverse transcription of retroviral RNA[citation needed]. (wikipedia.org)
  • molecule
  • To specify the 3-D structure of their organoids, Gartner's team makes use of a familiar molecule: DNA. (healthcanal.com)
  • 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)
  • cDNA
  • Complementary DNA is often used in gene cloning or as gene probes or in the creation of a cDNA library. (wikipedia.org)
  • When scientists transfer a gene from one cell into another cell in order to express the new genetic material as a protein in the recipient cell, the cDNA will be added to the recipient (rather than the entire gene), because the DNA for an entire gene may include DNA that does not code for the protein or that interrupts the coding sequence of the protein (e.g., introns). (wikipedia.org)
  • This is achieved by designing sequence-specific DNA primers that hybridize to the 5' and 3' ends of a cDNA region coding for a protein. (wikipedia.org)
  • An example of this first step from viral DNA to cDNA can be seen in the HIV cycle of infection. (wikipedia.org)
  • While information in cDNA libraries is a powerful and useful tool since gene products are easily identified, the libraries lack information about enhancers, introns, and other regulatory elements found in a genomic DNA library. (wikipedia.org)
  • cDNA library lacks the non-coding and regulatory elements found in genomic DNA. (wikipedia.org)
  • Both the cDNA and the linker have blunt ends which can be ligated together using a high concentration of T4 DNA ligase. (wikipedia.org)
  • The LTRs are partially transcribed into an RNA intermediate, followed by reverse transcription into complementary DNA (cDNA) and ultimately dsDNA (double-stranded DNA) with full LTRs. (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)
  • cytosine
  • The four nitrogenous bases found in DNA are adenine, guanine, thymine and cytosine. (reference.com)
  • Chargaff's rules state that DNA from any cell of all organisms should have a 1:1 ratio (base Pair Rule) of pyrimidine and purine bases and, more specifically, that the amount of guanine should be equaled to cytosine and the amount of adenine should be equaled to thymine. (wikipedia.org)
  • In single stranded DNA, cytosine spontaneously slowly deaminates to adenosine (a C to A transversion). (wikipedia.org)
  • This process tends to yield one strand that is enriched in guanine (G) and thymine (T) with its complement enriched in cytosine (C) and adenosine (A), and this process may have given rise to the deviations found in the mitochondria. (wikipedia.org)
  • In the canonical Watson-Crick base pairing, adenine (A) forms a base pair with thymine (T) and guanine (G) forms one with cytosine (C) in DNA. (wikipedia.org)
  • Photolyases bind complementary DNA strands and break certain types of pyrimidine dimers that arise when a pair of thymine or cytosine bases on the same strand of DNA become covalently linked. (wikipedia.org)
  • genome
  • Enhancement was found to be independent of initial rAAV2 receptor binding stage or subsequent second-strand synthesis of target DNA, but was related to cell cycle retardation followed by blocked genome degradation. (mdpi.com)
  • Due to the complexity of rAAV's infection pathway, some stages can be biologic barriers to affect gene delivery and expression, like receptor binding stage [ 9 , 10 ] and genome conversion from single strand to double strand [ 11 , 12 ]. (mdpi.com)
  • Polyomaviruses are a family of small, nonenveloped viruses with a circular double-stranded DNA genome of ~ 5,000 base pairs protected by an icosahedral protein structure. (hindawi.com)
  • The viral life cycle can be divided in an early phase taking place before viral DNA replication and a late phase occurring after replication of the viral genome. (hindawi.com)
  • OU biases are characteristic features of a bacterial genome [ 4 , 11 ], but according to Chargaff's first and second parity rule [ 14 ] the complementary strands are believed to be symmetric. (biomedcentral.com)
  • In eukaryotes, ribonuclease H1 is involved in DNA replication of the mitochondrial genome. (wikipedia.org)
  • Parvovirus particles (virions) have a durable non-enveloped protein capsid ~20-30 nm in diameter that contains a single copy of the linear single-stranded ~ 5kb DNA genome, which terminates in small imperfect palindromes that fold into dynamic hairpin telomeres. (wikipedia.org)
  • These terminal hairpins are hallmarks of the family, giving rise to the viral origins of DNA replication and mediating multiple steps in the viral life cycle including genome amplification, packaging, and the establishment of transcription complexes. (wikipedia.org)
  • These signals ultimately mediate delivery of the intact virion into the cell nucleus, where genome uncoating allows the establishment of viral DNA replication and transcription complexes that rely predominantly upon the synthetic machinery of their host cell. (wikipedia.org)
  • It does not apply to organellar genomes (mitochondria and plastids) smaller than ~20-30 kbp, nor does it apply to single stranded DNA (viral) genomes or any type of RNA genome. (wikipedia.org)
  • Genome-wide analysis showed that intron-containing genes display decreased R-loop levels and decreased DNA damage compared to intronless genes of similar expression in both yeast and humans. (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)
  • molecules
  • Thymine is a nitrogenous base that is found in DNA molecules but not in RNA molecules, according to Vision Learning. (reference.com)
  • The hillocks are capable of binding to complementary portions of biological molecules or their component molecules. (google.com)
  • b) a multiplicity of hillocks, said hillocks comprising at least one atom specifically positioned on said surface to form a three-dimensional pattern, said pattern dimensioned to facilitate binding between clusters of said hillocks and regions on DNA or RNA molecules complementary to said hillock clusters wherein said binding is by hydrogen bonding. (google.com)
  • Entire disciplines have developed around obtaining a better understanding of molecules of biological significance including DNA (deoxyribonucleic acid), RNA (ribonucleic acid), proteins, and their respective component molecules. (google.com)
  • A DNA field-effect transistor (DNAFET) is a field-effect transistor which uses the field-effect due to the partial charges of DNA molecules to function as a biosensor. (wikipedia.org)
  • In a non-biological context, secondary structure is a vital consideration in the nucleic acid design of nucleic acid structures for DNA nanotechnology and DNA computing, since the pattern of basepairing ultimately determines the overall structure of the molecules. (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)
  • hydrogen bonds
  • 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)
  • 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
  • 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)
  • 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)
  • 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)
  • homologous recombination
  • 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)
  • protein
  • 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)
  • This protein is located in the cell nucleus and must dimerize with another bHLH protein in order to bind DNA. (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)
  • 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)
  • 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)
  • transcription
  • Human RAD52 also has an important role in repair of DNA double-strand breaks at active transcription sites during the G0/G1 phase of the cell cycle. (wikipedia.org)
  • Only one of the two DNA strands serve as a template for transcription. (wikipedia.org)
  • Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for copying DNA. (wikipedia.org)
  • As a result, transcription has a lower copying fidelity than DNA replication. (wikipedia.org)
  • The multi-step process of reverse transcription results in the placement of two identical LTRs, each consisting of a U3, R, and U5 region, at either end of the proviral DNA. (wikipedia.org)
  • mediate
  • The LTRs then mediate integration of the retroviral DNA via an LTR specific integrase into another region of the host chromosome. (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)
  • In the "closed complex" the promoter DNA is still fully double-stranded. (wikipedia.org)
  • unbound
  • These R-loops are visualized by electron microscopy and reveal intron regions of DNA by creating unbound loops at these regions. (wikipedia.org)