• genome
  • DNA mismatch repair (MMR) is an important DNA repair system that helps maintain genome plasticity by correcting mismatches, or non Watson-Crick base pairs in the a DNA duplex. (wikipedia.org)
  • Transposition is a precise process in which a defined DNA segment is excised from one DNA molecule and moved to another site in the same or different DNA molecule or genome. (wikipedia.org)
  • All of the DNA transposons identified in the human genome and other mammalian genomes are non-autonomous because even though they contain transposase genes, the genes are non-functional and unable to generate a transposase that can mobilize the transposon. (wikipedia.org)
  • The elevation of DNA-PKcs is thought to reflect the induction of a compensatory DNA repair capability, due to the genome instability in these cancers. (wikipedia.org)
  • As indicated in the article Genome instability, such genome instability may be due to deficiencies in other DNA repair genes present in the cancers. (wikipedia.org)
  • Φ29 is a bacteriophage of Bacillus subtilis with a sequenced, linear, 19,285 base pair DNA genome. (wikipedia.org)
  • sequences
  • The activated AhR/ARNT heterodimer complex is then capable of either directly and indirectly interacting with DNA by binding to recognition sequences located in the 5'- regulatory region of dioxin-responsive genes. (wikipedia.org)
  • The genomics era began in the 1990s, with the generation of DNA sequences of many organisms. (wikipedia.org)
  • 397 1: 161-78 Preferred sequences within a defined cleavage window specify DNA 3' end-directed cleavages by retroviral RNases H. Schultz SJ, Zhang M, Champoux JJ The Journal of Biological Chemistry. (wikipedia.org)
  • The Sleeping Beauty transposon system is a synthetic DNA transposon designed to introduce precisely defined DNA sequences into the chromosomes of vertebrate animals for the purposes of introducing new traits and to discover new genes and their functions. (wikipedia.org)
  • The Sleeping Beauty transposon system is composed of a Sleeping Beauty (SB) transposase and a transposon that was designed in 1997 to insert specific sequences of DNA into genomes of vertebrate animals. (wikipedia.org)
  • Further work has shown that the DNA-binding domain consists of two paired sequences, which are homologous to sequence motifs found in certain transcription factors. (wikipedia.org)
  • For example, mutational biases and purifying selection favoring conservative changes are probably both responsible for the relatively high rate of transitions compared to transversions in evolving sequences. (wikipedia.org)
  • Evolutionary analyses of sequences are conducted on a wide variety of time scales. (wikipedia.org)
  • Example: We would like to model the substitution process in DNA sequences (i.e. (wikipedia.org)
  • ii) In the context of nucleotide changes in DNA sequences, transition is a specific term that refers to the exchange between either the two purines (A ↔ G) or the two pyrimidines (C ↔ T) (for additional details, see the article about transitions in genetics). (wikipedia.org)
  • genes
  • One major source of epigenetic change is altered methylation of CpG islands at the promoter region of genes (see DNA methylation in cancer). (wikipedia.org)
  • DNA damage appears to be the primary underlying cause of cancer, and deficiencies in DNA repair genes likely underlie many forms of cancer. (wikipedia.org)
  • Human populations studies show that single-nucleotide polymorphisms in DNA repair genes, causing up-regulation of their expression, correlate with increases in longevity. (wikipedia.org)
  • strands
  • Nicks are also thought to play a role in the DNA mismatch repair mechanisms that fix errors on both the leading and lagging daughter strands. (wikipedia.org)
  • As their family name suggests, a highly conserved tyrosine nucleophile cleaves the DNA strands. (wikipedia.org)
  • These other residues are crucial to the correct orientation of Flp binding and positioning on the DNA strands. (wikipedia.org)
  • A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation cannot be repaired. (wikipedia.org)
  • catalytic
  • The three domains consist of an N-terminal DNA binding domain (DBD), and catalytic nucleotidyltransferase (NTase), and C-terminal oligonucleotide / oligosaccharide binding (OB) domains. (wikipedia.org)
  • Moreover, the identification of a cyclin binding (Cy) motif in the catalytic C-terminus domain was shown by mutational analysis to play a role in the phosphorylation of serines 91 and 76. (wikipedia.org)
  • methylation
  • A number of recently devised methods can assess the DNA methylation status in cancers versus normal tissues. (wikipedia.org)
  • backbone
  • This leads to a different DNA conformation, where a hydrogen bond forms in place of the missing piece of the DNA backbone in order to preserve the structure. (wikipedia.org)
  • Pinch: UDG scans DNA for uracil by nonspecifically binding to the strand and creating a kink in the backbone, thereby positioning the selected base for detection. (wikipedia.org)
  • This compression of the DNA backbone, or "pinch," allows for close contact between UDG and base of interest. (wikipedia.org)
  • covalently
  • An anionic oxygen on the 5' phosphate of the DNA nick serves as the nucleophile, attacking the alpha phosphate of the covalently bound AMP causing the AMP to be covalently bound intermediate (DNA-AMP intermediate). (wikipedia.org)
  • nucleophile
  • The resulting 5'-hydroxyl group of the cleaved DNA acts as the nucleophile and attacks the 3'-phosphate on the complementarily cleaved DNA strand, resulting in successful recombination. (wikipedia.org)
  • deamination
  • Current evidence suggests that, in human cells, TDG and SMUG1 are the major enzymes responsible for the repair of the U:G mispairs caused by spontaneous cytosine deamination, whereas uracil arising in DNA through dU misincorporation is mainly dealt with by UNG. (wikipedia.org)
  • occurs
  • In humans and other mammals, DNA damage occurs frequently and DNA repair processes have evolved to compensate. (wikipedia.org)
  • accumulation
  • Hypothesis that aging is caused by accumulated DNA danage The DNA damage theory of aging proposes that aging is a consequence of unrepaired accumulation of naturally occurring DNA damages. (wikipedia.org)
  • Overall, they concluded that while the complexity of responses to DNA damage remains only partly understood, the idea that DNA damage accumulation with age is the primary cause of aging remains an intuitive and powerful one. (wikipedia.org)
  • The accumulation of unrepaired DNA damage is more prevalent in certain types of cells, particularly in non-replicating or slowly replicating cells, such as cells in the brain, skeletal and cardiac muscle. (wikipedia.org)
  • Descriptions of reduced function, characteristic of aging and associated with accumulation of DNA damage, are given later in this article. (wikipedia.org)
  • accumulate
  • Given these properties of DNA damage and mutation, it can be seen that DNA damages are a special problem in non-dividing or slowly dividing cells, where unrepaired damages will tend to accumulate over time. (wikipedia.org)
  • Okazaki
  • On the lagging strand, nicks exist between Okazaki fragments and are easily recognizable by the DNA mismatch repair machinery prior to ligation. (wikipedia.org)
  • ligation
  • LigA drives the process of the ligation by wrapping its protein clamp around the DNA and creating large protein conformational changes and remodeling of the active site. (wikipedia.org)
  • favorable
  • The coupling of intercalation and eversion helps compensate for the disruption of favorable base stacking interactions within the DNA helix. (wikipedia.org)
  • cancers
  • DNA-PKcs expression was reduced by 23% to 57% in six cancers as indicated in the table. (wikipedia.org)
  • It is not clear what causes reduced expression of DNA-PKcs in cancers. (wikipedia.org)
  • Elevated DNA-PKcs expression is found in a large fraction (40% to 90%) of some cancers (the remaining fraction of cancers often has reduced or absent expression of DNA-PKcs). (wikipedia.org)
  • As indicated in a table listing 12 types of cancer reported in 20 publications, the fraction of cancers with over-expression of DNA-PKcs is often associated with an advanced stage of the cancer and shorter survival time for the patient. (wikipedia.org)
  • However, the table also indicates that for some cancers, the fraction of cancers with reduced or absent DNA-PKcs is also associated with advanced stage and poor patient survival. (wikipedia.org)
  • enzymes
  • DNA can be nicked by physical shearing, over-drying or enzymes. (wikipedia.org)
  • As an example, they described a study showing that centenarians of 100 to 107 years of age had higher levels of two DNA repair enzymes, PARP1 and Ku70, than general-population old individuals of 69 to 75 years of age. (wikipedia.org)
  • DNA damage can be recognized by enzymes, and thus can be correctly repaired using the complementary undamaged sequence in a homologous chromosome if it is available for copying. (wikipedia.org)
  • sequence
  • As do all other Tc1/mariner-type transposases, SB transposase inserts a transposon into a TA dinucleotide base pair in a recipient DNA sequence. (wikipedia.org)
  • In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. (wikipedia.org)
  • A number of different Markov models of DNA sequence evolution have been proposed. (wikipedia.org)
  • By expressing models in terms of the instantaneous rates of change we can avoid estimating a large numbers of parameters for each branch on a phylogenetic tree (or each comparison if the analysis involves many pairwise sequence comparisons). (wikipedia.org)
  • Consider a DNA sequence of fixed length m evolving in time by base replacement. (wikipedia.org)
  • organisms
  • Because the recombination activity can be targeted to a selected organ, or a low level of recombination activity can be used to consistently alter the DNA of only a subset of cells, Flp-FRT can be used to construct genetic mosaics in multicellular organisms. (wikipedia.org)
  • important
  • citation needed] To understand the DNA damage theory of aging it is important to distinguish between DNA damage and mutation, the two major types of errors that occur in DNA. (wikipedia.org)