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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
MicroRNAs are a family of ~22 nt small RNAs that can regulate gene expression at the post-transcriptional level. Identification of these molecules and their targets can aid understanding of regulatory processes. Recently, HTS has become a common identification method but there are two major limitatio...
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PMID: 21504621
PDF is available here.
PDF is available here.
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Abstract
Molecular dynamics simulations (90 ns) of different DNA complexes attached to a functionalized substrate in solution were performed in order to clarify the behavior of mismatched DNA sequences captured by a tethered DNA probe (biochip). Examination of the trajectories revealed that the substrate infl...
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PMID: 21660324
PDF is available here.
PDF is available here.
Abstract
Nucleic acids have been demonstrated to be versatile nanoscale engineering materials with the construction of dynamic DNA structures, motors, and circuits. These constructions generally rely on the clever use and integration of relatively few reaction mechanisms and design primitives...
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PMID: 21166410
PDF is available here.
PDF is available here.
Abstract
We previously showed by NMR and molecular modeling that the unexpectedly high binding affinity of 2'F-ANA is largely due to a C-H···F-C pseudohydrogen bond at pyrimidine-purine steps. Comparisons of the melting of duplexes with identical sequence composition but a rearranged sequence confirm that...
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PMID: 21171597
PDF is available here.
PDF is available here.
Abstract
We use molecular dynamics (MD) simulations to show that the surprisingly slow (∼10 ns) TDSS response of coumarin 102 (C102), a base pair replacement, reflects a distinct dynamical signature for DNA damage. When the C102 molecule is covalently incorporated into DNA, an abasic site is created on the...
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PMID: 21175205
PDF is available here.
PDF is available here.
Abstract
We investigate the links between chromosomal spatial organization and global transcriptional regulation. By means of a novel multi-scale spatial aggregation analysis, we uncover the existence of contiguous clusters of nucleoid-perturbation sensitive genes along the genome, whose expression is affect...
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PMID: 21165487
PDF is available here.
PDF is available here.
Abstract
We used single-molecule fluorescence assays to observe intrinsic B-to-Z transitions, protein association/dissociation events, and accompanying B-to-Z transitions. The results reveal that intrinsic Z-DNAs are dynamically formed and effectively stabilized by Z-DNA-binding proteins through efficient tr...
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PMID: 21171590
PDF is available here.
PDF is available here.
Abstract
We use standard molecular dynamics and replica exchange molecular dynamics to take a series of tests on the RNA stability under different combinations of Amber force field parameters (ff98, ff99 and ff99bsc0) and the general Born implicit solvent models (igb1, igb2 and igb5). It is found that only f...
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PMID: 20919758
PDF is available here.
PDF is available here.
Abstract
The conformations of the benzo[a]pyrene-7,8-quinone (BPQ) modified oligonucleotide were investigated using molecular dynamic simulation. In the initial structures, the central guanine base was modified with BPQ resulting in the formation of four structurally distinguishable 10-(N2-deoxyguanosyl)-9,1...
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PMID: 20919757
PDF is available here.
PDF is available here.
Abstract
We report a single-molecule study that monitors the dynamics of individual initiation complexes, comprised of vRNA, tRNA and HIV reverse transcriptase (RT). RT transitions between two opposite binding orientations on tRNA-vRNA complexes, and the prominent pausing events are related to RT binding in...
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PMID: 21102446
PDF is available here.
PDF is available here.
Abstract
We propose that AM AFM in high humidity will be a useful technique for probing DNA topology without some of the drawbacks of imaging under bulk solution....
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PMID: 20927466
PDF is available here.
PDF is available here.
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...
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PMID: 20835452
PDF is available here.
PDF is available here.
Abstract
We compared the overall pro-domain tertiary structure with several proteins belonging to the same fold in the structural classification of proteins (SCOP) database by using structure and sequence comparisons. The best score obtained was between the activation domain of human procarboxypeptidase A4 (...
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PMID: 21082207
PDF is available here.
PDF is available here.
Chemical Communications (46)42 2010
Abstract
A novel nucleoside analog with a disulfide bridge structure at the sugar moiety, which shows redox-responsive reversibility of the sugar conformation due to formation and scission of the disulfide bond, was designed and synthesized.
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PMID: 20871898
PDF is available here.
PDF is available here.
Abstract
We compare two different families of dendrons to explore the role played by architecture in influencing the ability of these molecules to optimize their surface to bind DNA-an indicator of rigid/flexible behaviour....
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PMID: 20856975
PDF is available here.
PDF is available here.
Abstract
Upon X-ray irradiation of hypoxic aqueous solution, modified oligodeoxynucleotides (ODNs) bearing a pair of disulfides at both ends of the strand that forms a stem-and-loop structure with a neighboring arrangement of α,ω-bis-disulfides underwent efficient cyclization via an intramolecular exchange...
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PMID: 20820660
PDF is available here.
PDF is available here.
Abstract
We prepared an oligodeoxyribonucleotide conjugate (5-3ant(2)18) carrying two anthracenes, each of which was tethered to both ends of the conjugate through hexamethylene linker chains. The conjugate has a mirror repeat of two heptamer sequences, such that it forms a bimolecular triplex with the singl...
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PMID: 20734012
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...
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PMID: 20838693
PDF is available here.
PDF is available here.
Abstract
Ru(ii) complexes that bring together the properties of the dppz (dipyrido[3,2-a:2',3'-c]phenazine) intercalating residue and the properties of metal-coordinating macrocycles (L = 4,4'-(2,5,8,11,14-pentaaza[15])-2,2'-bipyridilophane) have been synthesised and their protonation and affinity for copper...
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PMID: 20838679
PDF is available here.
PDF is available here.
Abstract
Ribosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the Escherichia coli 30S subunit suggest that ribosome assembly occurs via multiple parallel pathways rather than...
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PMID: 21030658
PDF is available here.
PDF is available here.
Systematic Parasitology (77)3 2010
Abstract
We also report what we interpret here as intraspecific variation in the ITS2 rDNA between individuals of E. manilensis from Lutjanus vitta recovered off the Great Barrier Reef and New Caledonia....
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PMID: 20960090
PDF is available here.
PDF is available here.
Nature Nanotechnology (5)11 2010
Abstract
We report using reconfigurable nucleic acid catalyst-based units to build a multipurpose reprogrammable molecular automaton that goes beyond single-purpose 'hard-wired' molecular automata. The automaton covers all possible responses to two consecutive sets of four inputs (such as four first and four...
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PMID: 20972436
PDF is available here.
PDF is available here.
Abstract
An efficient enzymatic synthesis of 6-chloropurine-2'-deoxyriboside from the reaction of 6-chloropurine with 2'-deoxycytidine catalyzed by nucleoside-2'-deoxyribosyltransferase (E.C. 2.4.2.6) followed by chemical conversion into the 5'-dimethoxytrityl 3'-(2-cyanoethyl-N,N-diisopropyl...
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PMID: 21128170
PDF is available here.
PDF is available here.
Abstract
MicroRNAs (miRNAs) are potent regulators of mRNA stability and thereby protein expression. As such, miRNAs have become of interest as possible therapeutics and/or therapeutic targets. In this context, small complementary miRNA sequences known as antagomirs could be used to inhibit miRNA activity, wh...
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PMID: 20978356
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...
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PMID: 20859255
PDF is available here.
PDF is available here.