Sequence-dependent DNA deformability studied using molecular dynamics simulations Export

@article{citeulike:1735956, abstract = {Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during proteinDNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of proteinDNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids. 10.1093/nar/gkm627}, author = {Fujii, Satoshi and Kono, Hidetoshi and Takenaka, Shigeori and Go, Nobuhiro and Sarai, Akinori}, citeulike-article-id = {1735956}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkm627}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/35/18/6063}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17766249}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17766249}, day = {30}, doi = {10.1093/nar/gkm627}, journal = {Nucl. Acids Res.}, keywords = {cap\_dna, dna, molecular\_dynamics}, month = {August}, pages = {gkm627+}, posted-at = {2008-09-15 11:02:35}, priority = {2}, title = {Sequence-dependent DNA deformability studied using molecular dynamics simulations}, url = {http://dx.doi.org/10.1093/nar/gkm627}, year = {2007} }

TY - JOUR ID - citeulike:1735956 L3 - citeulike-article-id:1735956 N2 - Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during proteinDNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of proteinDNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids. 10.1093/nar/gkm627 JF - Nucl. Acids Res. TI - Sequence-dependent DNA deformability studied using molecular dynamics simulations SP - gkm627 KW - cap_dna KW - dna KW - molecular_dynamics AU - Fujii, Satoshi AU - Kono, Hidetoshi AU - Takenaka, Shigeori AU - Go, Nobuhiro AU - Sarai, Akinori PY - 2007/08/30/ UR - http://dx.doi.org/10.1093/nar/gkm627 ER -