Dynamics of B-DNA on the Microsecond Time Scale Export

@article{citeulike:2136245, abstract = {Abstract: We present the first microsecond MD simulation of B-DNA. Trajectory shows good agreement with available data and clarifies the s dynamics of DNA. The duplex is sampling the B-conformation, but many relevant local transitions are found, including S N repuckers (up to 7 N-sugars are found simultaneously), local BII transitions (15\% of the dinucleotides are in BII-form; some of these forms are stable for up to 7 ns), and sequence-dependent / transitions (happening in the 7-50 ns time scale, and being stable for up to 80 ns). Partial and total openings are often detected, but no base flipping is found. A·T openings happen after amplification of propeller twist movements, while G·C pairs (which can be opened for up to 1 ns) are opened by a complex mechanism which is often catalyzed by cations. A high affinity Na+ binding site is found in the center of the minor groove. Access to this site by cations is difficult (average entry time 400 ns), but once inside, the ion remains for long periods of time (10-15 ns), producing a sizable narrowing of the minor groove. The essential dynamics of DNA fits well with the pattern of deformation needed to (i) sample uncommon right-handed forms and (ii) sample conformations adopted by DNA when bound to proteins. Clearly, DNA has evolved to be not only a stable structure able to maintain and transmit the genetic information but also a flexible entity whose intrinsic pattern of deformability matches its functional needs.}, address = {Contribution from the Institut de Recerca Biom\`{e}dica and Instituto Nacional de Bioinformtica, Parc Cient\'{\i}fic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, Computational Biology Program, Barcelona Supercomputer Center, Jordi Girona 31, Edifici Torre Girona, Barcelona 08028, Spain, Departament de Fisicoqu\'{\i}mica, Facultat de Farm\`{a}cia, Avgda Diagonal sn, Barcelona 08028, Spain, and Departament de Bioqu\'{\i}mica, Facultat de Biolog\'{\i}a, Avgda Diagonal 647, Barcelona 08028, Spain}, author = {Perez, A. and Luque, F. J. and Orozco, M.}, citeulike-article-id = {2136245}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/ja0753546}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ja0753546}, day = {28}, doi = {10.1021/ja0753546}, journal = {J. Am. Chem. Soc.}, keywords = {dna, dna\_md}, month = {November}, number = {47}, pages = {14739--14745}, posted-at = {2008-12-24 21:10:03}, priority = {2}, title = {Dynamics of B-DNA on the Microsecond Time Scale}, url = {http://dx.doi.org/10.1021/ja0753546}, volume = {129}, year = {2007} }

TY - JOUR ID - citeulike:2136245 L3 - citeulike-article-id:2136245 N2 - Abstract: We present the first microsecond MD simulation of B-DNA. Trajectory shows good agreement with available data and clarifies the s dynamics of DNA. The duplex is sampling the B-conformation, but many relevant local transitions are found, including S N repuckers (up to 7 N-sugars are found simultaneously), local BII transitions (15% of the dinucleotides are in BII-form; some of these forms are stable for up to 7 ns), and sequence-dependent / transitions (happening in the 7-50 ns time scale, and being stable for up to 80 ns). Partial and total openings are often detected, but no base flipping is found. A·T openings happen after amplification of propeller twist movements, while G·C pairs (which can be opened for up to 1 ns) are opened by a complex mechanism which is often catalyzed by cations. A high affinity Na+ binding site is found in the center of the minor groove. Access to this site by cations is difficult (average entry time 400 ns), but once inside, the ion remains for long periods of time (10-15 ns), producing a sizable narrowing of the minor groove. The essential dynamics of DNA fits well with the pattern of deformation needed to (i) sample uncommon right-handed forms and (ii) sample conformations adopted by DNA when bound to proteins. Clearly, DNA has evolved to be not only a stable structure able to maintain and transmit the genetic information but also a flexible entity whose intrinsic pattern of deformability matches its functional needs. IS - 47 JF - J. Am. Chem. Soc. AD - Contribution from the Institut de Recerca Biomèdica and Instituto Nacional de Bioinformtica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, Computational Biology Program, Barcelona Supercomputer Center, Jordi Girona 31, Edifici Torre Girona, Barcelona 08028, Spain, Departament de Fisicoquímica, Facultat de Farmàcia, Avgda Diagonal sn, Barcelona 08028, Spain, and Departament de Bioquímica, Facultat de Biología, Avgda Diagonal 647, Barcelona 08028, Spain EP - 14745 TI - Dynamics of B-DNA on the Microsecond Time Scale VL - 129 SP - 14739 KW - dna KW - dna_md AU - Perez, A AU - Luque, FJ AU - Orozco, M PY - 2007/11/28/ UR - http://dx.doi.org/10.1021/ja0753546 ER -