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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 Conformation (3):
Recent article
Nucleic Acid Conformation
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...
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PMID: 21998393
PDF is available here.
PDF is available here.
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Abstract
Translation initiation dependent on the foot-and-mouth disease virus (FMDV) internal ribosome entry site (IRES) occurs at two sites (Lab and Lb), 84 nucleotides (nt) apart. In vitro translation of an mRNA comprising the IRES and Lab-Lb intervening segment fused to a chloramphenicol acetyltransferase...
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PMID: 21813609
PDF is available here.
PDF is available here.
FEBS Journal (278)19 2011
Abstract
Through its capability to transiently pack and unpack our genome, chromatin is a key player in the regulation of gene expression. Single-molecule approaches have recently complemented conventional biochemical and biophysical techniques to decipher the complex mechanisms ruling chroma...
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PMID: 21810177
PDF is available here.
PDF is available here.
FEBS Journal (278)19 2011
Abstract
We discuss nucleosome dynamics from two angles. First, we describe the dynamical modes of nucleosomes in the absence of remodelers that are experimentally fairly well characterized and theoretically understood. Then, we discuss remodelers and describe recent insights about the possible schemes that...
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PMID: 21812931
PDF is available here.
PDF is available here.
Abstract
We show that labile S4 complexes rearrange into stable complexes within a few minutes at 42 °C, with longer coincubation leading to an increased population of stable complexes. In contrast, prefolding the rRNA has a smaller effect on stable S4 binding. Experiments with minimal rRNA fragments show...
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PMID: 21821049
PDF is available here.
PDF is available here.
Abstract
We were able, for the first time, to observe spontaneous, ATP-independent unwrapping of nucleosomes. However, low temporal resolution did not allow visualization of various pathways of nucleosome dynamics. In the studies described here, we applied high-speed time-lapse AFM (HS-AFM) capable of visual...
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PMID: 21846149
PDF is available here.
PDF is available here.
Biochemistry (Washington) (50)37 2011
Abstract
We benchmark the method using six molecules for which crystallographic data are available: tRNA(phe) and 5S rRNA from Escherichia coli, the P4-P6 domain of the Tetrahymena group I ribozyme, and ligand-bound domains from riboswitches for adenine, cyclic di-GMP, and glycine. SHAPE-directed modeling of...
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PMID: 21842868
PDF is available here.
PDF is available here.
Abstract
We report on an in vitro study, which combined RNase footprinting, gel shift binding assays, and processing assays, to investigate the molecular basis and function of the interaction between the native let-7g precursor (pre-let-7g) and LIN28. We have mapped the structure of pre-let-7g and identified...
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PMID: 21815640
PDF is available here.
PDF is available here.
Abstract
We have solved the crystal structure of the RNA recognition and leucine-rich repeat motifs of TAP bound to one symmetrical half of the CTE RNA. L-shaped conformations of protein and RNA are involved in a mutual molecular embrace on complex formation. We have monitored the impact of structure-guided...
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PMID: 21822283
PDF is available here.
PDF is available here.
Nature Reviews: Genetics (12)9 2011
Abstract
RNA structure is crucial for gene regulation and function. In the past, transcriptomes have largely been parsed by primary sequences and expression levels, but it is now becoming feasible to annotate and compare transcriptomes based on RNA structure. In addition to computational pred...
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PMID: 21850044
PDF is available here.
PDF is available here.
Abstract
We report 3.15-Å crystal structures of this ligase trapped in catalytically viable preligation states, with the 3'-hydroxyl nucleophile positioned for in-line attack on the 5'-triphosphate. Guided by metal- and solvent-mediated interactions, the 5'-triphosphate hooks into the major groove of the ad...
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PMID: 21857665
PDF is available here.
PDF is available here.
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.
Abstract
We investigated a large family affected with autosomal-dominant adermatoglyphia (absence of fingerprints) also known as the "immigration delay disease." Using linkage and haplotype analyses, we mapped the disease phenotype to 4q22. One of the genes located in this interval is SMARCAD1, a member of t...
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PMID: 21820097
PDF is available here.
PDF is available here.
Journal of Cell Biology (194)3 2011
Abstract
We find here that in a key dendritic RNA transport pathway (exemplified by BC1 RNA, a dendritic regulatory RNA, and protein kinase M ζ [PKMζ] mRNA, a dendritic mRNA), noncanonical purine•purine nucleotide interactions are functional determinants of RNA targeting motifs. These motifs are specific...
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PMID: 21807882
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...
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PMID: 21793786
PDF is available here.
PDF is available here.
Abstract
Base pairs formed by the inosine nucleoside (I) play an important role in many physiological processes as well as in various DNA technologies. Relative stabilities and favored base pair geometries of free inosine wobble base pairs in aprotic solvents have been determined through (1)H NMR measurements...
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PMID: 21644523
PDF is available here.
PDF is available here.
Abstract
RNA regulation has been increasingly recognized as a potential and perhaps overlooked genetics of higher organisms. Noncoding RNAs (ncRNA) may play various catalytic and regulatory roles in the genetic operating system. Recent studies using comparative genomics and molecular genetics show evidence of...
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PMID: 21041153
PDF is available here.
PDF is available here.
Abstract
Yeast ribosomal protein L11 is positioned at the intersubunit cleft of the large subunit central protuberance, forming an intersubunit bridge with the small subunit protein S18. Mutants were engineered in the central core region of L11 which interacts with Helix 84 of the 25S rRNA. N...
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PMID: 21519857
PDF is available here.
PDF is available here.
Abstract
We describe structural and functional analyses of the Thermus thermophilus CRISPR Cse3 endonuclease. High-resolution X-ray structures of Cse3 bound to repeat RNAs model both the pre- and post-cleavage complexes associated with processing the pre-crRNA. These structures establish the molecular basis...
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PMID: 21572444
PDF is available here.
PDF is available here.
Abstract
We show that Cse3 type CRISPR-specific endoRNases bind a hairpin structure and residues downstream of the cleavage site within the repetitive segment of cognate CRISPR RNA. Cocrystal structures of Cse3-RNA complexes reveal an RNA-induced conformational change in the enzyme active site that aligns th...
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PMID: 21572442
PDF is available here.
PDF is available here.
Abstract
We propose the existence of a dynamic DNA readout mechanism, wherein distant segments modulate conformational preferences, flexibility or spacing of the DNA binding motifs or serve as competitive partners. Despite their low sequence similarity, these intrinsically disordered regions are often conser...
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PMID: 21620710
PDF is available here.
PDF is available here.
Abstract
We extensively characterize alternative first exons of the mouse GR to reveal homology to the rat and human. We further find that, although most promoters are broadly expressed in various tissues, transcription of individual promoters can be differentially regulated by growth factor- and depolarizat...
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PMID: 21527501
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.
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences (369)1944 2011
Abstract
The effect of a slit-like confinement on the relaxation dynamics of DNA is studied via a mesoscale model in which a bead and spring model for the polymer is coupled to a particle-based Navier-Stokes solver (multi-particle collision dynamics). The confinement is found to affect the equilibrium stretch...
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PMID: 21536580
PDF is available here.
PDF is available here.
Abstract
We have carried out ∼3 microsecond long all atom replica exchange molecular dynamics (REMD) simulations for each of four histone tails, H4, H3, H2B, and H2A, and probed their intrinsic conformational preferences. Our subsequent free energy landscape analysis demonstrated that most tails are not fu...
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PMID: 21517079
PDF is available here.
PDF is available here.
Abstract
We report a first atomistic and statistical analysis of the unfolding of the pseudoknot within gene 32 mRNA of bacteriophage T2. Multiple unfolding pathways, diverse transition states, and various intermediate structures were observed. Water molecules were found to be coupled with the unfolding proc...
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PMID: 21500824
PDF is available here.
PDF is available here.
Abstract
Deoxyribonucleic acid (DNA) is composed of five major elements carbon, hydrogen, nitrogen, oxygen, and phosphorus. The substitution of any of these elements in DNA would be anticipated to have major biological implications. However, recent studies have suggested that the substitution of arsenic into...
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PMID: 21443192
PDF is available here.
PDF is available here.
Biopolymers (95)8 2011
Abstract
We consider the Porod-Debye law as a powerful tool for detecting biopolymer flexibility in SAS experiments. We show that the Porod-Debye region fundamentally describes the nature of the scattering intensity decay by capturing the information needed for distinguishing between folded and flexible part...
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PMID: 21509745
PDF is available here.
PDF is available here.
Abstract
We review modern developments in genomics and systems biology that have revolutionized our understanding of the multiple means by which translation is regulated. We suggest new means to model the process of translation in a richer framework that will incorporate information about gene sequences, the...
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PMID: 21487400
PDF is available here.
PDF is available here.
Biopolymers (95)9 2011
Abstract
We present results of the molecular electrostatic potential (MEP), together with the HOMO and LUMO frontier orbitals, which are physical quantities of concern in the docking of compounds on the G-quadruplex. The calculations are performed in the frame of density functional theory at the B88LYP/6-31G...
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PMID: 21480192
PDF is available here.
PDF is available here.
Abstract
We report on a crucial structural feature of the bent DNA required for strong binding to HMGB1. NMR structures of two bent DNA oligomers, only one of which binds strongly to HMGB1, revealed that the presence of a pocket structure on the minor groove is crucial for strong binding through penetration...
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PMID: 21443191
PDF is available here.
PDF is available here.
Abstract
We have studied by rapid scan FTIR spectroscopy the isothermal B(I)-B(II) transition on its intrinsic time scale. Correlation analysis of IR absorption changes occurring within seconds after a reversible incremental growth of the DNA hydration shell identifies water populations w(1) (PO(2)(-)-bound)...
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PMID: 21446714
PDF is available here.
PDF is available here.
Abstract
We investigate the folding mechanism of the preQ(1) riboswitch aptamer domain using all-atom Go̅-model simulations. The folding pathway of such a single domain is found to be cooperative and sequentially coordinated, as the folding proceeds in the 5' → 3' direction. This kinetically efficient fol...
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PMID: 21375305
PDF is available here.
PDF is available here.
Abstract
I photocleavage in a dinucleotide, single-stranded, and double-stranded RNA. This radical is a model of the major hydroxyl radical adduct of uridine. Tandem lesions resulting from addition of the peroxyl radical derived from 1 to the 5'-adjacent nucleotide are observed by ESI-MS. Radical 1 produces...
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PMID: 21391681
PDF is available here.
PDF is available here.
Biopolymers (95)9 2011
Abstract
Molecular dynamics (MD) simulations were carried out to compare the free and bound structures of wild type U1A protein with several Phe56 mutant U1A proteins that bind the target stem loop 2 (SL2) RNA with a range of affinities. The simulations indicate the free U1A protein is more flexible than the...
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PMID: 21384338
PDF is available here.
PDF is available here.
Abstract
We report the design and construction of a novel DNA cross tile, called the double-decker tile. Its arms are symmetric and have four double helices each. Using its sticky ends, large two-dimensional square lattices have been constructed which are on the order of tens of micrometers. Furthermore, it...
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PMID: 21355587
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...
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PMID: 21517523
PDF is available here.
PDF is available here.
Abstract
We report here on the existence of a high-level compositional organization of isochores in the human genome. By using a segmentation algorithm incorporating the long-range correlations existing in human DNA, we find that every chromosome is composed of a few huge segments (~ 10^{7} bp) of relatively...
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PMID: 21517526
PDF is available here.
PDF is available here.
Abstract
We use a lattice Boltzmann based Brownian dynamics simulation to investigate the dependence of DNA thermophoresis on its interaction with dissolved salts. We find the thermal diffusion coefficient D_{T} depends on the molecule size, in contrast with previous simulations without electrostatics. The m...
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PMID: 21517533
PDF is available here.
PDF is available here.
Abstract
We provide a practical guide for design and assembly of scaffolded DNA origami objects. We also introduce a computational tool for predicting the structure of DNA origami objects and provide information on the conditions under which DNA origami objects can be expected to maintain their structure....
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PMID: 21358626
PDF is available here.
PDF is available here.
Abstract
We separate the individual contributions of single- and multistep channels to DNA charge transport and find that with 7 or 8 intervening adenines the charge transport is a coherent, single-step process. Moreover, a transition occurs from multistep to single-step charge transport with increasing dono...
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PMID: 21348520
PDF is available here.
PDF is available here.
Mutation Research (711)1-2 2011
Abstract
The most aggressive product of water radiolysis, the hydroxyl (OH) radical, is responsible for the indirect effect of ionizing radiations on DNA in solution and aerobic conditions. According to radiolytic footprinting experiments, the resulting strand breaks and base modifications are inhomogeneously...
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PMID: 21329707
PDF is available here.
PDF is available here.
Molecular Cell (41)2 2011
Abstract
We show that the ORF of histone mRNA contains two structural elements critical for translation initiation. One of the two structures binds eIF4E without the need of the cap. Ribosomal 43S particles become tethered to this site and directly loaded in the vicinity of the AUG. The other structure, 19 n...
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PMID: 21255730
PDF is available here.
PDF is available here.
Abstract
We have therefore developed a different combination approach for the treatment of HIV infection in which an RNA aptamer, with high binding affinity to the HIV-1 envelope (gp120) protein and virus neutralization properties, is attached to and delivers a small interfering RNA (siRNA) that triggers seq...
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PMID: 21248316
PDF is available here.
PDF is available here.
Abstract
We hypothesized that biotinylation modifies the physical structure of nucleosomes, and that biotin-induced conformational changes contribute to gene silencing associated with histone biotinylation....
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PMID: 21298003
PDF is available here.
PDF is available here.
Abstract
We demonstrate that, beyond the obvious difference in transcriptional and translational modulation, both adenine riboswitches exhibit different ligand binding properties and appear to operate under different regulation regimes (kinetic versus thermodynamic). While the B. subtilis pbuE riboswitch ful...
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PMID: 21283784
PDF is available here.
PDF is available here.
Abstract
We investigated the prevalence of anti-core and anti-core+1/ARFP antibodies in HCV-positive blood donors from Cambodia, using peptide and recombinant protein-based ELISAs. We detected unusual serological profiles in 3 out of 58 HCV positive plasma of genotype 1a. These patients were negative for ant...
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PMID: 21283512
PDF is available here.
PDF is available here.
Abstract
Iron is one of the most important minor elements in the shells of bivalves. This study was designed to investigate the involvement of ferritin, the principal protein for iron storage, in shell growth. A novel ferritin subunit (Fth1) cDNA from the freshwater pearl mussel (Hyriopsis cu...
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PMID: 21818403
PDF is available here.
PDF is available here.
Abstract
Our novel DNAzyme constructs could efficiently silence the expression of target genes, proving a powerful tool for gene silencing. The results showed that the six oligo bulge was the most effective when the six oligo bulge was 12-15 bp away from the core catalytic domain....
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PMID: 21490924
PDF is available here.
PDF is available here.
Abstract
We show that in an exponentially growing Escherichia coli rpoZ mutant lacking the polymerase ω subunit, the impact of the Eσ(38) holoenzyme on transcription is enhanced in parallel with overall DNA relaxation. Conversely, overproduction of σ(70) in an rpoZ mutant increases both overall DNA superc...
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PMID: 21810966
PDF is available here.
PDF is available here.
Abstract
We need to look for other reasons behind the giant panda's diet switch....
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PMID: 21818345
PDF is available here.
PDF is available here.
Abstract
We analysed for the first time the complete transcriptome of human trisomic endothelial progenitor cells to an unprecedented level of resolution and sensitivity by RNA-sequencing. Our analysis allowed us to detect differential expression of even low expressed genes crucial for the pathogenesis, to d...
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PMID: 21533138
PDF is available here.
PDF is available here.
Abstract
We describe the identification of the agr as a quorum sensing system in Staphylococcus aureus and the isolation of agr autoinducers and inhibitors by northern blotting, real-time RT-PCR, and β-lactamase reporter cells assays....
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PMID: 21031303
PDF is available here.
PDF is available here.
Abstract
We analysed for the first time the complete transcriptome of human trisomic endothelial progenitor cells to an unprecedented level of resolution and sensitivity by RNA-sequencing. Our analysis allowed us to detect differential expression of even low expressed genes crucial for the pathogenesis, to d...
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PMID: 21533138
PDF is available here.
PDF is available here.
BMC Medical Genomics (4)1 2011
Abstract
We suggest their control by a miRNA dominated feedback loop, which might be linked to the dramatically different miRNA amounts seen between low and high-grade MDS.
The presented results provide novel findings that build a basis of further investigations of diagnostic biomarkers, targ...
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PMID: 21342535
PDF is available here.
PDF is available here.
Molecular Plant (4)1 2011
Abstract
We report here that the expression of endogenous microRNAs (miRNAs) can be efficiently silenced in Arabidopsis thaliana (Arabidopsis) using artificial miRNA (amiRNA) technology. We demonstrate that an amiRNA designed to target a mature miRNA directs silencing against all miRNA family members, wherea...
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PMID: 20943811
PDF is available here.
PDF is available here.
Biology Direct (6) 2011
Abstract
We review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. PROPOSAL: The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. T...
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PMID: 21303550
PDF is available here.
PDF is available here.
Abstract
We describe a novel approach to predict the structure of key TR features and to aid the identification of TRs in genomes, using a program we developed, TRFolder. We applied our method to confirm and improve previously studied core structures from Saccharomyces and Kluyveromyces TRs. We made novel st...
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PMID: 21441097
PDF is available here.
PDF is available here.
Abstract
We also focused on exploring dominating set of features using principal component analysis and Info gain in our earlier work, with the assumption that it will reduce complexity of the model and may increase prediction accuracy. In this chapter, we have used attribute relevance analysis techniques fo...
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PMID: 21431548
PDF is available here.
PDF is available here.
Abstract
We have carried out computer simulations of drug and DNA alone and also in complex mode in water as a medium. All the simulations are being carried out using molecular operating environment (MOE) and X3DNA software tools on SUN SOLARIS platform. Interaction energy of all the drug molecules with DNA...
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PMID: 21431579
PDF is available here.
PDF is available here.