Find your PDFs fast.
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.
Base Pairing (0):
Recent article
Base Pairing
Abstract
We developed a nuclear magnetic resonance approach that enabled direct detection of structural elements within the intact leader (712-nucleotide dimer) that are critical for genome packaging. Residues spanning the gag start codon (AUG) form a hairpin in the monomeric leader and base pair with residu...
|
PMID: 21998393
PDF is available here.
PDF is available here.
| < More recent | Older article > |
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....
|
PMID: 21819995
PDF is available here.
PDF is available here.
Abstract
We use cryo-electron microscopy to determine the subnanometre structures of Cascade before and after binding to a target sequence. These structures reveal a sea-horse-shaped architecture in which the crRNA is displayed along a helical arrangement of protein subunits that protect the crRNA from degra...
|
PMID: 21938068
PDF is available here.
PDF is available here.
Abstract
The Hepatitis Delta Virus (HDV) ribozyme, which is well adapted to the environment of the human cell, is an excellent candidate for the future development of gene-inactivation systems. On top of this, a new generation of HDV ribozymes now exists that benefits from the addition of a s...
|
PMID: 21793786
PDF is available here.
PDF is available here.
Abstract
We sequenced the exome of a patient who died at the age of 10 months of hypertrophic mitochondrial cardiomyopathy with combined cardiac respiratory chain complex I and IV deficiency. Rigorous data analysis allowed us to identify a homozygous missense mutation in AARS2, which we showed to encode the...
|
PMID: 21549344
PDF is available here.
PDF is available here.
Abstract
The intermolecular interactions of the photodamaged cyclobutane pyrimidine dimer (CPD) lesion with adjacent nucleobases in the native intrahelical DNA double strand are investigated at the level of density functional theory symmetry-adapted perturbation theory (DFT-SAPT) and compared to the original...
|
PMID: 21452189
PDF is available here.
PDF is available here.
Abstract
We investigate DNA breathing dynamics by suggesting and examining several Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base pairs. The walk takes place on the Poland-Scheraga free-energy landsca...
|
PMID: 21517523
PDF is available here.
PDF is available here.
Abstract
Many biomolecules have specific binding properties in the nanostructure formation; they are attractive materials for nanotechnology. One such promising construction material for growing a well-defined nanostructure is deoxyribonucleic acid, due to its π-electron hydrophobic core and predictable reco...
|
PMID: 21382609
PDF is available here.
PDF is available here.
Biopolymers (95)4 2011
Abstract
We report a new Monte-Carlo approach that takes direct account of this information to extract the distortions of covalent structure, base pairing, and dinucleotide geometry intrinsic to regularly organized double-helical molecules. We present new methods to test the validity of the anisotropic param...
|
PMID: 21280021
PDF is available here.
PDF is available here.
Abstract
We add several significant extensions to the work reported in Daniel Pasailă et al. Proceedings of the International (SYNASC) 2008, pp. 519-525: testing this classifier on a more recent version of miRBase (12.0), evaluating the effect of using probabilistic patterns instead of non-probabilistic one...
|
PMID: 21431542
PDF is available here.
PDF is available here.
Abstract
We propose a novel method for sRNA target prediction, termed sTarPicker, which was based on a two-step model for hybridization between an sRNA and an mRNA target. This method first selects stable duplexes after screening all possible duplexes between the sRNA and the potential mRNA target. Next, hyb...
|
PMID: 21799937
PDF is available here.
PDF is available here.
Abstract
We demonstrate that period-doubled discrete breathers appear from the anticontinuum limit of the driven Peyrard-Bishop-Dauxois model of DNA. These novel breathers result from a stability overlap between subharmonic solutions of the driven Morse oscillator. Subharmonic breathers exist whenever a stab...
|
PMID: 21405710
PDF is available here.
PDF is available here.
American Surgeon (12) 2011
Abstract
Abstract
3-Aminophenyl-modified analogues of the bicyclic nucleoside N-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one were synthesised and incorporated directly into triplex-forming oligonucleotides in order to utilise their extended hydrogen bonding motif for recognition of the CG base pair. All analogues demo...
|
PMID: 20835452
PDF is available here.
PDF is available here.
Abstract
We used IRMPD spectroscopy and ion mobility spectrometry to assess whether i-motif structures were preserved in the gas phase. We first investigated the IRMPD spectral signature of the tetramer [dC(6)](4), which can only be formed via C-H(+)-C base pairing, compared to the single strand dC(6). The I...
|
PMID: 20838693
PDF is available here.
PDF is available here.
Abstract
We consider an elastic chain at thermodynamic equilibrium with a heat bath, and derive an approximation to the probability density function, or pdf, governing the relative location and orientation of the two ends of the chain. Our motivation is to exploit continuum mechanics models for the computati...
|
PMID: 21230517
PDF is available here.
PDF is available here.
EMBO Journal (29)21 2010
Abstract
Tethered hydroxyl-radical probing has been used to determine the orientation of binding of polypyrimidine tract-binding protein (PTB) to the poliovirus type 1 (Mahoney) (PV-1(M)) internal ribosome entry site/segment (IRES)-the question of which RNA-binding domain (RBD) binds to which sites on the IR...
|
PMID: 20859255
PDF is available here.
PDF is available here.
Abstract
The base specificity and energetics of DNA binding of the phenazinium dyes phenosafranine and safranine-O have been studied using various biophysical tools. The guanine-cytosine base specificity of both compounds was established from binding affinity values and competition dialysis results and also...
|
PMID: 20730145
PDF is available here.
PDF is available here.
Abstract
The objective of this paper was to evaluate the sequence of feline prepro-adrenomedullin (AM) and its tissue distribution and to investigate whether expression of feline AM mRNA increases in association with spontaneous cardiomyopathy. The feline prepro-AM cDNA sequence and deduced amino acids were...
|
PMID: 20460835
PDF is available here.
PDF is available here.
Abstract
I small heat shock protein (sHSP-CI) genes were found to be selectively induced by L-azetidine-2-carboxylic acid (AZC) on chromosome 3 but not chromosome 1. Here it is shown that a novel cis-responsive element contributed to the differential regulation. By serial deletion and computational analysis,...
|
PMID: 20643810
PDF is available here.
PDF is available here.
Abstract
We succeeded in the synthesis of triplex-forming oligonucleotides (TFOs) that contain a deoxyribonucleotide (Py) bearing a 2-pyridine nucleobase or the 2',4'-BNA congener (Py(B)). By UV melting experiments, it was found that 2-pyridine was a very promising nucleobase for the sequence-selective recog...
|
PMID: 20648389
PDF is available here.
PDF is available here.
Journal of Molecular Biology (402)1 2010
Abstract
We performed molecular dynamics simulations on the hepatitis delta virus ribozyme in the product form and assessed communication between a distal structural portion of the ribozyme-the protonated C41 base triple-and the active site containing the critical C75. We varied the ionization state of C41 i...
|
PMID: 20643139
PDF is available here.
PDF is available here.
Abstract
The aim of this study was to develop in situ hybridization for detection of Mycoplasma hyorhinis in formalin-fixed, paraffin-wax-embedded tissues from pigs with polyserositis. M. hyorhinis was isolated from the spleen (2 pigs) and pericardium (1 pig). M. hyorhinis DNA was detected 16 out of 20 pigs...
|
PMID: 20424392
PDF is available here.
PDF is available here.
Abstract
This review deals with 2-azapurine (imidazo[4,5-d] [1,2,3]triazine) nucleosides and closely related analogs. Different routes are described to yield the desired target compounds, including a sequence of ring-opening and ring-closure reactions performed on purine nucleosides or dire...
|
PMID: 20860023
PDF is available here.
PDF is available here.
Abstract
As calculated by the density functional theory (DFT), the acidity of cytosine's exocyclic amine group (C-N(4)H2) in the base pair G-C is considerably increased upon its one-electron oxidation. The proton affinity (PA) of the amine moiety is lowered by ionisation of G-C (which yields G(*+)-C) from -3...
|
PMID: 20532316
PDF is available here.
PDF is available here.
Abstract
We demonstrate that 19-bp siRNAs are more active silencers than shorter corresponding duplexes. The discrepancy between our results and those questioned appears to be due to different modes of shortening the duplex (either at the 3'-end or at the 5'-end, with respect to polarity of the guide strand)...
|
PMID: 20575617
PDF is available here.
PDF is available here.
Abstract
We use an algorithm now commonly used in microbial ecology, UniFrac, to cluster 175 genomes spanning all three domains of life based on the phylogenetic relationships among their complete tRNA pools. We find that the overall pattern of similarities and differences in the tRNA pools recaptures univer...
|
PMID: 20558546
PDF is available here.
PDF is available here.
Abstract
We have developed amber, opal, and ochre suppressor tRNAs derived from Escherichia coli, and yeast tRNA(Cys) that incorporate a chemically modified cysteine residue with high selectivity at the cognate UAG, UGA, and UAA stop codons in an in vitro translation system. These synthetic tRNAs were aminoa...
|
PMID: 20581130
PDF is available here.
PDF is available here.
Abstract
We show that an LTR retrotransposon of ERV-9 human endogenous retrovirus located 40-70 kb upstream of the human fetal gamma- and adult beta-globin genes serves a long-range, host function. The ERV-9 LTR contains multiple CCAAT and GATA motifs and competitively recruits a high concentration of NF-Y a...
|
PMID: 20615953
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)29 2010
Abstract
We identified genes regulated by the unliganded and liganded forms of ERalpha and ERbeta in U2OS cells. Microarray data demonstrated that virtually no gene regulation occurred with unliganded ERalpha, whereas many genes were regulated by estradiol (E(2)). These results demonstrated that ERalpha requ...
|
PMID: 20404318
PDF is available here.
PDF is available here.
Abstract
We performed Brownian dynamics simulations of the R.P(c) --> R.P(o) transition. In the fast trajectories, unwinding of the promoter DNA begins by local melting around the -10 element, which is followed by sequential unzipping of DNA till the +2 site. The R.P(c) --> R.P(o) transition occurs in three...
|
PMID: 20615963
PDF is available here.
PDF is available here.
Abstract
Abstract
Abstract
Abstract
Abstract
Abstract
Abstract
Abstract
Abstract
Abstract
Abstract
Abstract
We find that extensive complementarity between a target RNA and an Argonaute1-bound miRNA triggers miRNA tailing and 3'-to-5' trimming. In flies, Argonaute2-bound small RNAs--but not those bound to Argonaute1--bear a 2'-O-methyl group at their 3' ends. This modification blocks target-directed small...
|
PMID: 20558712
PDF is available here.
PDF is available here.
Abstract
An improved method of non-radioactive identification of transcription start sites is presented in which the use of 7-deaza dGTP in the primer extension reaction allows the product to be directly aligned to cycle sequencing traces on an automated sequencer. This removes the documented need to apply c...
|
PMID: 20385179
PDF is available here.
PDF is available here.
Abstract
We focus on DNA conformational signals found in the growing library of known high-resolution core-particle structures and the ways in which these features may contribute to the positioning of nucleosomes on specific DNA sequences. We survey the chemical composition of the protein-DNA assemblies and...
|
PMID: 20232929
PDF is available here.
PDF is available here.
Abstract
We propose a new non-coding RNA named B2 discovered by differential display. B2 is a nuclear RNA which is 51,011 bp long with no significant open reading frame. This RNA has a continuous homology with the genomic DNA of the HEF1/ NEDD9/Cas-L gene located on 6p24-p25. This homology has enabled us to...
|
PMID: 20428794
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...
|
PMID: 20423977
PDF is available here.
PDF is available here.
Abstract
We report a novel finding of an antisense oligonucleotide (ASO) microwalk in which we examined the position-specific role of intronic residues downstream from the 5' splice site (5' ss) of SMN2 exon 7, skipping of which is associated with spinal muscular atrophy (SMA), a leading genetic cause of inf...
|
PMID: 20413618
PDF is available here.
PDF is available here.
Nucleic Acids Research (38)11 2010
Abstract
We investigated the thermodynamic stability of the temperature labile hairpin 2 of the Salmonella fourU RNA thermometer over a broad temperature range and determined free energy, enthalpy and entropy values for the base-pair opening of individual nucleobases by measuring the temperature dependence o...
|
PMID: 20211842
PDF is available here.
PDF is available here.
Abstract
We have used ultrafast multidimensional NMR techniques to monitor the adenine-induced folding of an adenine-sensing riboswitch in real time, with nucleotide-resolved resolution. By following changes in 2D spectra at rates of approximately 0.5 Hz, we identify distinct steps associated with the ligand...
|
PMID: 20439766
PDF is available here.
PDF is available here.
Neurological Research (32)4 2010
Abstract
We set out to investigate two variations within the TLR3 gene, an 8 bp insertion-deletion [-/A](8) and a single base-pair variation C1236T, in subjects with MS and matched healthy controls to determine whether significant differences exist in these markers in an Australian population. We used capill...
|
PMID: 20483009
PDF is available here.
PDF is available here.
Abstract
We observed that approximately 85 and 87% of the phenotypic variation in seed set was associated with the major Rf gene on SBI-02. Some evidence for modifier genes was also observed since a continuum of partial restored fertility was exhibited by lines in both RIL populations. With the prior report...
|
PMID: 20091293
PDF is available here.
PDF is available here.
Abstract
We present a benchmark consisting of two sets of simulated genomic sequences for testing the performances of segmentation algorithms. Sequences in the first set are composed of fixed-sized homogeneous domains, distinct in their between-domain guanine and cytosine (GC) content variability. The sequen...
|
PMID: 20018981
PDF is available here.
PDF is available here.
Abstract
We study the thermally driven denaturation of a double-stranded polymer in the presence of a stretching force via Monte-Carlo simulations. When one strand only is stretched, the denaturation transition is first order, while when both strands are stretched, melting is second order. By revisiting the...
|
PMID: 20866280
PDF is available here.
PDF is available here.
Abstract
We genotyped families of cystic fibrosis sib pairs homozygous for F508del-CFTR who represent extreme clinical phenotypes at informative microsatellite markers spanning a 38 Mb region between CFTR and 7qtel. Recombination events on both parental chromosomes were compared between siblings with concord...
|
PMID: 20051989
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (114)16 2010
Abstract
These results suggest that the positive charge on A(+)(*) in ODNs is delocalized as the dimer is stabilized by pi-orbital stacking between adjacent A's. The rate constants for deprotonation of A(+)(*) in ODNs containing AA and AAA (0.9-1.1 x 10(7) s(-1)) were a factor of 2 smaller than the rate cons...
|
PMID: 20369809
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (114)16 2010
Abstract
Our results also indicate that the presence of the thymine 5-methyl group is necessary for calibrating the backbone conformation and the basepair and dinucleotide step geometry of the core A-tract as well as the flanking CA/TG and the neighboring GC/GC steps, as observed in free and protein-bound DN...
|
PMID: 20373819
PDF is available here.
PDF is available here.
Developmental Biology (340)2 2010
Abstract
We investigated the regulation of Dkk1 expression during embryonic development. We identified nine conserved non-coding elements (CNEs), located 3' to the Dkk1 locus. Analyses of the regulatory potential revealed that four of these CNEs in combination drive reporter expression very similar to Dkk1 e...
|
PMID: 20144607
PDF is available here.
PDF is available here.
Abstract
We evaluated the energetic contributions of unsatisfied hydrogen bonding groups by placing chemically modified substituents in select internal positions in RNA helices and conducting thermodynamic studies. We find that unsatisfied carbonyl groups make exceptional contributions to structure formation...
|
PMID: 20345162
PDF is available here.
PDF is available here.
Abstract
Tillering is one of the most important agronomic traits related to grain production in rice (Oryza sativa L.). A japonica-type variety, Aikawa 1, is known to have low-tiller number. The detailed location of a low-tillering gene, Ltn, which has been localized on chromosome 8 in Aikawa 1, was confirme...
|
PMID: 20062964
PDF is available here.
PDF is available here.