Base pair mismatches. Medical search. Frequent questions

We demonstrate that relatively short single-stranded oligodeoxynucleotides, 25-61 bases homologous to the target sequence except for a single mismatch to the targeted base, are capable of correcting a single point mutation (G to A) in the mutant beta-galactosidase gene, in nuclear extracts, episome, and chromosome of mammalian cells, with correction rates of approximately 0.05%, 1% and 0.1%, respectively. (nih.gov)
The requirement for a total of 6-12 fingers, each of which binds three base pairs, provides enough specificity to address a unique sequence in a genome as complex as the three billion base pairs of human DNA. (ddw-online.com)
We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. (cdc.gov)

Intestinal-type poorly differentiated gastric adenocarcinoma with microsatellite instability and defective DNA mismatch repair proteins expression. (embl-heidelberg.de)
This study investigated the concordance in microsatellite instability (MSI) and mismatch repair (MMR) status between primary and corresponding metastatic colorectal cancer (CRC). (jnccn.org)

Adenine-guanine base pairing ribosomal RNA. (wikidata.org)
Adenine is converted to adenosine or inosine monophosphate (IMP), either of which, in turn, is converted into inosine (I), which pairs with Adenine (A), cytosine (C), and uracil (U). (wikidoc.org)
When designing primers for polymerase chain reaction , inosine is useful in that it can pair with adenine, thymine, or cytosine. (wikidoc.org)
The DNA glycosylase MutY repairs the DNA damage by removing adenine from mismatched adenine:8-oxoganine base pair. (rutgers.edu)

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. (rcsb.org)
Polymerase discovery and engineering efforts have produced high fidelity polymerases, which rarely make base substitution mistakes, requiring DNA sequencing methods to read millions of synthesized bases to detect any errors by the polymerase Advancements in measuring fidelity by single-molecule sequencing has identified Q5 ® High-Fidelity DNA Polymerase as having fidelity 280X greater than Taq DNA polymerase (12). (neb.com)
Using the base-pairing and active site molecular checkpoints described above, Taq DNA polymerase is incredibly accurate, but proofreading enzymes can have even higher fidelity. (neb.com)
Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. (embl-heidelberg.de)

The gene products are, therefore, called the "Mut" proteins, and are the major active components of the mismatch repair system. (wikipedia.org)
Three of these proteins are essential in detecting the mismatch and directing repair machinery to it: MutS, MutH and MutL (MutS is a homologue of HexA and MutL of HexB). (wikipedia.org)
DNA recognition in these proteins is provided by modules, each of which binds a single base pair, and there is a robust code to address each of the four base pairs (2,3). (ddw-online.com)

In animals, the degree of base pairing between a miRNA and its target messenger RNA seems to determine whether the regulation occurs through cleavage or translation inhibition 1 . (nature.com)
Other mismatches allow for RNA extension but are inefficiently formed and efficiently proofread by RNA cleavage. (cipsm.de)
We wanted to determine the effect of crRNA mismatches on target cleavage in vitro. (billfryer.com)
Mismatched crRNAs may also provide low-level immunity through continued target cleavage. (billfryer.com)

MutS forms a dimer (MutS2) that recognises the mismatched base on the daughter strand and binds the mutated DNA. (wikipedia.org)
The crystal structure of MutS reveals that it is exceptionally asymmetric, and, while its active conformation is a dimer, only one of the two halves interacts with the mismatch site. (wikipedia.org)
The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. (embl-heidelberg.de)

The continuous effort to improve the overall mixture was mainly aimed to enhance reactions, diminish unnecessary primer dimers, reduce nonspecific binds due to mismatches, and block efficiency drops occurred by high G/C rates [6, 7]. (researchsquare.com)

DNA mismatch repair (MMR) is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage. (wikipedia.org)
Mismatches are commonly due to tautomerization of bases during DNA replication. (wikipedia.org)
Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. (rcsb.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. (rcsb.org)
Löwdin proposed that the base pair double proton transfer (DPT) tautomers, A*T* and G*C*, may cause mutations during the replication process via mismatches, e.g. the pairing of A* with C, and G* with T. This thesis uses multiscale modelling techniques to study base pair tautomerism in a realistic DNA system. (ucl.ac.uk)

X-ray analysis reveals that a T⋅U mismatch impairs RNA extension by forming a wobble base pair at the Pol II active center that dissociates the catalytic metal ion and misaligns the RNA 3′ end. (cipsm.de)
Inosine is commonly found in tRNAs and is essential for proper translation of the genetic code in wobble base pairs . (wikidoc.org)

The damage is repaired by recognition of the deformity caused by the mismatch, determining the template and non-template strand, and excising the wrongly incorporated base and replacing it with the correct nucleotide. (wikipedia.org)
The removal process involves more than just the mismatched nucleotide itself. (wikipedia.org)
The mismatch can also stabilize a paused state of Pol II with a frayed RNA 3′ nucleotide. (cipsm.de)

Such unexpected editing was not previously reported in vitro, presumably because the common use of artificially tight mRNA:gRNA base pairing precludes alternate alignments. (tamu.edu)
Detect if there is a mismatch between two VERIFIED alignments. (lu.se)

Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. (rcsb.org)
In contrast, the selection of regulatory mechanisms is independent of the degree of mismatch between a plant miRNA and its target transcript 5 . (nature.com)

The first evidence for mismatch repair was obtained from S. pneumoniae (the hexA and hexB genes). (wikipedia.org)
They identified, for example, 23 genes responsible for excising erroneous bases, 36 genes needed for mending double-strand breaks, and 16 genes involved in mismatch repair, or the re-aligning of complementary base pairs. (damonrunyon.org)
DNA mismatch repair genes and colorectal cancer. (ox.ac.uk)

Mismatch repair is strand-specific. (wikipedia.org)
In order to begin repair, the mismatch repair machinery distinguishes the newly synthesised strand from the template (parental). (wikipedia.org)
Examples of mismatched bases include a G/T or A/C pairing (see DNA repair). (wikipedia.org)
Mismatch repair is a highly conserved process from prokaryotes to eukaryotes. (wikipedia.org)
Repair of defined single base-pair mismatches in Escherichia coli. (wikidata.org)

While most of the issues were solved, primer template mismatches constantly tamper the overall specificity, resulting in unwanted false-positives. (researchsquare.com)

It is suspected that, in eukaryotes, newly synthesized lagging-strand DNA transiently contains nicks (before being sealed by DNA ligase) and provides a signal that directs mismatch proofreading systems to the appropriate strand. (wikipedia.org)
Loaded PCNA then directs the action of the MutLalpha endonuclease to the daughter strand in the presence of a mismatch and MutSalpha or MutSbeta. (wikipedia.org)
A few or up to thousands of base pairs of the newly synthesized DNA strand can be removed. (wikipedia.org)
The entire MutSHL complex then slides along the DNA in the direction of the mismatch, liberating the strand to be excised as it goes. (wikipedia.org)
Here, single-molecule high-resolution optical trapping measurements reveal that Mtr4p unwinds RNA duplexes by 3′-to-5′ translocation on the loading strand, that strand separation occurs in discrete steps of 6 base pairs and that a single Mtr4p molecule performs consecutive unwinding steps. (nature.com)
The general concept for copying DNA was evident upon the elucidation of DNA's double helical structure and the identification of base pair complementarity (1): one strand of nucleobases could serve as the template for synthesis of a new strand. (neb.com)
After each round of dNTP addition to the growing strand, the chip is imaged, and the emission wavelength from each DNA cluster is used to identify the base. (jove.com)
Paired-end, strand specific sequencing for total RNA was performed on Illumina HiSeq 2500 with 100 bp read lengths. (nih.gov)

We show that RNA polymerase (Pol) II prevents erroneous transcription in vitro with different strategies that depend on the type of DNA⋅RNA base mismatch. (cipsm.de)

RenLab-H3K4me1-spleen-DM378.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches. (nih.gov)

This alignment for catalysis is sensitive to distortions in position caused by incorrect Watson-Crick base pairing, allowing for kinetic stalling at incorrect or non-cognate base pairs. (neb.com)

If a mismatch is detected the DNA is transferred from the polymerization domain to an N-terminal 3´→5´ exonuclease domain of the polymerase. (neb.com)

An ensemble of reaction coordinates and the rate coefficients of tautomerism for each base pair in aqueous DNA is calculated using quantum mechanics/molecular mechanics (QM/MM) methods. (ucl.ac.uk)
Unlike non- ionizing radiation (such as microwaves and ultraviolet radiation), which has insufficient energy to eject molecular electrons, ionizing radiation deposits sufficient energy to remove electrons from atomic orbits and create molecular ion pairs along particle tracks. (cdc.gov)

If, however, the nick is on the 3' end of the mismatch, ExoI (a 3' to 5' enzyme) is used. (wikipedia.org)

The application of larger electric fields (10⁹ V/m) parallel to base pair hydrogen bonds is found to increase the lifetime of the tautomers by one order of magnitude at most. (ucl.ac.uk)

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. (rcsb.org)

fastq: Illumina's Genome Analyzer Pipeline bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. (nih.gov)

The stability of a model substrate for topoisomerase 1-mediated DNA religation depends on the presence of mismatched base pairs. (wakehealth.edu)
Gmeiner WH, Salsbury F, Olsen CM, Marky LA. The stability of a model substrate for topoisomerase 1-mediated DNA religation depends on the presence of mismatched base pairs. (wakehealth.edu)

The ensemble-based methodology utilised in this study has shown that several different proton transfer reaction pathways, each with varying probabilities, occur within the same base pair. (ucl.ac.uk)

In reversible terminator sequencing - pure genomic DNA is first cut into smaller fragments of 100-1000 base pairs. (jove.com)

The aims of this thesis are to i) reassess the viability of base pair tautomerism as a contributory mechanism towards spontaneous single point mutations in DNA and ii) predict how external electric fields (ranging from strengths of 10⁴ V/m to 10⁹ V/m) influence the thermodynamic stability of the tautomers and the kinetics of the DPT reaction. (ucl.ac.uk)
The results show that DPT between base pairs has a negligible contribution towards spontaneous mutations in DNA. (ucl.ac.uk)
In the context of mutations in human beings, the effect of external electric fields on base pair tautomerism is deemed insignificant. (ucl.ac.uk)

When bound, the MutS2 dimer bends the DNA helix and shields approximately 20 base pairs. (wikipedia.org)
High-resolution structure of a DNA helix containing mismatched base pairs. (wikidata.org)

Each row tells whether the affyprobe is a perfect match or mismatch, what number it has in the list of probes for this probeset (so that pm/mm pairs can be identified), and what feature defines its position. (lu.se)

The DNA is looped out to search for the nearest d(GATC) methylation site to the mismatch, which could be up to 1 kb away. (wikipedia.org)
33. Richardson, K. E. and Znosko, B. M. (2016) "Nearest-neighbor parameters for 7-deaza-adenosine·uridine base pairs in RNA duplexes," RNA 22 , 934-942. (slu.edu)
26. Hudson, G. A., Bloomingdale, R. J., and Znosko, B. M. (2013) Thermodynamic contribution and nearest neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides , RNA 19 , 1474-1482. (slu.edu)

The entire process ends past the mismatch site - i.e., both the site itself and its surrounding nucleotides are fully excised. (wikipedia.org)

It is exactly solvable for homogeneous DNA (with only one type of basepairs), and predicts a first-order phase transition. (mpg.de)

Messages that lead to a "Verified mismatch" are not trusted, which is indicated with line-through styled text. (lu.se)

As a threshold of statistical significance, we look for daily mismatches of at least two standard deviations of the price variation over the past 21 trading days. (cxoadvisory.com)

To do this, the team created two groups of complementary nanoparticles: one batch containing complementary base pairs, called "seed" PAEs, and the other containing mismatched base pairs to make "growth" PAEs. (phys.org)

For this pair of ETFs, only the XLB side of the trade is profitable on average, but 2007-2008 trades drive the unprofitability of the XLI side. (cxoadvisory.com)

Arthur Genthon of the Max Planck Institute for the Physics of Complex Systems, Albertas Dvirnas and Tobias Ambjörnsson (Lund University, Sweden) have now derived an exact equilibrium solution of an extended Poland-Scheraga model that describes DNA with a defect site that could, for instance, result from DNA basepair mismatching, cross-linking, or the chemical modifications from attaching fluorescent labels, such as fluorescent-quencher pairs, to DNA. (mpg.de)

A standalone pairs trading strategy appears to require a large inventory of pairs at all times in order to keep capital largely engaged in trades. (cxoadvisory.com)

Although not quite the lowest, we select XLB and XLI for pair trading because it seems logical that materials demand (XLB) would mirror industrial activity (XLI). (cxoadvisory.com)

Orange detailing appears on the tongue tags and heel tabs paired with a white sole unit. (newjordansretro.com)

dbOligo") to increase the discrimination between matched and mismatched PCR. (researchsquare.com)

Anatomy1

Organisms1

Chemicals and Drugs17

Analytical, Diagnostic and Therapeutic Techniques and Equipment6

Phenomena and Processes20

Information Science3

Sequence3

Microsatellite instability2

Adenine4

Fidelity4

Proteins3

Cleavage4

MutS3

Binds1

Replication5

Wobble2

Nucleotide3

Alignments2

Mechanisms2

Genes3

Repair5

Specificity1

Strand8

Transcription1

Bases1

Distortions1

Exonuclease1

Molecular2

Enzyme1

Hydrogen1

Primer1

Genome1

Presence2

Proton1

Fragments1

Mutations3

Helix2

Position1

Nearest3

Process1

Type1

Lead1

Past1

Make1

Side1

Chemical1

Order1

Activity1

Appears1

Increase1