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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.
DNA, A-Form (0):
Recent article
DNA, A-Form
Abstract
Most of the dinucleotide steps in free DNA display high flexibility, assuming different conformations in a sequence-dependent fashion. With the exception of the AA/TT and GA/TC steps, which are 'A-phobic', and the GG/CC step, which is 'A-philic', the dinucleotide steps show no preference for A or B...
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PMID: 19393049
PDF is available here.
PDF is available here.
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ChemPhysChem (9)18 2008
Abstract
In recent years, significant progress has been made towards uncovering the physical mechanisms of low-hydration polymorphism in double-helical DNA. The effect appears to be mechanistically similar in different biological systems, and it is due to the ability of water to form spanning H-bonded networ...
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PMID: 19006154
PDF is available here.
PDF is available here.
Biophysical Journal (95)1 2008
Abstract
We predict that the mechanism of the transition involves a series of A/B hybrid forms and is sequential in nature, similar to previous crystallographic studies of derivatized duplexes. A simulation in which waters were restrained in the major groove of B DNA shows a rapid, spontaneous change from B...
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PMID: 18326653
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)11 2008
Abstract
We have also identified combined A + B backbone-deformed conformers, e.g. with alpha/gamma switches, and a few conformers with a syn orientation of bases occurring e.g. in G-quadruplex structures. A plethora of A- and B-like conformers show a close relationship between the A- and B-form double helic...
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PMID: 18477633
PDF is available here.
PDF is available here.
The Journal of Chemical Physics (128)19 2008
Abstract
Elastic scattering of 5-30 eV electrons within the B-DNA 5'-CCGGCGCCGG-3' and A-DNA 5'-CGCGAATTCGCG-3' DNA sequences is calculated using the separable representation of a free-space electron propagator and a curved wave multiple scattering formalism. The disorder brought about by the surrounding wat...
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PMID: 18500900
PDF is available here.
PDF is available here.
Abstract
We examined the effect of 5-bromouracil on nucleosome positioning in vivo using TALS plasmid in yeast cells. This plasmid can stably and precisely be assembled nucleosomes aided by the alpha2 repressor complex bound to its alpha2 operator. Insertion of AT-rich sequences into a site near the operator...
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PMID: 18258180
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)6 2008
Abstract
We have determined the structure of fully modified 4'-thioDNA with the sequence of d(CGCGAATTCGCG) by NMR. Most sugars take on the C3'-endo conformation. The major groove is narrow and deep, while the minor groove is wide and shallow. Thus, fully modified 4'-thioDNA takes on the A-form characteristi...
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PMID: 18252770
PDF is available here.
PDF is available here.
Abstract
The dynamics of ions and water at the surface of DNA are studied by computer simulations in a wide range of hydrations involving the zone of low-hydration polymorphism in DNA. The long-range mobility of ions exhibits a stepwise increase at three distinct hydration levels. The first of them is close...
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PMID: 18052374
PDF is available here.
PDF is available here.
FEBS Letters (581)30 2007
Abstract
Three types of DNA: approximately 2700 bp polydeoxyguanylic olydeoxycytidylic acid [poly(dG)-poly(dC)], approximately 2700 bp polydeoxyadenylic polydeoxythymidylic acid [poly(dA)-poly(dT)] and 2686 bp linear plasmid pUC19 were deposited on a mica surface and imaged by atomic force microscopy. Contou...
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PMID: 18053809
PDF is available here.
PDF is available here.
Abstract
We examined short deoxyribooligonucleotide duplexes containing single, site-specific cross-link by Raman spectroscopy and assigned the spectral alterations to conformational changes induced in DNA by 1,2-GG or 1,3-GTG intrastrand CLs determined earlier by other biochemical and biophysical methods. T...
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PMID: 17321149
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (111)22 2007
Abstract
A comprehensive conformational analysis of isolated 2'-beta-deoxy-6-azacytidine (d6AC), an analogue of therapeutically active 6-azacytidine (6AC), has been performed by means of ab initio calculations at the MP2/6-311++G(2df,pd)//DFT B3LYP/6-31G(d,p) level of theory. Among the 81 conformers located...
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PMID: 17503799
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)6 2007
Abstract
We have determined the X-ray crystal structures of DNA:DNA duplexes containing either (N)U or (N)U(m) and of DNA:RNA hybrid duplexes containing (N)U(m). The aminohexyl chains are fixed in the major groove through hydrogen bonds between the carbamoyl amino groups and the uracil O4 atoms. The terminal...
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PMID: 17341465
PDF is available here.
PDF is available here.
Biophysical Chemistry (125)1 2007
Abstract
We induced the B-to-A conformational transition by ethanol in a linearized pUC19 DNA. A primer extension method was used in combination with UV light irradiation to follow the transition, based on pausing of DNA synthesis due to the presence of damaged bases in the template. Primer extension data hi...
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PMID: 16962700
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)10 2007
Abstract
We explore here the possibility of determining theoretically the free energy change associated with large conformational transitions in DNA, like the solvent-induced B<-->A conformational change. We find that a combination of targeted molecular dynamics (tMD) and the weighted histogram analysis meth...
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PMID: 17459891
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)14 2007
Abstract
The behaviour of the d(GGTATACC) oligonucleotide has been investigated by X-ray crystallography at 295 K in the range from ambient pressure to 2 GPa (approximately 20,000 atm). Four 3D-structures of the A-DNA form (at ambient pressure, 0.55, 1.09 and 1.39 GPa) were refined at 1.60 or 1.65 A resoluti...
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PMID: 17617642
PDF is available here.
PDF is available here.
Abstract
We examined now an ultraweak thermalized neutron field (UTNF) affects the structural transformation in DNA macromolecules at room temperature. IR-spectroscopy, electrophoresis, and filtration through nitrocellulose filter measurements revealed that UTNF irradiation with a fluence of F(n) - 1.0 - 3.7...
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PMID: 17969916
PDF is available here.
PDF is available here.
Physical Review Letters (97)26 2006
Abstract
We demonstrate apertureless near-field microscopy of single molecules at sub-10 nm resolution. With a novel phase filter, near-field images of single organic fluorophores were obtained with approximately sixfold improvement in the signal-to-noise ratio. The improvement allowed pairs of molecules sep...
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PMID: 17280412
PDF is available here.
PDF is available here.
Mathematical Biosciences (204)1 2006
Abstract
We investigate the use of algebraic state-space models for the sequence dependent properties of DNA. By considering the DNA sequence as an input signal, rather than using an all atom physical model, computational efficiency is achieved. A challenge in deriving this type of model is obtaining its str...
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PMID: 16603205
PDF is available here.
PDF is available here.
Nucleic Acids Research (34)13 2006
Abstract
We report here, for the first time, that DNA destabilization and conformational transition induced by SWNTs are sequence-dependent. Contrasting changes for SWNTs binding to poly[dGdC]:poly[dGdC] and poly[dAdT]:poly[dAdT] were observed. For GC homopolymer, DNA melting temperature was decreased 40 deg...
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PMID: 16885240
PDF is available here.
PDF is available here.
Abstract
The dynamics of the B-A transition of DNA double helices with different GC contents and various chain lengths has been characterized by an electric field pulse technique. The field-induced B-A reaction is separated from orientation effects using the magic angle technique. Amplitudes reflecting the B...
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PMID: 16287299
PDF is available here.
PDF is available here.
ChemBioChem (6)8 2005
Abstract
Biopolymers (78)3 2005
Abstract
We have shown that the stretched intermediate model of the B-Z transition is more probable than other B-Z transition models such as the Harvey model. This is accomplished by comparing potential energy profiles of various B-Z DNA transition models and calculating relative probabilities based on the s...
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PMID: 15759288
PDF is available here.
PDF is available here.
Abstract
The interconversion between the well-characterized A- and B-forms of DNA is a structural transition for which the intermediate states and the free energy difference between the two endpoints are not known precisely. In the present study, the difference between the Root Mean Square Distance (RMSD) fro...
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PMID: 15869310
PDF is available here.
PDF is available here.
Biophysical Journal (88)5 2005
Abstract
DNA geometry depends on relative humidity. Using the CHARMM22 force field to push B-DNA to A-DNA, a molecular dynamics simulation of a mixed-sequence 24-basepair DNA double-stranded oligomer, starting from B-DNA, was carried out to explore both the mechanism of the transition and the evolution of hy...
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PMID: 15749779
PDF is available here.
PDF is available here.
Nucleic Acids Research (33)1 2005
Abstract
We illustrate properties of the method with the B-A conformational transition induced by ethanol in linearized pUC19 plasmid DNA. At various ethanol concentrations, the DNA was irradiated with ultraviolet light, transferred to a restriction endonuclease buffer and the irradiated DNA was cleaved by 1...
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PMID: 15644308
PDF is available here.
PDF is available here.
Biochemistry (Washington) (43)30 2004
Abstract
Members of the Sso7d/Sac7d protein family and other related proteins are believed to play an important role in DNA packaging and maintenance in archeons. Sso7d/Sac7d are small, abundant, basic, and nonspecific DNA-binding proteins of the hyperthermophilic archeon Sulfolobus. Structures of several co...
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PMID: 15274614
PDF is available here.
PDF is available here.
Journal of Molecular Biology (332)5 2003
Abstract
We have constructed the potential energy surfaces for all unique tetramers, hexamers and octamers in double helical DNA, as a function of the two principal degrees of freedom, slide and shift at the central step. From these potential energy maps, we have calculated a database of structural and flexi...
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PMID: 14499606
PDF is available here.
PDF is available here.
Biophysical Journal (85)3 2003
Abstract
DNA structure is known to be sensitive to hydration and ionic environment. To explore the dynamics, hydration, and ion binding features of A-tract sequences, a 7-ns Molecular dynamics (MD) study has been performed on the dodecamer d(CGCAAATTTGCG)(2). The results suggest that the intrusion of Na(+) i...
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PMID: 12944294
PDF is available here.
PDF is available here.