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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.
Templates, Genetic (0):
Recent article
Templates, Genetic
Abstract
We demonstrate that a single, site-specific, cyclobutane pyrimidine dimer leading-strand template lesion provides only a transient block to fork progression in vitro. The replisome remains stably associated with the fork after collision with the lesion. Leading-strand synthesis is then reinitiated d...
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PMID: 21998391
PDF is available here.
PDF is available here.
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Biochimica et Biophysica Acta (1809)3 2011
Abstract
An unusual enterovirus 71 (EV71) epidemic has begun in China since 2008. EV71 RNA polymerases (3D(pol)) showed polymerase activity with an Mn(2+). Little activity was detected with Co(2+), and no activity was detected with Mg(2+), Ca(2+), Cu(2+), Ni(2+), Cd(2+), or Zn(2+). It is a primer-dependent po...
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PMID: 21220056
PDF is available here.
PDF is available here.
Nature Nanotechnology (5)11 2010
Abstract
We show that a DNA mechanical device--a DNA walker moving along a DNA track--can be used to perform a series of amine acylation reactions in a single solution without any external intervention. The products of these reactions are programmed by the sequence of the DNA track, but they are not related...
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PMID: 20935654
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1799)1-2 2010
Abstract
We review the role of HMGN in chromatin structure, the link between HMGN proteins and histone modifications, and discuss the consequence of this link on nuclear processes and cellular phenotype....
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PMID: 19948260
PDF is available here.
PDF is available here.
Biophysical Journal (99)4 2010
Abstract
We hypothesize that tightly looping DNA is alone sufficient to repress transcription. To test this hypothesis, we have developed an assay to quantify transcription elongation by bacteriophage T7 RNAP on small, circular DNA templates approximately 100 bp in size. From these highly bent transcription...
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PMID: 20712997
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)30 2010
Abstract
We have previously shown that the mutagenic potential of DinB is regulated by the DNA damage response protein UmuD(2). In the current study, we employ a pre-steady-state fluorescence approach to gain a mechanistic understanding of DinB regulation by UmuD(2). Our results suggest that DinB, like its m...
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PMID: 20467052
PDF is available here.
PDF is available here.
Abstract
We describe two inexpensive, sensitive methods for rapidly discriminating between paralogous miRNAs or other closely related miRNAs and for quantifying their abundance. The first approach is a sequential ribonuclease-protection and primer-extension assay; the second approach is a primer-extension as...
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PMID: 20423977
PDF is available here.
PDF is available here.
Abstract
We introduce a constructive approach to understand how biological molecules can be arranged to achieve a higher-order biological function: replication of genetic information....
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PMID: 20516136
PDF is available here.
PDF is available here.
Abstract
During the past four decades, Tomato yellow leaf curl disease has become one of the major constraints in tomato production worldwide. In the Mediterranean basin, several isolates from two major Begomovirus species are involved in outbreaks and persistent epidemics. A real-time TaqMan PCR assay was d...
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PMID: 20153376
PDF is available here.
PDF is available here.
Methods in Molecular Biology (629)629 2010
Abstract
We recently demonstrated that the activation of RIG-1 by siRNA-bearing 5'-triphosphate can be used to enhance dendritic cell maturation and function. Indeed, immature DCs that had been transfected with siRNA-bearing 5'-triphosphate activated T cells, indicating that, even in the absence of external...
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PMID: 20387164
PDF is available here.
PDF is available here.
Methods in Molecular Biology (629)629 2010
Abstract
We describe a small RNA cloning method that can be used to generate small RNA cDNA libraries for both conventional and next generation (deep) sequencing. It can also be used for detection and quantitative analyses of small RNAs using PCR....
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PMID: 20387155
PDF is available here.
PDF is available here.
Abstract
We assume that activated monomers are produced by prebiotic chemistry. These monomers can undergo spontaneous polymerization, a system that we call "prelife." Adding template-directed polymerization changes the equilibrium structure of prelife if the rate constants meet certain criteria. In particul...
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PMID: 20034501
PDF is available here.
PDF is available here.
Methods in Molecular Biology (630)630 2010
Abstract
Reverse transcription (RT) is the synthesis of complementary deoxyribonucleic acids (DNA) from single-stranded ribonucleic acid (RNA) templates. This process is catalyzed by the reverse transcriptase enzyme, which is the replicating enzyme of retroviruses. Reverse transcriptase was discovered in 197...
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PMID: 20301003
PDF is available here.
PDF is available here.
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics (27)1 2010
Abstract
The nonspecific product of negative control presented an average call rate of 3.2%. The genome coverage of the MDA product increased from 86.4% to 96.4% with the increasing number of template from 1 to 10 cells, while the LOH rate and ADO rate decreased significantly (P<0.05). CONCLUSION: MDA is a h...
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PMID: 20140866
PDF is available here.
PDF is available here.
Journal of Virology (84)4 2010
Abstract
Purified nucleocapsid protein (N protein) from transmissible gastroenteritis virus (TGEV) enhanced hammerhead ribozyme self-cleavage and favored nucleic acid annealing, properties that define RNA chaperones, as previously reported. Several TGEV N-protein deletion mutants were expressed in Escherichi...
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PMID: 19955314
PDF is available here.
PDF is available here.
Abstract
We demonstrate, using biochemical and genetic approaches, that the formation of stable RNA.DNA hybrids enhances the instability of CTG.CAG repeat tracts. In vitro transcribed CG-rich repeating sequences, unlike AT-rich repeats and nonrepeating sequences, form stable, ribonuclease A-resistant structu...
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PMID: 20080737
PDF is available here.
PDF is available here.
Abstract
We show here that both autocatalysis and organocatalysis can be engineered into a synthetic structure. The compound is shown to selectively accelerate its own formation and catalyze either hydrogenation or nucleophilic addition to alpha,beta-unsaturated aldehydes. The observed reactivity indicates t...
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PMID: 20018652
PDF is available here.
PDF is available here.
Abstract
We show that parental 'Watson' and 'Crick' DNA template strands can be identified in sister chromatids of murine metaphase chromosomes using CO-FISH (chromosome orientation fluorescence in situ hybridization) with unidirectional probes specific for centromeric and telomeric repeats. All chromosomes...
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PMID: 20016487
PDF is available here.
PDF is available here.
Abstract
We have developed a HIV-1 marker system by making a small number of codon modifications in gag which allow recombination to be measured over various lengths between closely related viral genomes. We have developed statistical tools to measure recombination rates that can compensate for the possibili...
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PMID: 20442872
PDF is available here.
PDF is available here.
BMC Microbiology (10) 2010
Abstract
These results highlight the PCR conditions, particularly the polymerase, have significant effect on the analysis of microbial diversity with next generation sequencing methods....
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PMID: 20937143
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 showed that initiation of R-loop formation at an R-loop initiation zone (RIZ) is favored by G clusters. Here, using a purified in vitro system with T7 RNA polymerase, we show that increased distance between the promoter and the R-loop-supporting G-rich region reduces R-loop formation. When the G-...
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PMID: 19841062
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)33 2009
Abstract
We applied single-molecule time-lapse atomic force microscopy (AFM) imaging to directly visualize the dynamics of nucleosomes and identify the mechanism of the large range DNA exposure. With this technique, we are able to observe the process of unwrapping of nucleosomes. The unwrapping of nucleosome...
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PMID: 19618963
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (284)31 2009
Abstract
We report on the conformational dynamics of a model Y-family polymerase Dpo4 from Sulfolobus solfataricus. Hydrogen-deuterium exchange in tandem with mass spectrometry was used to monitor changes in Dpo4 structure as a function of time and the presence or absence of specific substrates and ligands....
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PMID: 19515847
PDF is available here.
PDF is available here.
Journal of Molecular Biology (390)4 2009
Abstract
We show here that many of the key elements of this highly unusual strategy are conserved between yeast and human Rev1, including the eviction of template G from the DNA helix and the pairing of incoming deoxycytidine 5'-triphosphate with a surrogate arginine residue. We also show that the catalytic...
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PMID: 19464298
PDF is available here.
PDF is available here.
Abstract
We demonstrate that a previously predicted bacterial transcriptional regulator, NrtR, represses the transcription of NAD biosynthetic genes in vitro. The NAD metabolite ADP-ribose functions as an activator suppressing NrtR repressor activity. The presence of high ADP-ribose levels in the cell is ind...
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PMID: 19604474
PDF is available here.
PDF is available here.
Audio, Transactions of the IRE Professional Group on (Chapter 18) 2009
Abstract
We describe a set of improvements we have made to the standard Illumina Genome Analyzer protocols to make the sequencing process more reliable in a high-throughput environment, reduce amplification bias, narrow the distribution of insert sizes, and reliably obtain high yields of data....
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PMID: 19582764
PDF is available here.
PDF is available here.
BioTechniques (47)1 2009
Abstract
The predominant method for DNA cloning is by propagation in biological hosts, but this method has limitations because certain sequences are difficult to clone using any combination of available hosts or vectors. Recently, multiply-primed rolling circle amplification (MPRCA) has been applied to overc...
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PMID: 19594445
PDF is available here.
PDF is available here.
Croatian Medical Journal (50)3 2009
Abstract
Amplification of 100 pg or less of DNA generated reproducible results with anticipated stochastic effects. Down to 25 pg of DNA, 92% or more of the expected alleles were consistently detected while lower amounts yielded concordant partial profiles. Although spurious alleles were sometimes observed w...
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PMID: 19480021
PDF is available here.
PDF is available here.
Human Molecular Genetics (18)12 2009
Abstract
We investigated the potential mechanisms for MECP2 duplication and examined whether genomic architectural features may play a role in their origin using a custom designed 4-Mb tiling-path oligonucleotide array CGH assay. Each of the 30 patients analyzed showed a unique duplication varying in size fr...
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PMID: 19324899
PDF is available here.
PDF is available here.
Nucleic Acids Research (37)8 2009
Abstract
The effects of photocaged nucleosides on the DNA polymerization reaction was investigated, finding that most polymerases are unable to recognize and read through the presence of a single caging group on the DNA template. Based on this discovery, a new method of introducing mutations into plasmid DNA...
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PMID: 19293272
PDF is available here.
PDF is available here.
Methods in Molecular Biology (543)543 2009
Abstract
We describe a method for quantitative analysis of the rate of distant communication in cis on saturated arrays of nucleosomes capable of forming the 30-nm chromatin fibers in vitro....
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PMID: 19378187
PDF is available here.
PDF is available here.
Nucleic Acids Research (37)7 2009
Abstract
We conclude that DNA-binding activity of RPA2 is dispensable in yeast and that the essential function of DBD D is intra- and/or inter-protein interactions....
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PMID: 19244309
PDF is available here.
PDF is available here.
Abstract
Obtaining genetic profiles from samples containing minimal amounts of DNA can be difficult. In forensic science, the vast majority of genetic profiles are generated using commercial kits that have been optimized for the amplification of a specific range of DNA concentrations. DNA ext...
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PMID: 19215883
PDF is available here.
PDF is available here.
Journal of Virology (83)4 2009
Abstract
We propose that a nucleotide template-based mechanism facilitates the acquisition of the K65R mutation in subtype C human immunodeficiency virus type 1 (HIV-1). Different patterns of DNA synthesis were observed using DNA templates from viruses of subtype B or C origin. When subtype C reverse transcr...
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PMID: 19073730
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
We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides (Figur...
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PMID: 19820685
PDF is available here.
PDF is available here.
Abstract
We briefly review patents that can enrich target genomic regions of interest to harness the power of NextGen sequencing technology for basic and translational biomedical research....
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PMID: 19149736
PDF is available here.
PDF is available here.
Abstract
We examined their base recognition ability by DNA polymerase reactions. It was found that these modified derivatives were incorporated into the 3'-terminal site of an ODN by DNA polymerase selecting accurately the complementary G or T base on a template ODN. In the incorporation reaction using templ...
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PMID: 19749293
PDF is available here.
PDF is available here.
Abstract
We were able to detect single-stranded-DNA (ssDNA)-guest complexes for strands with lengths of up to 20 bases, in which the highest complex mass detected was 15 kDa; these complexes constitute 20-component self-assembled objects. Gas-phase breakdown experiments on single- and multiple-guest-DNA asse...
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PMID: 19040227
PDF is available here.
PDF is available here.
Abstract
The in cellulo analysis of DNA protein interactions and chromatin structure is very important to better understand the mechanisms involved in the regulation of gene expression. The nuclease-hypersensitive sites and sequences bound by transcription factors often correspond to genetic regulatory eleme...
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PMID: 19378174
PDF is available here.
PDF is available here.
Abstract
Several methods have been developed to site-specifically incorporate photoreactive nucleotide analogs into DNA for the purpose of identifying the proteins and their domains that are in contact with particular regions of DNA. The synthesis of several deoxynucleotide analogs that have a photoreactive...
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PMID: 19378181
PDF is available here.
PDF is available here.
Abstract
We have shown that during lineage progression from a quiescent adult muscle satellite cell to a differentiated myofibre, both symmetric and asymmetric divisions take place. Furthermore, we provide evidence that a sub-population of label retaining satellite cells co-segregate template DNA strands to...
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PMID: 19089364
PDF is available here.
PDF is available here.
Abstract
We describe several recently developed procedures for obtaining and analysis of mononucleosomes that are uniquely positioned on 150-600 bp DNA fragments....
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PMID: 19381918
PDF is available here.
PDF is available here.
Abstract
We have discussed a method to evaluate the role of histone chaperone NPM1 (the only known chaperone to get acetylated with functional consequence) in the transcriptional activation which is acetylation dependent....
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PMID: 19381933
PDF is available here.
PDF is available here.
Abstract
We describe three robust methods for target amplification from purified genomic DNA or pre-amplified DNA. The protocols include incorporation of biotin labels in the target molecules and allow for biotin/streptavidin chemistry to be utilized for flexibility in choice of visualization strategy....
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PMID: 19381981
PDF is available here.
PDF is available here.
Abstract
We used in vitro reconstituted solid-phase transcription elongation/termination system. This approach allows for direct monitoring of ligand binding and riboswitch functioning, establishing the working concentration of a ligand as a function of RNA polymerase speed, and also probing RNA structure of...
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PMID: 19381551
PDF is available here.
PDF is available here.
Abstract
DNA footprinting is a widely used method to locate the binding sites of protein on the DNA. It is based on the observation that a protein bound to DNA protects it from degradation by an enzyme or chemical reagent.Exonuclease III is a suitable probe to analyze the boundaries of a protein when it is n...
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PMID: 19378158
PDF is available here.
PDF is available here.
Abstract
The microinjection of mRNA that is transcribed and capped in vitro into fertilized eggs and embryos of Xenopus laevis provides a powerful means for discovering the function of proteins during early development. Proteins may be overexpressed for a gain-of-function effect or exogenous protein function...
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PMID: 19085142
PDF is available here.
PDF is available here.
Mikrobiologiia (78)3 2009
Abstract
Journal of Molecular Biology (384)5 2008
Abstract
We previously provided support for an induced-fit mechanism for pol X in the presence of the correct incoming nucleotide. Here, we perform molecular dynamics simulations of pol X/DNA complexes with different incoming incorrect nucleotides in various orientations [C•C, A•G, and G•G (anti) and A...
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PMID: 18955064
PDF is available here.
PDF is available here.
FEBS Letters (582)30 2008
Abstract
Our results show that misalignment occurs only in the 5'-G(Sp) and 5'-T(Sp) templates, providing structural insights into the observed differences in mutagenicity of Sp and oG during DNA replication....
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PMID: 19041867
PDF is available here.
PDF is available here.
Abstract
We show, using genetic and physical approaches, that in budding yeast (Saccharomyces cerevisiae) Rad18 is required for the formation of X-shaped sister chromatid junctions (SCJs) at damaged replication forks through a process involving PCNA polyubiquitylation and the ubiquitin-conjugating enzymes Mm...
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PMID: 19092928
PDF is available here.
PDF is available here.
Journal of Molecular Biology (384)1 2008
Abstract
We test an RNA looping model for this N-dependent "action at a distance" by cleaving the nascent transcript between boxB and RNAP during transcript elongation. Cleavage decreases antitermination, showing that an intact RNA transcript is required to stabilize the interaction of boxB-bound N with RNAP...
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PMID: 18922547
PDF is available here.
PDF is available here.
Journal of Molecular Biology (384)1 2008
Abstract
We previously showed that it is possible to delete a complete module without affecting the overall structure of the interface. Here, we replace a complete module with structure fragments taken from nonrelated proteins. Nature-optimized fragments were chosen from 10(7) starting templates found in the...
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PMID: 18804117
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)21 2008
Abstract
We have developed a novel approach for analysis of beta transcript diversity in mice with a real-time PCR-based method that uses a matrix of BV- and BJ-specific primers to amplify 240 distinct BV-BJ combinations. Defined endpoints (Ct values) and dissociation curves are generated for each BV-BJ comb...
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PMID: 18835849
PDF is available here.
PDF is available here.
ChemBioChem (9)17 2008
Abstract
ChemBioChem (9)17 2008
Abstract
We investigated whether the A, C, T and U analogues of this phosphonate nucleoside (PMdN) series can function as substrates of natural DNA polymerases. PMdT and PMdU could only be polymerized enzymatically to a limited extent. Nevertheless, PMdA and PMdC could be incorporated into a DNA duplex with...
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PMID: 19006151
PDF is available here.
PDF is available here.
ChemBioChem (9)17 2008
Abstract
We reported messenger RNA (mRNA)-directed polyester synthesis by using the new emerging method of genetic-code reprogramming in which alpha-hydroxy acids with various kinds of side-chains are assigned to arbitrarily chosen codons. In this work, we have achieved the ribosomal synthesis of polyesters...
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PMID: 18985645
PDF is available here.
PDF is available here.
Abstract
We show that this domain is the main structural determinant that dictates the internal 3' nucleotide used as template during initiation....
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PMID: 19011105
PDF is available here.
PDF is available here.