DNA conformations and their sequence preferences.
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.
Svozil
Daniel
D
Institute 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, Czech Republic.
Kalina
Jan
J
Omelka
Marek
M
Schneider
Bohdan
B
D001483:Base Sequence; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D044704:DNA, A-Form / Q000737:chemistry; D045566:DNA, Cruciform / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry; D003854:Deoxyribonucleotides / Q000737:chemistry; D054856:G-Quadruplexes; D008024:Ligands; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry; D012313:RNA / Q000737:chemistry
D044704:DNA, A-Form; D045566:DNA, Cruciform; D004268:DNA-Binding Proteins; D003854:Deoxyribonucleotides; D008024:Ligands; D009707:Nucleosomes; D012313:RNA; D003596:Cytosine; D004247:DNA