DNA conformations and their sequence preferences

@article{citeulike:2795271, abstract = {The geometry of the phosphodiester backbone was analyzed for 7739 dinucleotides from 447 selected crystal structures of naked and complexed DNA. Ten torsion angles of a near-dinucleotide unit have been studied by combining Fourier averaging and clustering. Besides the known variants of the A-, B- and Z-DNA forms, 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 helices. A comparison of the populations of the conformers occurring in naked and complexed DNA has revealed a significant broadening of the DNA conformational space in the complexes, but the conformers still remain within the limits defined by the A- and B- forms. Possible sequence preferences, important for sequence-dependent recognition, have been assessed for the main A and B conformers by means of statistical goodness-of-fit tests. The structural properties of the backbone in quadruplexes, junctions and histone-core particles are discussed in further detail. 10.1093/nar/gkn260}, author = {Svozil, Daniel and Kalina, Jan and Omelka, Marek and Schneider, Bohdan }, citeulike-article-id = {2795271}, doi = {10.1093/nar/gkn260}, journal = {Nucl. Acids Res.}, keywords = {dna}, month = {May}, pages = {gkn260+}, posted-at = {2008-05-13 16:06:34}, priority = {2}, title = {DNA conformations and their sequence preferences}, url = {http://dx.doi.org/10.1093/nar/gkn260}, year = {2008} }

TY - JOUR ID - citeulike:2795271 L3 - citeulike-article-id:2795271 TI - DNA conformations and their sequence preferences JF - Nucl. Acids Res. SP - gkn260 N2 - The geometry of the phosphodiester backbone was analyzed for 7739 dinucleotides from 447 selected crystal structures of naked and complexed DNA. Ten torsion angles of a near-dinucleotide unit have been studied by combining Fourier averaging and clustering. Besides the known variants of the A-, B- and Z-DNA forms, 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 helices. A comparison of the populations of the conformers occurring in naked and complexed DNA has revealed a significant broadening of the DNA conformational space in the complexes, but the conformers still remain within the limits defined by the A- and B- forms. Possible sequence preferences, important for sequence-dependent recognition, have been assessed for the main A and B conformers by means of statistical goodness-of-fit tests. The structural properties of the backbone in quadruplexes, junctions and histone-core particles are discussed in further detail. 10.1093/nar/gkn260 KW - dna AU - Svozil, Daniel AU - Kalina, Jan AU - Omelka, Marek AU - Schneider, Bohdan PY - 2008/05/13/ UR - http://dx.doi.org/10.1093/nar/gkn260 ER -