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Base Pair Mismatch (0):
Recent article
Base Pair Mismatch
Abstract
O(6)-methylguanine (O(6)-MeG) is a miscoding DNA lesion arising from the alkylation of guanine. This report uses the bacteriophage T4 DNA polymerase as a model to probe the roles of hydrogen-bonding interactions, shape/size, and nucleobase desolvation during the replication of this miscoding lesion....
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PMID: 21819995
PDF is available here.
PDF is available here.
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Abstract
We report on the use of 3,4,9,10-perylenetetracarboxylic diimide microfibers (PDIMs) as an effective fluorescent sensing platform for DNA detection for the first time. This sensing system exhibits a detection limit as low as 15 nmol L(-1) and has a high selectivity down to single-base mismatch. The...
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PMID: 21819867
PDF is available here.
PDF is available here.
Abstract
We disclose a strategy that harnesses an intramolecular β-CD/adamantane host-guest interaction to generate a stabilized DNA hairpin (ΔT(m) = 17 °C) that undergoes an input oligonucleotide (ODN)-selective structural transformation from a stem-loop conformation to a duplex. This ODN-induced conform...
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PMID: 21534531
PDF is available here.
PDF is available here.
Abstract
The review concerns the use of the affinity modification method as an integral part of the modern proteomic analysis to search for and identification of proteins belonging to protein ensembles of DNA repair. Affinity modification is based on the preliminary formation of specific non-covalent complex...
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PMID: 21460885
PDF is available here.
PDF is available here.
Voprosy Virusologii (56)1 2011
Abstract
A real-time fluorescent polymerase chain reaction was used to develop a RealBest HIV RNA kit that was clinically suitable for the detection of HIV-1 RNA and for the estimation of virus load in plasma and serum samples. Due to the selection of a highly conserved target region and to the experimental s...
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PMID: 21427951
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (135)11 2010
Abstract
A simple and sensitive approach for the recognition of single base mismatches in duplex DNA was developed. The single base mismatched double-strand (ds) DNA and the completely complementary dsDNA can quench the fluorescence of methylene blue to the different values, so the point mutation dsDNA can b...
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PMID: 20830326
PDF is available here.
PDF is available here.
Abstract
We find that an L-system generated sequence can be inserted into the OR1D2 subfamily-specific star model and novel full-length olfactory receptors can be generated. This remarkable mathematical principle could be utilized for making new subfamily olfactory receptor members from any olfactory recepto...
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PMID: 20826948
PDF is available here.
PDF is available here.
Abstract
Nanotechnology (21)24 2010
Abstract
We report here on our investigations, via the I-V characteristics, of the effect of a mispair on the electrical properties of homogeneous and generic DNA molecules. The I-V characteristics of DNA were studied numerically within the double-stranded tight-binding model. The parameters of the tight-bin...
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PMID: 20484790
PDF is available here.
PDF is available here.
Abstract
A chronocoulometric DNA sensor was constructed based on doped screen-printed electrode (SPE). Polyaniline nanotubes (PANINTs) and ionic liquid (IL) [C12mim][PF6] were doped into the commercial graphite ink (Electrodag 423SS) for the printing of the SPE, and chitosan was covered on the electrode surf...
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PMID: 20219343
PDF is available here.
PDF is available here.
Abstract
We used this assay for genotyping mutations in the Duchenne muscular dystrophy (DMD) gene, the largest known in the human genome. Our results show that conjugating the gold nanoparticles with short DNA probes of 18 bases and 70 bases complimentary to target sequences allows specific discrimination b...
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PMID: 20219341
PDF is available here.
PDF is available here.
Chemical Communications (46)18 2010
Abstract
A highly sensitive and selective electrochemiluminescent biosensor was designed for mercury(ii) based on T-Hg(2+)-T complex by using Ru(bpy)(3)(2+)-doped silica nanoparticles (Ru-SNPs) to label the oligonucleotides in order to improve the sensitivity.
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PMID: 20424756
PDF is available here.
PDF is available here.
Interaction between human mismatch repair recognition proteins and checkpoint sensor Rad9-Rad1-Hus1.
Abstract
We show that each subunit of the human 9-1-1 complex physically interacts with hMSH2, hMSH3, and hMSH6. The 9-1-1 complex from both humans and Schizosaccharomyces pombe can stimulate hMutS alpha binding with G/T-containing DNA. Rad9, Rad1, and Hus1 individual subunits can also stimulate the DNA bind...
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PMID: 20188637
PDF is available here.
PDF is available here.
Abstract
A new label-free, optical method was developed to detect sequence-specific DNA based on supramolecular self-assembly. A cationic phenylene ethynylene oligomer with two pairs of positively charged side chains (OPE-2) can form a J-dimer or J-aggregate with negatively charged DNA by a combination of el...
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PMID: 20030336
PDF is available here.
PDF is available here.
Abstract
We show that the theoretical limit on genomic information content may increase substantially as a consequence of dramatically slowed polymerization after mismatches. As a result of postmismatch stalling, accurate copies of a template tend to be completed more rapidly than mutant copies and the accur...
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PMID: 20359213
PDF is available here.
PDF is available here.
Abstract
We prepared and studied 5-chloro-2'-deoxyuridine (CldU) and ClU-containing oligonucleotide templates. We demonstrate that human K-562 cells grown in culture with 10 muM CldU incorporate substantial amounts of CldU without significant toxicity. When in the template, ClU residues pair with dATP but al...
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PMID: 20104909
PDF is available here.
PDF is available here.
Abstract
We hypothesized that ACVR2 frameshifts were influenced by DNA sequences surrounding the microsatellite. We constructed plasmids in which exons 3 or 10 of ACVR2 were cloned +1 bp out of frame of enhanced green fluorescent protein (EGFP), allowing -1 bp frameshift to express EGFP. Plasmids were stably...
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PMID: 20140012
PDF is available here.
PDF is available here.
Chemical Communications (46)15 2010
Abstract
We succeeded for the first time in achieving single-molecule imaging of DNA duplexes vertically oriented on surfaces, with an in situ scanning tunneling microscope (STM), and demonstrated that this observation clearly revealed the surface hybridization behavior for both perfectly matched and mismatc...
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PMID: 20449314
PDF is available here.
PDF is available here.
Abstract
We have developed a novel DNA-based nanomechanical device that measures the amount of work that a DNA-bending protein can do when it binds to the double helix. The device we report here is a scissors-like device consisting of two double-crossover (DX) molecules connected to each other by a flexible...
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PMID: 20205420
PDF is available here.
PDF is available here.
Abstract
Abstract
Although tetraloops are one of the most frequently occurring secondary structure motifs in RNA, less than one-third of the 30 most frequently occurring RNA tetraloops have been thermodynamically characterized. Therefore, 24 stem-loop sequences containing common tetraloops were optically melted, and...
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PMID: 20047989
PDF is available here.
PDF is available here.
Abstract
We report application of stopped-flow kinetics to probe the mechanism of action of Msh2-Msh6, a eukaryotic DNA repair protein that recognizes base-pair mismatches and insertion/deletion loops in DNA and signals mismatch repair (MMR)(3-5). In doing so, Msh2-Msh6 increases the accuracy of DNA replicat...
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PMID: 20357752
PDF is available here.
PDF is available here.
Abstract
We now describe a method that allows mutagenesis on any DNA template (e.g. cDNA, genomic DNA, and plasmid DNA), and is highly efficient for multiple-site mutagenesis (up to 100%). The technology takes advantage of the requirement that, in order for DNA polymerases to elongate, it is crucial that the...
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PMID: 20676982
PDF is available here.
PDF is available here.
Abstract
We present the routine diagnostic application of EMMA (Enhanced Mismatch Mutation Analysis, Fluigent), a new, fast, reliable, and cost-effective method for mutation screening. This method is based on heteroduplex analysis by capillary electrophoresis and relies on the use of innovative matrices incr...
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PMID: 20721742
PDF is available here.
PDF is available here.
Abstract
The analysis resulted in identification of a 1975C>T mutation in exon 17, resulting in substitution of arginine residue with stop codon at codon 659. 655A>G substitution was also observed, resulting in replacement of isoleucine with valine at codon 219. Similar analysis on 250 ethnically matched con...
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PMID: 20167975
PDF is available here.
PDF is available here.
Abstract
We have found that shRNAs with 19-bp or shorter stems (sshRNAs) possess some unique structure-activity features that depend on whether the antisense strand is positioned 5' or 3' to the loop (L- or R-type sshRNAs, respectively). L sshRNAs can have IC(50)s in the very low picomolar range, and sshRNAs...
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PMID: 19952116
PDF is available here.
PDF is available here.
Abstract
We obtain a mesoscopic model of the DNA duplex close to that observed in experiments and all-atom molecular dynamics simulations. The mesoscopic model is calibrated to data from the all-atom molecular dynamics package AMBER for a variety of twist angles of the DNA duplex. Defects are considered in t...
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PMID: 20365189
PDF is available here.
PDF is available here.
Analytical Biochemistry (398)2 2009
Abstract
We employed chemically-modified nucleobases, such as oxanine and hypoxanthine, at the end of a ligation fragment, and analyzed their influence on the ligation efficiency between G:C and G:T. Successful ligation for G:C and no ligation for G:T were observed, when oxanine was employed adjacent to guan...
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PMID: 19917262
PDF is available here.
PDF is available here.
Abstract
To determine the prevalence of Lynch syndrome mutations in a Canadian hereditary cancer clinic population, and to determine the effectiveness of the program's referral criteria and testing algorithm.
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PMID: 19893772
PDF is available here.
PDF is available here.
Abstract
We investigate the interplay between charge transport through the ordered backbone and disordered base stacks with random sequences. By analytical and numerical calculations, we find that the coupling between the backbone and base-pair channels plays an important role in charge transport. The backbo...
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PMID: 20365000
PDF is available here.
PDF is available here.
FEBS Journal (276)22 2009
Abstract
We studied the relationship between the silencing efficiency of the siRNAs and their binding to the RNA-induced silencing complex loading complex proteins HIV transactivating response RNA-binding protein and Dicer in H1299 cytoplasmic extracts. Binding of siRNA and the transactivating response RNA-b...
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PMID: 19811537
PDF is available here.
PDF is available here.
Analytical Biochemistry (398)1 2009
Abstract
We describe a novel method for SNP genotyping, based on differential fluorescence emission due to cleavage by Thermus thermophilus RNase HII (TthRNase HII) of DNA heteroduplexes containing a SNP-site-specific chimeric DNA-rN(1)-DNA molecular beacon (cMB). We constructed a loop sequence for a cMB tha...
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PMID: 19891952
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)40 2009
Abstract
We measured Cd(2+) binding to Msh2-Msh6, directly and by monitoring changes in protein structure and enzymatic activity. Global fitting of the data to a multiligand binding model revealed that binding of about 100 Cd(2+) ions per Msh2-Msh6 results in its inactivation. This finding indicates that the...
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PMID: 19320425
PDF is available here.
PDF is available here.
Abstract
One nucleotide difference was shown at position 594 in exon 3 from C to T between human leukocyte antigen (HLA)-B*550203 and HLA-B*550201, which does not alter amino acids in the mature protein.
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PMID: 19497036
PDF is available here.
PDF is available here.
Abstract
DRB1*1532 allele was identified in a Mexican unrelated marrow donor from the Gulf of Mexico.
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PMID: 19523021
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)33 2009
Abstract
We suggest that the junction itself is not responsible for this unusual conformation but served as a vehicle for the study of this CG-rich sequence as a B-DNA duplex, mimicking the form that would be present in a replication complex. The existence of this unusual base lends credence to and defines a...
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PMID: 19580331
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)31 2009
Abstract
We have constructed oligonucleotides containing 5-chlorouracil (ClU), one of the known inflammation damage products. The thermodynamic stability, base pairing configuration, and duplex conformation of oligonucleotides containing ClU paired opposite adenine have been examined. NMR spectra reveal that...
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PMID: 19618901
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (134)7 2009
Abstract
We studied the EIS of ds-DNA films containing a single A-C mismatch in the presence and absence of Ca2+, Zn2+, Cd2+ and Hg2+. DeltaR(ct) values for ds-DNA films with a single A-C mismatch is smaller than those of fully matched ds-DNA films....
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PMID: 19562195
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
The cyclobutane pyrimidine dimer (CPD) is one of the major classes of cytotoxic and carcinogenic DNA photoproducts induced by UV light. Hydrogen exchange rates of the imino protons were measured for various CPD-containing DNA duplexes to better understand the mechanism for CPD recogn...
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PMID: 19450588
PDF is available here.
PDF is available here.
Methods in Molecular Biology (554)554 2009
Abstract
We describe a strategy for the rapid identification of heteroplasmic mtDNA mutations that can be used routinely in molecular genetic laboratories. This protocol involves the following three steps: (i) PCR amplification of the entire human mitochondrial genome with 17 overlapping PCR products, (ii) l...
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PMID: 19513682
PDF is available here.
PDF is available here.
Abstract
The effects of local structural disorder on excess electron transfer (EET) in DNA were investigated by evaluating photoinduced electron transfer in phenothiazine (PTZ)-modified oligodeoxynucleotides bearing single-base mismatches. Unexpectedly, more efficient electron transfer was observed for the m...
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PMID: 19421445
PDF is available here.
PDF is available here.
Abstract
We need high-throughput, high-accuracy resequencing technologies. Although array-based genotyping has allowed genomewide association studies of common SNPs in tens of thousands of samples, array-based resequencing has been limited for 2 main reasons: the lack of a fully multiplexed pipeline for high...
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PMID: 19342489
PDF is available here.
PDF is available here.
Abstract
We first studied the role of mismatch repair proteins, MSH2, MSH3, MSH6, PMS2 and MLH1, since they would recognize mismatches. The MSH2-MSH6 heterodimer is involved in hypermutation by binding to U:G and other mismatches generated during repair synthesis, but the other proteins are not necessary. Se...
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PMID: 19008198
PDF is available here.
PDF is available here.
Abstract
Probing ds-DNA films in the presence of Zn(2+) ions by scanning electrochemical microscopy (SECM) allows the unequivocal detection of a single-nucleotide mismatch and provides information about its position within the duplex.
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PMID: 19240869
PDF is available here.
PDF is available here.
Abstract
Using classic DNA-intercalating dye and carbon nanotubes, a simple, but efficient, method for fluorescent detection of DNA hybridization has been developed.
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PMID: 19322415
PDF is available here.
PDF is available here.
Abstract
We discuss the binding properties with abasic sites and single base bulges of Rh(bpy)(2)(chrysi)(3+), a complex previously shown to bind thermodynamically destabilized mismatch sites via metalloinsertion. Photocleavage experiments show that Rh(bpy)(2)(chrysi)(3+) selectively binds abasic sites with...
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PMID: 19146409
PDF is available here.
PDF is available here.
Audio, Transactions of the IRE Professional Group on (11 Suppl 1) 2009
Abstract
The T1DGC MHC Fine Mapping project resulted in a 2300 family, 9992 genotyped individuals database comprising of two 1536 SNP panels and a 66 microsatellite panel to densely cover the 4 Mb MHC core region for use in statistical genetic analyses....
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PMID: 19143809
PDF is available here.
PDF is available here.
Abstract
We chose the surface of a positively charged liposome as a scaffold, which we recently demonstrated to be able to catalyze the exchange of fully complementary DNA oligonucleotides. We here study how single base pair mismatches affect the rate of strand exchange on the liposome surface. Interestingly...
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PMID: 19123801
PDF is available here.
PDF is available here.
Abstract
The (6S,8R,11S) 1,N2-HNE-dGuo adduct of trans-4-hydroxynonenal (HNE) was incorporated into the duplex 5′-d(GCTAGCXAGTCC)-3′·5′-d(GGACTAGCTAGC)-3′ [X = (6S,8R,11S) HNE-dG], in which the lesion was mismatched opposite dAdo. The (6S,8R,11S) adduct maintained the ring-closed 1,N2-HNE-dG structur...
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PMID: 19053179
PDF is available here.
PDF is available here.
Abstract
We found that insertion of dCTP was the least favored insertion product opposite the M1dG lesion (800-fold less efficient than opposite dG). Extension from M1dG·dC was equally as efficient as from control primer-templates (dG·dC). dATP insertion opposite M1dG was the most favored insertion product...
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PMID: 19108641
PDF is available here.
PDF is available here.
Abstract
Abstract
An analysis of the stability of a duplex containing G x A mispairs or G x A/A x G tandem during the DNA melting has shown that the duplex stability depends on both DNA sequences and the conformations of the G x A mispairs. The thermodynamics of single pair opening for the G(anti) x A(syn) and G(anti...
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PMID: 19140634
PDF is available here.
PDF is available here.
Abstract
We have already found that Hg(II) cation specifically binds to T:T mismatch base pair in heteroduplex DNA, which increases the melting temperature of heteroduplex DNA involving T:T mismatch base pair by about 4 degrees C. We have also found that Ag(I) cation specifically binds to C:C mismatch base p...
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PMID: 19749241
PDF is available here.
PDF is available here.
Abstract
We defined the mutations in mtDNA of X-irradiated mice brair using mismatch-specific endonuclease (CEL I-nuclease method) and by temporal temperature gradient gel electrophoresis (TTGE-technique). The comparison of the received by both methods, allows to conclude, that CEL I-nuclease method gives mo...
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PMID: 19368317
PDF is available here.
PDF is available here.
Journal of Gastroenterology (44 Suppl 19) 2009
Abstract
Characterization of this cPLA2-alpha deficiency provides support for the importance of prostaglandins in protecting small intestinal integrity and indicates that loss of prostaglandin biosynthesis is sufficient to produce small intestinal ulcers....
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PMID: 19148786
PDF is available here.
PDF is available here.
Abstract
ChemBioChem (10)1 2009
Abstract
The activity of the anticancer drug cisplatin is a consequence of its ability to bind DNA. Platinum adducts bend and unwind the DNA duplex, creating recognition sites for nuclear proteins. Following DNA damage recognition, the lesions will either be repaired, facilitating cell viability, or if repai...
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PMID: 19053130
PDF is available here.
PDF is available here.
BMC Bioinformatics (10)1 2009
Abstract
About 250 different GeneChip hybridizations performed at the VIB Microarray Facility for Homo sapiens, Drosophila melanogaster, and Arabidopsis thaliana were analyzed. The investigation of such a large set of data from the same source minimizes systematic experimental variations that may arise from...
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PMID: 19123958
PDF is available here.
PDF is available here.
Genetics in Medicine (11)1 2009
Abstract
We found insufficient evidence to recommend a specific genetic testing strategy among the several examined. RATIONALE: Genetic testing to detect Lynch syndrome in individuals with newly diagnosed colorectal cancer (CRC) is proposed as a strategy to reduce CRC morbidity and mortality in their relativ...
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PMID: 19125126
PDF is available here.
PDF is available here.
Biophysical Chemistry (139)1 2009
Abstract
We show that tC(O) is an excellent probe for the detection of individual melting processes of complex nucleic acid structures containing a large number of separate secondary structure motifs. Since conventional UV-melting investigations merely monitor the global melting process of the whole nucleic...
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PMID: 18963381
PDF is available here.
PDF is available here.