Base Pair Mismatch
The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).
Nucleic Acid Heteroduplexes
Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.
Base Sequence
Oligodeoxyribonucleotides
DNA Repair
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
DNA Mismatch Repair
A DNA repair pathway involved in correction of errors introduced during DNA replication when an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. Excinucleases recognize the BASE PAIR MISMATCH and cause a segment of polynucleotide chain to be excised from the daughter strand, thereby removing the mismatched base. (from Oxford Dictionary of Biochemistry and Molecular Biology, 2001)
Base Pairing
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Nucleic Acid Conformation
MutS DNA Mismatch-Binding Protein
MutS Homolog 2 Protein
Mutation
Cloning, Molecular
Escherichia coli
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Amino Acid Sequence
DNA-Binding Proteins
Plasmids
Transcription, Genetic
Promoter Regions, Genetic
Hydrogen Bonding
Genes
Oligonucleotides
Models, Molecular
DNA Restriction Enzymes
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Nucleic Acid Denaturation
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
Restriction Mapping
DNA Repair Enzymes
Binding Sites
Sequence Homology, Nucleic Acid
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Skull Base
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Schiff Bases
RNA
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Adenosine Triphosphatases
Thermodynamics
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
Repair of large insertion/deletion heterologies in human nuclear extracts is directed by a 5' single-strand break and is independent of the mismatch repair system. (1/1695)
The repair of 12-, 27-, 62-, and 216-nucleotide unpaired insertion/deletion heterologies has been demonstrated in nuclear extracts of human cells. When present in covalently closed circular heteroduplexes or heteroduplexes containing a single-strand break 3' to the heterology, such structures are subject to a low level repair reaction that occurs with little strand bias. However, the presence of a single-strand break 5' to the insertion/deletion heterology greatly increases the efficiency of rectification and directs repair to the incised DNA strand. Because nick direction of repair is independent of the strand in which a particular heterology is placed, the observed strand bias is not due to asymmetry imposed on the heteroduplex by the extrahelical DNA segment. Strand-specific repair by this system requires ATP and the four dNTPs and is inhibited by aphidicolin. Repair is independent of the mismatch repair proteins MSH2, MSH6, MLH1, and PMS2 and occurs by a mechanism that is distinct from that of the conventional mismatch repair system. Large heterology repair in nuclear extracts of human cells is also independent of the XPF gene product, and extracts of Chinese hamster ovary cells deficient in the ERCC1 and ERCC4 gene products also support the reaction. (+info)Mismatch repair and differential sensitivity of mouse and human cells to methylating agents. (2/1695)
The long-patch mismatch repair pathway contributes to the cytotoxic effect of methylating agents and loss of this pathway confers tolerance to DNA methylation damage. Two methylation-tolerant mouse cell lines were identified and were shown to be defective in the MSH2 protein by in vitro mismatch repair assay. A normal copy of the human MSH2 gene, introduced by transfer of human chromosome 2, reversed the methylation tolerance. These mismatch repair defective mouse cells together with a fibroblast cell line derived from an MSH2-/- mouse, were all as resistant to N-methyl-N-nitrosourea as repair-defective human cells. Although long-patch mismatch repair-defective human cells were 50- to 100-fold more resistant to methylating agents than repair-proficient cells, loss of the same pathway from mouse cells conferred only a 3-fold increase. This discrepancy was accounted for by the intrinsic N-methyl-N-nitrosourea resistance of normal or transformed mouse cells compared with human cells. The >20-fold differential resistance between mouse and human cells could not be explained by the levels of either DNA methylation damage or the repair enzyme O6-methylguanine-DNA methyltransferase. The resistance of mouse cells to N-methyl-N-nitrosourea was selective and no cross-resistance to unrelated DNA damaging agents was observed. Pathways of apoptosis were apparently intact and functional after exposure to either N-methyl-N-nitrosourea or ultraviolet light. Extracts of mouse cells were found to perform 2-fold less long-patch mismatch repair. The reduced level of mismatch repair may contribute to their lack of sensitivity to DNA methylation damage. (+info)MSH3 deficiency is not sufficient for a mutator phenotype in Chinese hamster ovary cells. (3/1695)
In the yeast Saccharomyces cerevisiae, the mutS homolog protein products MSH3 and MSH6, each in cooperation with MSH2, play well-defined and specific roles in the repair of DNA mismatches and nucleotide loops. The discrete functions of the human homologs hMSH3 and hMSH6 are less clear and current evidence suggests that the substrate specificity of these proteins may be less strict. To determine the role of MSH3 in mammalian mismatch repair, we employed MSH3-deficient Chinese hamster ovary (CHO) cell lines. No significant changes in mutation rate were detected in the MSH3-deficient strain and there were no differences in sensitivity to DNA-damaging agents. Further analysis of hprt mutants did not show a MSH3-dependent shift in the mutant spectrum. Interestingly, thorough examination of four dinucleotide microsatellite regions revealed instability at only one locus in one of the MSH3-deficient cell lines. These data support the idea of a high degree of redundancy in the function of the MutS homologs MSH3 and MSH6, at least with respect to the control of microsatellite instability. (+info)Mouse MutS-like protein Msh5 is required for proper chromosome synapsis in male and female meiosis. (4/1695)
Members of the mammalian mismatch repair protein family of MutS and MutL homologs have been implicated in postreplicative mismatch correction and chromosome interactions during meiotic recombination. Here we demonstrate that mice carrying a disruption in MutS homolog Msh5 show a meiotic defect, leading to male and female sterility. Histological and cytological examination of prophase I stages in both sexes revealed an extended zygotene stage, characterized by impaired and aberrant chromosome synapsis, that was followed by apoptotic cell death. Thus, murine Msh5 promotes synapsis of homologous chromosomes in meiotic prophase I. (+info)Mutator phenotypes of yeast strains heterozygous for mutations in the MSH2 gene. (5/1695)
Heterozygosity for germ-line mutations in the DNA mismatch repair gene MSH2 predisposes humans to cancer. Here we use a highly sensitive reporter to describe a spontaneous mutator phenotype in diploid yeast cells containing a deletion of only one MSH2 allele. We also identify five MSH2 missense mutations that have dominant mutator effects in heterozygous cells when expressed at normal levels from the natural MSH2 promoter. For example, a 230-fold mutator effect is observed in an MSH2/msh2 diploid strain in which Gly693, which is invariant in MutS homologs and involved in ATP hydrolysis, is changed to alanine. DNA binding data suggest that mismatch repair is suppressed by binding of a mutant Msh2-Msh6 heterodimer to a mismatch with subsequent inability to dissociate from the mismatch in the presence of ATP. A dominant mutator effect also is observed in yeast when Gly693 is changed to serine. An early onset colorectal tumor is heterozygous for the analogous Gly --> Ser mutation in hMSH2, and a second hMSH2 mutation was not found, suggesting that this missense mutation may predispose to cancer via a dominant mutator effect. The mutator effects of the deletion mutant and the Gly --> Ala missense mutant in yeast MSH2 are enhanced by heterozygosity for a missense mutation in DNA polymerase delta that reduces its proofreading activity but is not a mutator in the heterozygous state. The synergistic effects of heterozygosity for mutations in two different genes that act in series to correct replication errors may be relevant to cancer predisposition. (+info)Hypermutation in Ig V genes from mice deficient in the MLH1 mismatch repair protein. (6/1695)
During somatic hypermutation of Ig V genes, mismatched nucleotide substitutions become candidates for removal by the DNA mismatch repair pathway. Previous studies have shown that V genes from mice deficient for the MSH2 and PMS2 mismatch repair proteins have frequencies of mutation that are comparable with those from wild-type (wt) mice; however, the pattern of mutation is altered. Because the absence of MSH2 and PMS2 produced different mutational spectra, we examined the role of another protein involved in mismatch repair, MLH1, on the frequency and pattern of hypermutation. MLH1-deficient mice were immunized with oxazolone Ag, and splenic B cells were analyzed for mutations in their V kappa Ox1 light chain genes. Although the frequency of mutation in MLH1-deficient mice was twofold lower than in wt mice, the pattern of mutation in Mlh1-/- clones was similar to wt clones. These findings suggest that the MLH1 protein has no direct effect on the mutational spectrum. (+info)Are adaptive mutations due to a decline in mismatch repair? The evidence is lacking. (7/1695)
The levels of proteins required for methyl-directed mismatch repair appear to decline in stationary-phase and nutritionally-deprived cells of Escherichia coli. It has been hypothesized that error-correction by the system also declines, and this decline is responsible for adaptive or stationary-phase mutations. However, evidence in support of this hypothesis is lacking. The mismatch repair system is no less effective in correcting errors during prolonged selection than it is during growth. Furthermore, mismatch repair proteins supplied in excess reduce both growth-dependent and adaptive mutation. (+info)MED1, a novel human methyl-CpG-binding endonuclease, interacts with DNA mismatch repair protein MLH1. (8/1695)
The DNA mismatch repair (MMR) is a specialized system, highly conserved throughout evolution, involved in the maintenance of genomic integrity. To identify novel human genes that may function in MMR, we employed the yeast interaction trap. Using the MMR protein MLH1 as bait, we cloned MED1. The MED1 protein forms a complex with MLH1, binds to methyl-CpG-containing DNA, has homology to bacterial DNA repair glycosylases/lyases, and displays endonuclease activity. Transfection of a MED1 mutant lacking the methyl-CpG-binding domain (MBD) is associated with microsatellite instability (MSI). These findings suggest that MED1 is a novel human DNA repair protein that may be involved in MMR and, as such, may be a candidate eukaryotic homologue of the bacterial MMR endonuclease, MutH. In addition, these results suggest that cytosine methylation may play a role in human DNA repair. (+info)
Base pair
Examples include ethidium bromide and acridine.[citation needed] Mismatched base pairs can be generated by errors of DNA ... kb (= kbp) = kilo-base-pair = 1,000 bp Mb (= Mbp) = mega-base-pair = 1,000,000 bp Gb = giga-base-pair = 1,000,000,000 bp. For ... The GU pairing, with two hydrogen bonds, does occur fairly often in RNA (see wobble base pair). Paired DNA and RNA molecules ... In addition to the canonical pairing, some conditions can also favour base-pairing with alternative base orientation, and ...
DNA mismatch repair
A few or up to thousands of base pairs of the newly synthesized DNA strand can be removed. Mismatch repair is a highly ... Examples of mismatched bases include a G/T or A/C pairing (see DNA repair). Mismatches are commonly due to tautomerization of ... When bound, the MutS2 dimer bends the DNA helix and shields approximately 20 base pairs. It has weak ATPase activity, and ... that recognises the mismatched base on the daughter strand and binds the mutated DNA. MutH binds at hemimethylated sites along ...
Adaptive evolution in the human genome
DNA repair mechanisms are biased towards repairing a mismatch to the CG base pair. This will lead allele frequencies to change ... Meiotic recombination between homologous chromosomes that are heterozygous at a particular locus can produce a DNA mismatch. ...
Infectious causes of cancer
Thus, it changes a C:G base pair into a mutagenic U:G mismatch. In a still further cause of DNA damage, HCV core protein binds ... AID creates mutations in DNA by deamination (a DNA damage) of the cytosine base, which converts cytosine into uracil. ... including the base of the tongue and tonsils). Each year in the United States, about 39,800 new cases of cancer are found in ...
Nucleotide excision repair
Similarly, the MMR pathway only targets mismatched Watson-Crick base pairs. Nucleotide excision repair (NER) is a particularly ... Base excision repair (BER) Mismatch repair (MMR) Fuss JO, Cooper PK (June 2006). "DNA repair: dynamic defenders against cancer ... Karahalil B, Bohr V, Wilson D (October 2012). "Impact of DNA polymorphisms in key DNA base excision repair proteins on cancer ... Zhang Y, Rohde LH, Wu H (June 2009). "Involvement of nucleotide excision and mismatch repair mechanisms in double strand break ...
Tom Brown (chemist)
In early part of his academic career, Brown studied base-pair mismatch and DNA repair. Later he worked on the mutagenic effect ... Hunter, William N. (10 April 1986). "Structure of an adenine˙cytosine base pair in DNA and its implications for mismatch repair ... "High-resolution structure of a DNA helix containing mismatched base pairs". Nature. 315 (6020): 694-606. Bibcode:1985Natur.315 ... Savva, Renos (9 February 1995). "The Structural Basis of Specific Base-Excision Repair by Uracil-DNA Glycosylase". Nature. 373 ...
Paul L. Modrich
Su, SS; Modrich, P (July 1986). "Escherichia coli mutS-encoded protein binds to mismatched DNA base pairs". Proceedings of the ... He works primarily on strand-directed mismatch repair. His lab demonstrated how DNA mismatch repair serves as a copyeditor to ... He is known for his research on DNA mismatch repair. Modrich received the Nobel Prize in Chemistry 2015, jointly with Aziz ... They later searched for proteins associated with mismatch repair in humans. Honors and awards received by Modrich include: 1983 ...
Deepak T. Nair
Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA polymerase iota. ... MsDpo4-a DinB Homolog from Mycobacterium smegmatis-Is an Error-Prone DNA Polymerase That Can Promote G:T and T:G Mismatches. J ... Human DNA polymerase iota incorporates dCTP opposite template G via a G.C + Hoogsteen base pair. Structure. 2005 Oct;13(10): ... Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing. Nature. 2004 Jul 15;430(6997):377-80. PMID 15254543 ...
MutS-1
It involves the correction of mismatched base pairs that have been missed by the proofreading element (Klenow fragment) of the ... MutS is a mismatch DNA repair protein, originally described in Escherichia coli. Mismatch repair contributes to the overall ... Nag N, Rao BJ, Krishnamoorthy G (November 2007). "Altered dynamics of DNA bases adjacent to a mismatch: a cue for mismatch ... "The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch". Nature. 407 (6805): 711-7. doi:10.1038/ ...
DNA polymerase
Mismatches in DNA base pairing can potentially result in dysfunctional proteins and could lead to cancer. Many DNA polymerases ... When an incorrect base pair is recognized, DNA polymerase moves backwards by one base pair of DNA. The 3'-5' exonuclease ... Hydrogen bonds play a key role in base pair binding and interaction. The loss of an interaction, which occurs at a mismatch, is ... which acts in detecting base pair mismatches and further performs in the removal of the incorrect nucleotide to be replaced by ...
Activation-induced cytidine deaminase
G base pair into a U:G mismatch. The cell's DNA replication machinery recognizes the U as a T, and hence C:G is converted to a ... This allows the generation of mutations at AT base pairs. The level of AID activity in B cells is tightly controlled by ... This heterodimer is able to recognize mostly single-base distortions in the DNA backbone, consistent with U:G DNA mismatches. ... The U:G mismatch may also be recognized by the DNA mismatch repair (MMR) machinery, to be specific by the MutSα(alpha) complex ...
Allele-specific oligonucleotide
... the effect of single base pair mismatch". Nucleic Acids Research. 6 (11): 3543-3558. doi:10.1093/nar/6.11.3543. PMC 327955. ... The Illumina Methylation Assay technology takes advantage of ASO to detect one base pair difference (cytosine versus thymine) ... The mismatched ASOs are washed off of the blots, while the matched ASOs (and their labels) remain. In the second diagram, six ... These probes can usually be designed to detect a difference of as little as 1 base in the target's genetic sequence, a basic ...
Biomolecular engineering
... uses an oligonucleotide that is complementary to a bacterial plasmid with a single base pair mismatch or a series of mismatches ... This primer will have a base pair mismatch at the site where the replacement is desired. The primer must also be long enough ... A single base-pair replacement will change the codon, potentially replacing an amino acid in a protein. Mutagenesis can help ... PCR paired with Western blotting and ELISA help define the relationship between cancer cells and IL-6. Enzyme-linked ...
Surveyor nuclease assay
... single base pair mismatches, and insertions and deletions at low frequencies. Several such enzymes have been discovered ( ... Surveyor nuclease assay is an enzyme mismatch cleavage assay used to detect single base mismatches or small insertions or ... Enzymatic mismatch cleavage assays exploit the properties of mismatch-specific endonucleases to detect and cleave mismatches. ... All types of mismatches are identifiable by Surveyor nuclease, although the mismatch cutting preferences fall into four groups ...
DNA-binding metallo-intercalators
Complex for High-affinity DNA Base-pair Mismatch Recognition". Proceedings of the National Academy of Sciences. 100 (7): 3737- ... of metallo-intercalators is to combat cancerous tumor cells within the body by targeting specific mismatched DNA base pairs; ... This ability to bind to specific DNA base pairs allows for potential therapeutic applications of metallo-intercalators. In the ... metallo-intercalator and DNA can substantially decrease the proliferation of cells containing DNA with mismatched base pairs. ...
Lorena S. Beese
This finding suggests a mechanism by which polymerases are able to detect incorrect base pairing. Beese had an integral role in ... Through her research, Beese found that the hExo1 enzyme binds the DNA near the site of mismatched pairing, and through ... the enzyme is able to assist in the identification and replacement of incorrect base pairs. By integrating high-resolution X- ... They are using DNA polymerase as a model system to study molecular mechanisms of DNA mis-pair incorporation and action of ...
Kataegis
It can slip at sequence or insert A or C base pairs into a distorted region on DNA strand; ss shown in Figure 3, TLS DNA ... A collection of enzymes from the DNA repair system will come in to excise the mismatch basepair. When these enzymes try to mend ... If the C→U mutation error is detected by its specific glycosylase, the glycosylase will cut the base pair and form an abasic ... The original CG pair will become a TA pair after one round of replication, hence the predominantly seen C→T mutation in ...
Sequencing by ligation
... relies upon the sensitivity of DNA ligase for base-pairing mismatches. The target molecule to be ... Instead, the mismatch sensitivity of a DNA ligase enzyme is used to determine the underlying sequence of the target DNA ... This sequences every Nth base, where N is the length of the probe left behind after cleavage. To sequence the skipped positions ... Although commonly represented as joining two pairs of ends at once, as in the ligation of restriction enzyme fragments, ligase ...
List of restriction enzyme cutting sites: A
"Hydrolysis by restriction endonucleases at their DNA recognition sequences substituted with mismatched base pairs". Nucleic ... Bilcock DT, Daniels LE, Bath AJ, Halford SE (December 1999). "Reactions of type II restriction endonucleases with 8-base pair ... T basepairs". FEBS Lett. 143 (2): 296-300. doi:10.1016/0014-5793(82)80120-8. PMID 6288466. Marks P, McGeehan J, Wilson G, ...
Mung bean nuclease
Cleavage of single-basepair mismatches, as a replacement for CEL 1 Nuclease in TILLING. Unidirectional deletion of large DNA ( ... Some is known about its structure, with one exposed Cysteine residue and 3 pairs of disulfide bonds. Some is known about its ... Its ability to recognise double-stranded nucleic acids depends on the base sequence. It tends to cleave at ApN and at T(U) pN. ...
GABRA3
The region that base pairs with the editing region is known as an Editing Complementary Sequence (ECS). The editing site was ... The predicted double-stranded RNA structure is interrupted by three bulges and a mismatch at the editing site. The double- ... The double-stranded regions of RNA are formed by base-pairing between residues in the close to region of the editing site, with ... stranded region is 22 base pairs in length. As with editing of the KCNA1 gene product, the editing region and the editing ...
Gene conversion
... occurs during meiosis when homologous recombination between heterozygotic sites results in a mismatch in base pairing. This ... For example, when a T:G mismatch occurs, it would be more or less likely to be corrected to a C:G pair than a T:A pair. This ... Conversion of one allele to the other is often due to base mismatch repair during homologous recombination: if one of the four ... When mismatches occur in heteroduplex DNA, the sequence of one strand will be repaired to bind the other strand with perfect ...
DNA methylation
G pair into a T:A pair, effectively changing a base and introducing a mutation. This misincorporated base will not be corrected ... This results in a T:G mismatch. Repair mechanisms then correct it back to the original C:G pair; alternatively, they may ... If there is a mismatch, it is recorded and the percentage of DNA for which the mismatch is present is noted. This gives the ... Bisulfite-treated DNA is hybridized to probes on "BeadChips." Single-base base extension with labeled probes is used to ...
AP endonuclease
... exonuclease activity that acts preferentially on mismatched base pairs". Nucleic Acids Res. 34 (9): 2508-15. doi:10.1093/nar/ ... Apurinic/apyrimidinic (AP) endonuclease is an enzyme that is involved in the DNA base excision repair pathway (BER). Its main ... Because APE1 performs an essential function in DNA base-excision repair pathway, it has become a target for researchers looking ... Mark R. Kelley; Melissa L. Fishel (2007). "The DNA base excision repair protein Ape1/Ref-1 as a Therapeutic and chemopreventive ...
Off-target genome editing
However, target sequence binding can tolerate mismatches up to several base pairs, meaning there are often thousands of ... Off-target binding mechanisms can be grouped into two main forms: base mismatch tolerance, and bulge mismatch. While the Cas9 ... off-target mutations are still prevalent and could occur with as many as 3-5 base pair mismatches (out of 20) between the sgRNA ... showed that in a catalytically dead Cas9 only 1-5 base pairs of seed sequence is required for specificity. This was later ...
RNA editing
Inosine is a modification that is able to base-pair with cytosine, adenine, and uridine. Another commonly modified base in tRNA ... The mechanism of the editosome involves an endonucleolytic cut at the mismatch point between the guide RNA and the unedited ... The wobble base pairing causes deaminated RNA to have a unique but different structure, which may be related to the inhibition ... The inserted uridines will base-pair with the guide RNA, and insertion will continue as long as A or G is present in the guide ...
Hematopoietic stem cell transplantation
In addition, a genetic mismatch as small as a single DNA base pair is significant, so perfect matches require knowledge of the ... A mismatch of an HLA type II gene (i.e. HLA-DR or HLA-DQB1) increases the risk of graft-versus-host disease. ... The HLA genes fall in two categories (types I and II). In general, mismatches of the type-I genes (i.e. HLA-A, HLA-B, or HLA-C ... Even so-called "perfect matches" may have mismatched minor alleles that contribute to graft-versus-host disease.[citation ...
Nucleic acid secondary structure
The base pairing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. ... The only other possible pairings are GT and AC; these pairings are mismatches because the pattern of hydrogen donors and ... In the canonical Watson-Crick base pairing, adenine (A) forms a base pair with thymine (T) and guanine (G) forms one with ... such as the wobble base pair and Hoogsteen base pair, also occur-particularly in RNA-giving rise to complex and functional ...
Nucleic acid analogue
... this is an example where a Watson-Crick basepair mismatch is stabilized by the formation of the metal-base pair. Another ... The asymmetric metal base pairing system is orthogonal to the Watson-Crick base pairs. Another example of an artificial ... base pair. One of the most common base analogs is 5-bromouracil (5BU), the abnormal base found in the mutagenic nucleotide ... which base pairs to cytosine instead of thymine. Cytosine is deaminated to uracil, which base pairs with Adenine instead of ...
Mutational signatures
DNA mismatch repair (MMR) deficiency: The mismatch repair machinery recognizes and repairs erroneous base pair insertion, ... MUTYH encodes the mutY adenine glycosylase enzyme which excise the mismatched adenine from 8-Oxoguanine:adenine base pairing, ... Taking the information from the 5' and 3' adjacent bases (also called flanking base pairs or trinucleotide context) lead to 96 ... base-pair substitution or substitution point mutation) in one of the 96 mutation types and counting the total number of ...
Benjamin Franklin
His reasons for vegetarianism were based on health, ethics, and economy: When about 16 years of age, I happen'd to meet with a ... he was shocked by a pair of Leyden jars, resulting in numbness in his arms that persisted for one evening, noting "I am Ashamed ... Pages using Sister project links with wikidata namespace mismatch, Pages using Sister project links with hidden wikidata, ... He tried to influence American moral life through the construction of a printing network based on a chain of partnerships from ...
Songs to No One 1991-1992
Whilst having a female lead vocalist made for a tactical development in a commercial sense, the pair had mismatched intentions ... Lucas describes the first phrasing of the song as "a questioning motif based on a diminished chord to a definitive answering ... Paired with Nichols on producing the 1991 season talent, the adoption of Willner's idea quickly became an exciting event to ... Recalling the first time hearing Jeff sing, Lucas stated "he closed his eyes and honey poured forth". The pair also jammed to a ...
Goal setting
Based initially on Drucker's management by objectives (MBO) model, a popular applied version of goal setting theory for ... the goal setter has established a desired future state which differs from their current state thus creating a mismatch which in ... and suggest new hypotheses regarding a pair of its moderators: goal difficulty and proximity. The effectiveness of goal setting ... In particular, setting life goals based on others leads to more positive emotions and therefore has a more positive impact on ...
Promoter (genetics)
On average, only 3 to 4 of the 6 base pairs in each consensus sequence are found in any given promoter. Few natural promoters ... 35 elements have been found to transcribe at lower frequencies than those with a few mismatches with the consensus. The optimal ... The TATA element and BRE typically are located close to the transcriptional start site (typically within 30 to 40 base pairs). ... Promoters can be about 100-1000 base pairs long, the sequence of which is highly dependent on the gene and product of ...
M551 Sheridan replacement process
Cadillac Gage Textron paired a Commando Stingray chassis to a LAV-105 turret. It had a fairly conventional layout with a four- ... "Army's AGS Will Be Based on Existing Platform, 'Air-Droppable' From C-17". Inside the Pentagon. Vol. 7, no. 15. Inside ... This move garnered consternation among both services who believed that the LAV-105 and heavier armored AGS were mismatched. The ... and air power in the area was limited to the B-52 Stratofortress flying from bases in the Indian Ocean, Naval air power could ...
Michelangelo
Pages using Sister project links with wikidata namespace mismatch, Pages using Sister project links with wikidata mismatch, ... Although the two angels form a pair, there is a great contrast between the two works, the one depicting a delicate child with ... The hypothesis on Michelangelo's possible involvement in the creation of the profile is based on the strong resemblance of the ... the latter based on a theme suggested by Poliziano and commissioned by Lorenzo de' Medici. Michelangelo worked for a time with ...
IQ imbalance
... the base-band signal consists of several sub-carriers. Complex-conjugating the base-band signal of the kth sub-carrier carrying ... Mismatches between the two LO signals and/or along the two branches of down-conversion mixers, and any following amplifiers, ... This process requires shifting the LO signal by 90° to produce a quadrature sinusoidal component, and a matched pair of mixers ... The time domain base-band signals with IQ imbalance can be represented by : z i , n = η α z ( t ) + η β z ∗ ( t ) , t = i ( N ...
Māori language
The lexical word forms the "base" of the phrase. Biggs identifies five types of bases. Noun bases include those bases that can ... The modern Māori alphabet has 15 letters, two of which are digraphs (character pairs). The five vowels have both short and long ... Pages using Sister project links with wikidata mismatch, Articles with GND identifiers, Articles with NDL identifiers, Articles ... Stative bases serve as bases usable as verbs but not available for passive use, such as ora, alive or tika, correct. Grammars ...
Antenna tuner
The technique is essentially to fix a mismatch by creating an opposite mismatch: A line segment with the proper impedance and ... At the base of the tower (in the "coupling hut") an ATU is used to match the antenna to the either 50 Ω or 300 Ω transmission ... Where paired components remain, they are "ganged" mechanically, so that one adjustment makes the same change to both. In the ... They are all based on tuned transformer circuits; none of the designs discussed in this section are balanced versions of the ...
RNA-targeting small molecule drugs
... creating a base triplet with the mismatch. The combined use of an acridine intercalator to pi-pi stack on the target gave a ... the guanosine analog prodrug is used to stop viral RNA synthesis and viral mRNA capping by incorporating into RNA and pairing ... Ratmeyer, L. S; Vinayak, R; Zon, G; Wilson, W. D (1992). "An ethidium analogue that binds with high specificity to a base- ... Through rational design, they utilized a triaminotriazine recognition unit to target TT or UU mismatches through a Janus Wedge ...
Cot filtration
... the molecular forces holding complementary base pairs together are disrupted, and the two strands of each double-helix ... The temperature at which renaturation occurs can be regulated so that little or no sequence mismatch is tolerated. The rate at ... In CF, genomic DNA is heat-denatured and allowed to renature to a Cot value (Cot = DNA concentration x time x a factor based on ... Cot-Based Cloning and Sequencing Plant Genome Mapping Laboratory v t e (Molecular biology, Laboratory techniques, All stub ...
Leonardo DiCaprio
Also in 2008, DiCaprio starred in Body of Lies, a spy film based on the novel of the same name. He played one of three agents ... DiCaprio liked working with Pitt, and Tarantino described the pair as the most exciting since Robert Redford and Paul Newman. ... Pages using Sister project links with wikidata namespace mismatch, Pages using Sister project links with hidden wikidata, ... DiCaprio reunited with Scorsese for the fifth time in The Wolf of the Wall Street, a film based on the life of stockbroker ...
Acis and Galatea
There are a pair by Jean-Baptiste Tuby in the Bosquet des Dômes in the Versailles gardens. Acis leans on a rock, casually ... ISBN 0-631-20102-5. Hard, Robin, The Routledge Handbook of Greek Mythology: Based on H.J. Rose's "Handbook of Greek Mythology ... Pages using Sister project links with wikidata namespace mismatch, Articles with J9U identifiers, Articles with LCCN ... They anticipate the tragic moment when he looms menacingly over the pair, having discovered the truth they have tried to ...
Wandsworth Bridge
It cost £40,000 (about £3.8 million in 2022) to build, and consisted of five identical spans, supported by four pairs of ... A utilitarian structure made of mismatched materials purchased for cheapness, the new bridge elicited unenthusiastic responses ... 138 UK Retail Price Index inflation figures are based on data from Clark, Gregory (2017). "The Annual RPI and Average Earnings ...
Robin Hood
In 1598, Anthony Munday wrote a pair of plays on the Robin Hood legend, The Downfall and The Death of Robert Earl of Huntington ... The overall picture from the surviving early ballads and other early references indicate that Robin Hood was based in the ... Pages using Sister project links with wikidata mismatch, Pages using Sister project links with default search, Articles with ... "being of a base stock and linaege, was for his manhood and chivalry advanced to the noble dignity of an Earl" and not the ...
Julia Roberts
Roberts paired with Hugh Grant for Notting Hill (1999), portraying a famous actress who falls in love with a struggling book ... Considered to be one of the best romantic comedies of all time, Rotten Tomatoes gave the film an approval rating of 73% based ... Pages using Sister project links with wikidata namespace mismatch, Internet Broadway Database person ID same as Wikidata, ... Emma Brookner, a character based on Dr. Linda Laubenstein, in the television adaptation of Larry Kramer's AIDS-era play, The ...
Whale
They have a pair of blowholes side by side and lack teeth; instead they have baleen plates which form a sieve-like structure in ... The whale is an albino sperm whale, considered by Melville to be the largest type of whale, and is partly based on the ... doi:10.2305/IUCN.UK.2018-2.RLTS.T2475A130482064.en.{{cite journal}}: CS1 maint: date and year (link),date= / ,doi= mismatch ... A pair of pygmy right whales were retained in an enclosed area (with nets); they were eventually released in South Africa. ...
Coding theory approaches to nucleic acid design
Such pairing is chemically very stable and strong. However, pairing of mismatching bases does occur at times due to biological ... denotes the Watson-Crick complement base pair of q i {\displaystyle {\mathit {q}}_{i}} . For any pair of length- n {\ ... Each purine base is the Watson-Crick complement of a unique pyrimidine base (and vice versa) - adenine and thymine form a ... This pairing can be described as follows - A ¯ = T , T ¯ = A , C ¯ = G , G ¯ = C {\displaystyle {\bar {A}}=T,{\bar {T}}=A,{\bar ...
A Midsummer Night's Dream (1999 film)
A Midsummer Night's Dream is a 1999 romantic comedy fantasy film based on the play of the same name by William Shakespeare. It ... Oberon tires of the sport and puts all to rights, pairing Lysander back with Hermia and Demetrius with Helena, and reconciling ... The hoodwinked characters of A Midsummer Night's Dream are meant to be mismatched much of the time. But not like this. The ... In the final part, Bottom and his troupe of "rude Mechanicals" perform their amateur play, based on the tragedy of Pyramus and ...
Syrah
Based on these findings, the researchers have concluded Syrah originated from northern Rhône. The DNA typing leaves no room for ... It is believed to be caused by mismatch between the rootstock and scion rather than an infection by a fungus or a virus. In ... "A Single Pair of Parents Proposed for a Group of Grapevine Varieties in Northeastern France". Acta Horticulturae (528): 129-132 ... Another legend of the grape variety's origin, based on the name Syrah, is that it was brought from Syracuse by the legions of ...
Tiger Woods
In the final round, he was paired with pro John Daly, who was then relatively unknown. The event's format placed a professional ... Pages using Sister project links with wikidata namespace mismatch, Pages using Sister project links with hidden wikidata, ... father was a member of the military and had playing privileges at the Navy golf course beside the Joint Forces Training Base in ... who had employed her as an au pair. They married on October 5, 2004, at the Sandy Lane resort in Barbados, and lived at ...
The Best Exotic Marigold Hotel
The screenplay, written by Ol Parker, is based on the 2004 novel These Foolish Things by novelist Deborah Moggach, and features ... whom he had to leave due to a scandal involving the pair. He, Evelyn, and Douglas eventually find Manoj, who has been happily ... mismatched local textiles, all mixed together with modern plastic bits and pieces, with everything distressed and weather ... The review aggregator website Rotten Tomatoes reported that 78% of critics gave the film a positive rating, based on 168 ...
DNA damage theory of aging
However, in vertebrates there are CpG islands, about 300 to 3,000 base pairs long, with interspersed DNA sequences that deviate ... "Elevated levels of mutation in multiple tissues of mice deficient in the DNA mismatch repair gene Pms2". Proceedings of the ... a mutation is a change in the base sequence of the DNA. A mutation cannot be recognized by enzymes once the base change is ... Swain, U; Subba Rao, K (Aug 2011). "Study of DNA damage via the comet assay and base excision repair activities in rat brain ...
Lattice network
To minimise the mismatch problem, various forms of image filter end terminations were proposed by Otto Julius Zobel and others ... A commonly used short-hand version is shown on the right, with dotted lines indicating the presence the second pair of matching ... In those early days, filter theory was based on image impedance concepts, or image filter theory, which was a design approach ... In the case of a low-pass filter, for example, where the mismatch is most severe near the cut-off frequency, the transition ...
Mismatched
... is a rom-com based on Sandhya Menon's best selling book 'When Dimple Met Rishi'. Dimple Ahuja (Prajakta Koli) wants ... "The fresh pairing of Rohit Saraf and Prajakta Koli is a delight to watch on screen - the duo shares a crackling chemistry and ... Mismatched is a 2020 Indian Hindi-language coming-of-age romantic drama web series on Netflix, based on Sandhya Menon's 2017 ... Mismatched' trailer: Series aimed at young adults is based on the novel 'When Dimple Met Rishi'". Scroll.in. Retrieved 21 ...
Augustin-Louis Cauchy
In the theory of numbers and complex quantities, he was the first to define complex numbers as pairs of real numbers. He also ... The young Duke had neither taste nor talent for either mathematics or science, so student and teacher were a perfect mismatch. ... where Napoleon intended to build a naval base. Here Augustin-Louis stayed for three years, and was assigned the Ourcq Canal ...
BCPL
The mismatch between BCPL's word orientation and byte-oriented hardware was addressed in several ways. One was by providing ... each paired with a number that associates the name with the corresponding numerically addressed word in the global vector. As ... was the language on which the C programming language was based. BCPL introduced several features of many modern programming ...
No-SCAR (Scarless Cas9 Assisted Recombineering) Genome Editing
Finally, the mismatch repair (MMR) machinery offers inherent protection to the cell against nucleotide base mismatch. Therefore ... First, optimal oligo length for the transfected linear DNA should be between 60 and 90 base pairs. This guideline is based on ... Of this sequence, at least 15 base pairs should be homologous to the target sequence at both the 5' and 3' ends to provide ... end of the PCR primer while the wild-type genotype results in mismatched DNA at the 3' end. The mismatch between the 3' end of ...
Brain-computer interface
EEG-based interfaces also require some time and effort prior to each usage session, whereas non-EEG-based ones, as well as ... Sabathiel N, Irimia DC, Allison BZ, Guger C, Edlinger G (17 July 2016). "Paired Associative Stimulation with Brain-Computer ... have been extensively tested in recent years in an effort to minimize brain tissue trauma related to mechanical mismatch ... Noninvasive EEG-based technologies and interfaces have been used for a much broader variety of applications. Although EEG-based ...
Standing wave
Similarly a cantilever beam can have a standing wave imposed on it by applying a base excitation. In this case the free end ... Lasers use optical cavities in the form of a pair of facing mirrors, which constitute a Fabry-Pérot interferometer. The gain ... when a wave is transmitted into one end of a transmission line and is reflected from the other end by an impedance mismatch, i. ... It can be used as a liquid-based template to assemble microscale materials. Index of wave articles: Amphidromic point Clapotis ...
Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches - PubMed
Damaged or mismatched DNA bases result in the formation of physical defects in double-stranded DNA. In vivo, defects in DNA ... Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches Parth Rakesh Desai 1 2 , Sumitabha ... Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches Parth Rakesh Desai et al. Nucleic ... Finding needles in a basestack: recognition of mismatched base pairs in DNA by small molecules. Granzhan A, Kotera N, Teulade- ...
Evaluation of a 3-base pair indel polymorphism within pre-microRNA-3131 in patients with prostate cancer using mismatch...
Evaluation of a 3-base pair indel polymorphism within pre-microRNA-3131 in patients with prostate cancer using mismatch ... Evaluation of a 3-base pair indel polymorphism within pre-microRNA-3131 in patients with prostate cancer using mismatch ... A mismatch polymerase chain reaction-restriction fragment length polymorphism method was designed for genotyping the 3-bp indel ... Detection of a 4-bp Insertion/deletion Polymorphism within the Promoter of EGLN2 Using Mismatch PCR-RFLP and Its Association ...
MeSH Coming Attractions. NLM Technical Bulletin. Sep-Oct 1998
Colorectal Tumors in Adolescents and Young Adults: Practice Essentials, Background, Polypoid Disease of the Gastrointestinal...
DNA mismatch repair (MMR) is defective in this syndrome. MMR promotes genomic stability by correcting acid-base and small ... Mistakes in base pairing occasionally occur. Some stretches of DNA are more likely to accumulate errors than others, ... This mismatch must be repaired in order to avoid mutations. The DNA mismatch repair system recognizes the DNA mismatch and ... this instability leads to a failure to recognize and repair these nucleotide mismatches. Mismatch repair defects are an early ...
NIH VideoCast - Two E. Coli Mismatch Repair Enzymes, DNA Helicase II and MUTL, Interact to Catalyze Efficient Unwinding of...
Coli Mismatch Repair Enzymes, DNA Helicase II and MUTL, Interact to Catalyze Efficient Unwinding of Duplex DNA ... Base Pair Mismatch. DNA Helicases--metabolism. DNA Repair. Escherichia coli Proteins--metabolism. Escherichia coli--metabolism ... Two E. coli mismatch repair enzymes, DNA helicase II and MUTL, interact to catalyze efficient unwinding of duplex DNA / Steve ... Two E. Coli Mismatch Repair Enzymes, DNA Helicase II and MUTL, Interact to Catalyze Efficient Unwinding of Duplex DNA. ...
Colorectal Tumors in Adolescents and Young Adults: Practice Essentials, Background, Polypoid Disease of the Gastrointestinal...
DNA mismatch repair (MMR) is defective in this syndrome. MMR promotes genomic stability by correcting acid-base and small ... Mistakes in base pairing occasionally occur. Some stretches of DNA are more likely to accumulate errors than others, ... This mismatch must be repaired in order to avoid mutations. The DNA mismatch repair system recognizes the DNA mismatch and ... this instability leads to a failure to recognize and repair these nucleotide mismatches. Mismatch repair defects are an early ...
Publication Detail
MeSH Terms: Base Pair Mismatch*; Catalysis; Catalytic Domain; Crystallography/methods; DNA Damage; DNA Glycosylases/chemistry; ... Abstract: Thymine:guanine base pairs are major promutagenic mismatches occurring in DNA metabolism. If left unrepaired, these ... In humans, T:G mismatches are repaired in part by mismatch-specific DNA glycosylases such as methyl-CpG-binding domain 4 (hMBD4 ... G-mismatch-specific DNA glycosylases specifically recognize both bases of the mismatch and remove the thymine but only from ...
Mechanisms of spontaneous human cancers. | Environmental Health Perspectives | Vol. 104, No. suppl 3
... deamination of 5-methylcytosine to produce C to T base pair substitutions; and damage to DNA and its replication imposed by ... Mure K and Rossman T (2001) Reduction of spontaneous mutagenesis in mismatch repair-deficient and proficient cells by dietary ... Endogenous causes of mutation include depurination and depyrimidation of DNA; proofreading and mismatch errors during DNA ...
Publication Detail
Base Pair Mismatch/genetics*; Carrier Proteins; DNA Repair Enzymes*; DNA Repair/genetics*; DNA-Binding Proteins/deficiency*; ... The insertion is adjacent to four existing G:C basepairs, so the allele has a tract of 11Gs. The G11 PLAP allele was studied in ... The allele does not produce enzyme because the reading frame is shifted by an insertion of 7 G:C basepairs. ... Title: Visualization of mosaicism in tissues of normal and mismatch-repair-deficient mice carrying a microsatellite-containing ...
Biomarkers Search
Generating and Viewing Sequence Overlap Alignment
In this example, zooming in on the lower graphical window reveals two base pair indel in the alignment at Sequence 2 ( ... Below is the Alignment Summary view filtered in the Search box for the alignments with mismatches (mismatches,0). ... Marks within the alignment bars in the graphical views indicate mismatches, insertions and gaps. You can see these alignment ... In the image below tooltip shows alignment information including percent of coverage and identity, mismatches, gaps and ...
Environmental Factor - January 2019: Intramural papers of the month
Accommodation of mismatched base pairing by DNA polymerase mu. NIEHS researchers have revealed that DNA polymerase mu (pol mu) ... pol mu could accommodate non-complementary base pairing of nucleotide dGTP with the DNA base T (dG:dT), a well-known DNA ... The mismatch insertion was subsequently followed by DNA ligation that sealed the break. In addition, they discovered that ... Pol mu dGTP mismatch insertion opposite T coupled with ligation reveals promutagenic DNA repair intermediate. Nat Commun 9(1): ...
DeCS - New Terms
MeSH Browser
Base Pair Mismatches See Also. Base Pairing. Heteroduplex Analysis. Nucleic Acid Heteroduplexes. Public MeSH Note. 99. History ... sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).. Terms. Base Pair ... Base Pair Mismatch Preferred Concept UI. M0029876. Scope Note. The presence of an uncomplimentary base in double-stranded DNA ... mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to ...
MeSH Browser
Base Pair Mismatches See Also. Base Pairing. Heteroduplex Analysis. Nucleic Acid Heteroduplexes. Public MeSH Note. 99. History ... sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).. Terms. Base Pair ... Base Pair Mismatch Preferred Concept UI. M0029876. Scope Note. The presence of an uncomplimentary base in double-stranded DNA ... mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to ...
DeCS - Termos Novos
DeCS - New Terms
DeCS - Termos Novos
DeCS - Termos Novos
DeCS - Termos Novos
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DeCS - Termos Novos
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DeCS - Términos Nuevos
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DeCS - Termos Novos
Nucleotide6
- Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. (jove.com)
- For example, if the nucleotide is 12 base pairs long, then the number of beats per measure will be 6 (time signature = 6/4). (rutgers.edu)
- In nucleotide excision repair, a unique excision nuclease activity produces cuts on either side of the damaged nucleotide(s) and excises an oligonucleotide containing the damaged base(s). (slideshare.net)
- In this study, the researchers found that during nucleotide incorporation, pol mu could accommodate non-complementary base pairing of nucleotide dGTP with the DNA base T (dG:dT), a well-known DNA mispairing that is prone to cause mutations in cells. (nih.gov)
- Using a DNA substrate with a single nucleotide gap with template base T, they observed that pol mu could efficiently insert the mismatched nucleotide dGTP, or oxidized dGTP, a common product generated from oxidative stress, into the gap. (nih.gov)
- and in the third family, a mutation in MSH2 at exon 3: the amino acid at nucleotide 530, codon 117, causing a frameshift and a premature stop codon eight base pairs later. (nih.gov)
Replication10
- Following proofreading, errors in DNA replication like pairing adenine with cytosine can persist and maybe fixed through a mechanism called mismatch repair. (jove.com)
- One example is where a trapped hole induces a hydrogen bond shift, known as tautomerization, which then triggers a base-pair mismatch during replication. (aps.org)
- The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. (nih.gov)
- 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. (proteopedia.org)
- Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. (proteopedia.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. (proteopedia.org)
- Structures of mismatch replication errors observed in a DNA polymerase. (proteopedia.org)
- The aim of my study was to develop a system that would overcome these difficulties and allow us to regulate replication fidelity by altering the base selectivity and/or the proofreading exonuclease activity of polymerase δ. (uzh.ch)
- Martin G. Marinus mainly investigates DNA mismatch repair, Escherichia coli, DNA, DNA repair and DNA replication. (research.com)
- They also study how DNA mismatch repair acts as a spell-checker to correct errors made during replication. (nih.gov)
Nucleotides5
- One type of error is the mismatch of nucleotides, for example, the pairing of A with G or T with C. Such mismatches are detected and repaired by the Mutator protein family. (jove.com)
- NIEHS researchers have revealed that DNA polymerase mu (pol mu) promotes insertion of mismatched nucleotides during repair of DNA damage. (nih.gov)
- DNA mutations occur when mismatched nucleotides are incorporated into the damaged DNA. (nih.gov)
- result of systematically lower-order parameters for purine of Utah on the occasion of his 75th birthday, in C8 compared to pyrimidine C6 sites, even for base-paired recognition of the outstanding contributions he has made nucleotides. (nih.gov)
- Chain extension of such termini begins only after all mispaired nucleotides have been removed and a base- paired terminus is reached. (nih.gov)
Cytosine1
- 12. Cytosine deamination in mismatched base pairs. (nih.gov)
Watson-Crick3
- Considerable impact frequencies in the 700-900 MHz range, the dipolar and of the electrostatic crystal potentials were shown in this chemical shift anisotropy (CSA) relaxation mechanisms for work, suggesting that some adjustment of the CSA values the protonated 13C nuclei in nucleic acid bases become may be required in hydrated Watson-Crick base-paired comparable in size, resulting in relatively large TROSY- oligonucleotides. (nih.gov)
- Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. (rcsb.org)
- This duplex, which contains six G.A mismatches and four Watson-Crick base pairs, is thermodynamically more stable than a decamer where T.A base pairs are substituted for the G.A mismatches, and is less stable than the duplex that contains G.C base pairs. (ox.ac.uk)
Polymerase5
- Despite the proofreading ability of the DNA polymerase, a copying error occurs approximately every 1 million base pairs. (jove.com)
- 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. (proteopedia.org)
- Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. (proteopedia.org)
- By the use of specifically labeled homopolymers and block copolymers as substrates we show in this report that under polymerizing conditions a mispaired primer terminus is quan- titatively removed by the DNA polymerase whereas a correctly base-paired primer terminus is completely conserved. (nih.gov)
- This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. (rcsb.org)
Sequence7
- For each feature on the source sequence, we perform a base-by-base analysis of each feature on the source sequence in order to project the feature through the alignment to the new sequence. (nih.gov)
- For each structure, there is a "Plain Melody," which follows a simple algorithm to highlight the structure's sequence, and a "Composition," which follows a more complicated algorithm that features the base pairing of the structure. (rutgers.edu)
- In each melody, each base in the sequence is played for one beat. (rutgers.edu)
- If a base repeats itself in a sequence, the repeated note is tied (ie. (rutgers.edu)
- This lets them ligate in an additional sequence precisely 13 base pairs from the first. (arstechnica.com)
- With that, they switch to EcoP15 I , and add a fourth and final insert, closing a circle that now has four pieces of known sequence separated by two 13 and two 26 base long inserts of genomic DNA. (arstechnica.com)
- Isolation of a human anti-haemophilic factor IX cDNA clone using a unique 52-base synthetic oligonucleotide probe deduced from the amino acid sequence of bovine factor IX. (wikidata.org)
Bases6
- Damaged or mismatched DNA bases result in the formation of physical defects in double-stranded DNA. (nih.gov)
- In this process, mispaired bases are identified due to their abnormal structure by a mismatch repair protein, such as MutS. (jove.com)
- In step 1, a DNA repair endonuclease or endonuclease-containing enzyme complex recognizes, binds to, and excises the damaged base or bases in DNA. (slideshare.net)
- There are two major types of excision repair: Base excision repair systems remove abnormal or chemically modified bases from DNA. (slideshare.net)
- Each glycosylase recognizes a specific type of altered base, such as deaminated bases, oxidized bases, and so on (step 2). (slideshare.net)
- The glycosylases cleave the glycosidic bond between the abnormal base and 2- deoxyribose, creating apurinic or apyrimidinic sites (AP sites) with missing bases (step 3). (slideshare.net)
Oligonucleotide2
- Properties of multiple G.A mismatches in stable oligonucleotide duplexes. (ox.ac.uk)
- The concepts of his Molecular biology study are interwoven with issues in Base pair, SOS Response, Oligonucleotide and DNA damage. (research.com)
Guanine1
- 1H-NMR spectroscopy revealed that the N1H groups of the mismatched guanine residues are not hydrogen bonded, and 31P-NMR showed the presence of BII phosphate conformations for the GpA steps. (ox.ac.uk)
20181
- 2018. Pol mu dGTP mismatch insertion opposite T coupled with ligation reveals promutagenic DNA repair intermediate. (nih.gov)
Polymerases1
- Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. (rcsb.org)
Mutation2
- His Molecular biology study combines topics in areas such as Plasmid, Mutation, Mutant and DNA repair, DNA mismatch repair. (research.com)
- The DNA damage study combines topics in areas such as MutS DNA Mismatch-Binding Protein and Mutation. (research.com)
Genes2
- We conclude that it is important to study HNPCC mismatch repair genes because of emerging evidence for genotypic and phenotypic heterogeneity, which will harbor the potential to eventually translate this knowledge into specific screening and management protocols. (nih.gov)
- DNA mismatch repair genes and colorectal cancer. (ox.ac.uk)
Pyrimidine1
- Pyrimidine.pyrimidine base-pair mismatches in DNA. (bvsalud.org)
Conformation2
- Project 1 focuses on B-DNA base pairing, while Project 2 uses a more detailed scheme to represent DNA conformation, mismatches, modifications, and more. (rutgers.edu)
- Circular-dichroism spectroscopy indicates an overall B-like conformation for the decamer, but stronger than usual base stacking. (ox.ac.uk)
Escherichia1
- His scientific interests lie mostly in DNA, DNA mismatch repair, Molecular biology, Escherichia coli and DNA repair. (research.com)
MUTL1
- Other mismatch repair proteins like MutL then identify the new strand so that the strand with the error is repaired while the template strand remains unchanged. (jove.com)
Repair8
- E. coli mismatch repair proteins detect the sequences that haven't been methylated yet, identifying the new strand. (jove.com)
- Eukaryotic mismatch repair proteins identify the nicked strand and target it for repair. (jove.com)
- Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes. (jove.com)
- Mutator S (MutS) initiates the mismatch repair (MMR) by identifying and binding to the mismatch. (jove.com)
- Postreplicative mismatch repair (MMR) then mediates the removal of mispairs that escaped proofreading. (uzh.ch)
- In addition, they discovered that unlike pol mu, other X-family repair enzymes pol beta and pol lambda were unable to accommodate the dG:dT mismatch, which suggested a unique feature of pol mu in NHEJ repair. (nih.gov)
- In his research on the topic of DNA mismatch repair, In vitro recombination is strongly related with Base pair. (research.com)
- His research in DNA mismatch repair is mostly concerned with MutS-1. (research.com)
Subsequently1
- The mismatch insertion was subsequently followed by DNA ligation that sealed the break. (nih.gov)
Sequences1
- The sequences used here all had an even number of base pairs. (rutgers.edu)
Detect1
- We learned that this chemistry was exquisitely sensitive to stacking within the helix, and we developed electrochemistry to detect single base mismatches in DNA and to monitor protein/DNA interactions. (nasonline.org)
Neutral2
- A nuclear magnetic resonance study of T.T pairing at neutral pH and C.C pairing at acidic pH in dodecanucleotide duplexes. (bvsalud.org)
- We love the neutral base with mismatched stripes of color. (aydinandella.com)
Genomes1
- Problematic base pair mismatches were identified between the assembled FCV genomes and RT-PCR primers. (avma.org)
Amino1
- The G.A mismatches pair in the amino form as originally proposed by Li et al. (ox.ac.uk)
Strand3
- When using VCF as input, left-shifted or multi-base alleles on the minus strand are not reverse-complemented in the output. (nih.gov)
- Each base of the asymmetric strand is given one note. (rutgers.edu)
- This strand is read 3' to 5' (essentially, it base pairs with the melody). (rutgers.edu)
Study1
- Here, we use coarse-grained molecular dynamics (MD) simulation and supporting statistical-mechanical theory to study the effect of mismatched base pairs on DNA supercoiling. (nih.gov)
Formation2
- Pre-steady-state kinetics, examination of the elemental effect using dNTPαS, and pulse-chase experiments indicate that a rapid phosphodiester bond formation step is flanked by slow conformational changes for both correct and incorrect base pair formation. (nih.gov)
- rapid phosphodiester bond formation occurs with a Keq of 2.2 and 1.7, and the second conformational change occurs with rate constants of 2.1 and 0.5 s(-1), for correct and incorrect base pair formation, respectively. (nih.gov)
Data1
- Read merging is only for paired-end data sets and is optional . (nih.gov)
Extensive1
- USA 88, 26-30], which results in extensive base-base stacking between the tandem G.A base pairs and their nearest neighbours. (ox.ac.uk)
Note1
- Using notes from the a minor scale, the base pairing note in the bass line is followed by specifically assigned notes to create counterpoint while the melody is being held. (rutgers.edu)
Correct1
- Kunkel's team studies how and how well the pairing choice is made, what happens when the wrong choice is made, and how to correct it (comparable to the backspace key). (nih.gov)
Long3
- The authors start by taking a complete genome, and using ultrasound to fragment the DNA into linear pieces that, on average, are about 450 base pairs long. (arstechnica.com)
- As long as a base has a value below this threshold the base is removed and the next base will be investigated. (nih.gov)
- As long as a base has a value below this threshold the base is removed and the next base (which as Trimmomatic is starting from the 3' end would be base preceding the just removed base) will be investigated. (nih.gov)
