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Welcome to the Pubget Medical Subject Headings (MESH) browser. Click on a topic or subtopic below to explore related papers. In the gold box is the most recent paper about the current MESH term, and below are 20 related papers.
Nucleic Acid Heteroduplexes (0):
Recent article
Nucleic Acid Heteroduplexes
Abstract
We describe the potential of estimating melting temperature (T(m)) for nonstandard oligonucleotides by using the correlation of the experimental T(m) with the calculated duplex binding energy (BE) for oligonucleotides of a given length. This method has been automated into a standardized molecular dy...
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PMID: 21702481
PDF is available here.
PDF is available here.
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Methods in Molecular Biology (629)629 2010
Abstract
We present a detailed procedure that allows the detection and quantification of RNA base modifications. This procedure involves a number of techniques, including oligonucleotide-affinity selection, site-specific cleavage and radiolabeling, nuclease digestion, and thin layer chromatography....
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PMID: 20387140
PDF is available here.
PDF is available here.
Abstract
The binding of the 18S RNA of the 40S subunits of wheat germ ribosomes to an oligodeoxyribonucleotide complementary to the 1112-1123 region of the central domain of this RNA molecule has been studied. The selective binding of this oligomer to the complementary RNA fragment and the inhibition of the...
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PMID: 20644591
PDF is available here.
PDF is available here.
Abstract
The DNA x RNA hybrid duplexes are functionally important structures in gene expression that are underutilized as potential drug targets. Several tools are described here for the discovery and characterization of small molecules capable of the selective recognition of DNA x RNA hybrid structures. Com...
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PMID: 19997877
PDF is available here.
PDF is available here.
Abstract
We find that removal of the anionic C-terminal domain (CTD) of HTLV-1 NC results in a protein with chaperone properties comparable with that of other retroviral NCs. Increasing the ionic strength of the solution also improves the chaperone activity of full-length HTLV-1 NC. To determine how the CTD...
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PMID: 19887455
PDF is available here.
PDF is available here.
Analytical Biochemistry (400)2 2010
Abstract
The present study investigated cDNA chimeras using two closely related members of the rice secretory protein gene family as an example. The chimeras detected in initial cDNA products that were amplified using LA Taq polymerase involved two categories: single-site type and multiple-si...
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PMID: 20045389
PDF is available here.
PDF is available here.
Abstract
We collected both steady-state and time-resolved fluorescence quenching titrations of 3MI and 6MI in solution with the mononucleotides AMP, CMP, GMP, and TMP. The dynamic quenching rank of the free probes (quenching constant, kq: T > A > G > C) is totally different from that of incorporated probes....
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PMID: 19610668
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)36 2009
Abstract
In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic fea...
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PMID: 19650666
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)35 2009
Abstract
Locked nucleic acids (LNA), conformationally restricted nucleotide analogues, are known to enhance pairing stability and selectivity toward complementary strands. With the aim to contribute to a better understanding of the origin of these effects, the structure, thermal stability, hybridization ther...
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PMID: 19670874
PDF is available here.
PDF is available here.
Journal of Neuroscience Research (65)Pt 9 2009
Abstract
Locked nucleic acids (LNAs) are modified nucleic acids which contain a modified sugar such as beta-D-2'-O,4'-C methylene-bridged ribofuranose or other sugar derivatives in LNA analogues. The beta-D-2'-O,4'-C methylene ribofuranose LNAs in particular possess high stability and melting temperatures, wh...
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PMID: 19724123
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)33 2009
Abstract
We term a "destabilized duplex", is involved in exonuclease-mediated strand degradation. We find that DNA strands in such a destabilized duplex can be displaced by the challenge of a molar excess of homologous single- and double-stranded DNA targets, in trans. Such an action of the UvrD protein is A...
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PMID: 19618961
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.
Biochemistry (Washington) (48)31 2009
Abstract
We studied the incorporation of the fluorescent cytidine analogues 1,3-diaza-2-oxophenothiazine (tC) and 1,3-diaza-2-oxophenoxazine (tCo) by human DNA polymerase alpha and Klenow fragment of DNA polymerase I (Escherichia coli). These tricyclic nucleobases possess the regular hydrogen bonding interfa...
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PMID: 19580325
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (284)31 2009
Abstract
We demonstrate here that MutSbeta displays identical biochemical and biophysical activities (including ATP-provoked conformational change, ATPase, ATP binding, and ADP binding) when interacting with a (CAG)(n) hairpin and a mismatch. More importantly, our in vitro functional hairpin repair assays re...
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PMID: 19525234
PDF is available here.
PDF is available here.
Genetika (Moskva) (45)7 2009
Abstract
These results indicate a reduction in the number of mtDNA copies with mutations in tissues of irradiated mice by day 28 of the postradiation period. The reduction in the level of mutant mtDNA copies by this term is especially significant in the spleen. The total number of mtDNA copies in the mouse b...
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PMID: 19705747
PDF is available here.
PDF is available here.
B M B Reports (42)6 2009
Abstract
These results suggest that 5-OHU from oxidative damage was mainly influenced by adenine mismatch....
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PMID: 19558797
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.
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.
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.
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.
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
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...
|
PMID: 19450588
PDF is available here.
PDF is available here.
Abstract
According to the results of this research, nucleotide substitutions were found in 5/72 (7%) of samples. The sporadic breast cancer patient was found to be heterozygote for the p.D92N, p.C105W, p.D107N, p.A121P and p.R130Q mutations. One novel mutation, p.D107N, was found in this study. CONCLUSION: L...
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PMID: 19471547
PDF is available here.
PDF is available here.
Abstract
We discovered a robust adenosine 5'-triphosphate-powered dsRNA translocation activity of RIG-I. The CARDs dramatically suppress translocation in the absence of 5'-triphosphate, and the activation by 5'-triphosphate triggers RIG-I to translocate preferentially on dsRNA in cis. This functional integra...
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PMID: 19119185
PDF is available here.
PDF is available here.
Abstract
We examine the ability of UvsW to translocate on ssDNA. Kinetic analysis indicates that the rate of ATP hydrolysis is strongly dependent on the length of the ssDNA lattice, whereas the K(M)-DNA remains relatively constant, demonstrating that UvsW translocates on ssDNA in an ATP-dependent fashion. Ex...
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PMID: 19154117
PDF is available here.
PDF is available here.
Malaria Journal (8)1 2009
Abstract
Thirty one clinical P. falciparum isolates (15 primary isolates and 16 recurrent isolates) from 17 Malagasy children treated with CQ for uncomplicated malaria were genotyped for the pfcrt K76T mutation. Two (11.7%) of 17 patients harboured genetically CQ-resistant P. falciparum strains after therapy...
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PMID: 19291288
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.
Analyst (Cambridge UK) (134)1 2009
Abstract
Thymidine glycol residues in DNA are biologically active oxidative molecular damage sites caused by ionizing radiation and other factors. One or two thymidine glycol residues were incorporated in 19- to 31-mer DNA fragments during automatic oligonucleotide synthesis. These oligonucleotide models wer...
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PMID: 19082173
PDF is available here.
PDF is available here.
Molecular Cell (32)6 2008
Abstract
We report that Salmonella RybB sRNA represses ompN mRNA translation by pairing with the 5′ coding region. Results of systematic antisense interference with 30S binding to ompN and unrelated mRNAs suggest that sRNAs can act as translational repressors by sequestering sequences within the mRNA down...
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PMID: 19111662
PDF is available here.
PDF is available here.
Journal of Molecular Biology (384)3 2008
Abstract
We employ calorimetric [isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC)] and spectroscopic (NMR and UV) methods to characterize the thermodynamics of the GAAA tetraloop-receptor interaction, utilizing a previously described bivalent construct. ITC studies indicate...
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PMID: 18845162
PDF is available here.
PDF is available here.
Journal of Molecular Biology (384)1 2008
Abstract
We showed that MutS bound to a 30-bp heteroduplex containing an unpaired T with a binding affinity approximately 400-fold stronger than to a 30-bp homoduplex, a much higher specificity than previously reported. The binding of nucleotide cofactors decreased both MutS specific and nonspecific binding...
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PMID: 18773911
PDF is available here.
PDF is available here.
Abstract
Junction ribonuclease (JRNase) recognizes the transition from RNA to DNA of an RNA-DNA/DNA hybrid, such as an Okazaki fragment, and cleaves it, leaving a mono-ribonucleotide at the 5' terminus of the RNA-DNA junction. Although this JRNase activity was originally reported in calf RNase H2, some other...
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PMID: 18959768
PDF is available here.
PDF is available here.
Abstract
It is demonstrated in our investigations that certain G-quadruplex structures formed by human telomeric repeats could perform self-cleaving actions. Our further studies verify that these reactions are site-specific and undergo hydrolytic pathways.
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PMID: 18812258
PDF is available here.
PDF is available here.
Abstract
We showed previously that treatment with the TLR9-agonistic ODN M362 (a CpG sequence containing oligonucleotide) induces matrix metalloproteinase-13-mediated invasion in TLR9-expressing human cancer cell lines. Here, we further characterized the role of the TLR9 pathway in this process. We show that...
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PMID: 18922969
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)17 2008
Abstract
We show how a new single molecule PCR (smPCR)-based procedure can be employed as a general substitute to in vivo cloning thereby allowing for the first time in vitro DNA synthesis. We integrated this rapid and high fidelity in vitro procedure into our earlier recursive DNA synthesis and error correc...
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PMID: 18667587
PDF is available here.
PDF is available here.
Abstract
We report a rapid redistribution of DDX1 in cells exposed to ionizing radiation, resulting in the formation of numerous foci that colocalize with gamma-H2AX and phosphorylated ATM foci at sites of DNA double-strand breaks (DSBs). The formation of DDX1 ionizing-radiation-induced foci (IRIF) is depend...
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PMID: 18710941
PDF is available here.
PDF is available here.
Biochemistry (Washington) (47)38 2008
Abstract
Due to their prevalence and roles in biological systems, single mismatches adjacent to G-U pairs are important RNA structural elements. Since there are only limited experimental values for the stability of single mismatches adjacent to G-U pairs, current algorithms using free energy minimization to...
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PMID: 18754680
PDF is available here.
PDF is available here.
Biochemistry (Washington) (47)38 2008
Abstract
We demonstrate that RPA is preferentially retained on a cisplatin interstrand cross-link (ICL) DNA column compared with undamaged DNA. The retention of RPA on cisplatin intrastrand and ICL containing DNA affinity columns is comparable. In vitro electrophoretic mobility shift assays (EMSAs) using syn...
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PMID: 18729380
PDF is available here.
PDF is available here.
Abstract
We have found that the efficiency of fluorescence resonance energy transfer between Cy3 and Cy5 terminally attached to the 5' ends of a DNA duplex is significantly affected by the relative orientation of the two fluorophores. The cyanine fluorophores are predominantly stacked on the ends of the heli...
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PMID: 18676615
PDF is available here.
PDF is available here.
Abstract
We monitored the interaction between MutS and DNA substrates using atomic force microscopy (AFM). An alpha-shaped DNA loop formed by the interaction between MutS and DNA, which was independent of whether or not a mismatch was present in the DNA substrate. These data indicate that MutS associates wit...
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PMID: 18514060
PDF is available here.
PDF is available here.
Abstract
Abstract
We found that roX RNAs of distant Drosophila species could complement D. melanogaster roX mutants despite low homology. Deletion of a conserved predicted stem-loop structure in roX2, containing a short GUb (GUUNUACG box) in its 3' stem, resulted in a defect in histone H4K16 acetylation on the X chro...
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PMID: 18541664
PDF is available here.
PDF is available here.
Biopolymers (89)8 2008
Abstract
The method of solution of the nonlinear Poisson-Boltzmann equation was used to calculate electrostatic energy of binding of various aromatic ligands with DNA oligomers of different length. Analysis of the electrostatic contribution was made in terms of a two-step DNA binding process: formation of th...
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PMID: 18351582
PDF is available here.
PDF is available here.