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Nucleic Acids Research Advance Access originally published online on May 13, 2008
Nucleic Acids Research 2008 36(11):3690-3706; doi:10.1093/nar/gkn260
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Nucleic Acids Research, 2008, Vol. 36, No. 11 3690-3706
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

DNA conformations and their sequence preferences

Daniel Svozil1, Jan Kalina2, Marek Omelka2 and Bohdan Schneider1,*

1Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, CZ-166 10 Prague and 2Jaroslav Hájek Center for Theoretical and Applied Statistics, Department of Probability and Mathematical Statistics, Faculty of Mathematics and Physics, Charles University, Sokolovská 83, CZ-186 75 Prague, Czech Republic

*To whom correspondence should be addressed. Tel: +420 728 303 566; Fax: +420 296 443 610; Email: bohdan{at}rcsb.rutgers.edu, bohdan.schneider{at}uochb.cas.cz

Received March 5, 2008. Revised April 17, 2008. Accepted April 18, 2008.

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.


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