Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG.
The crystal structure of the DNA dodecamer duplex CATGGGCCCATG lies on a structural continuum along the transition between A- and B-DNA. The dodecamer possesses the normal vector plot and inclination values typical of B-DNA, but has the crystal packing, helical twist, groove width, sugar pucker, slide and x-displacement values typical of A-DNA. The structure shows highly ordered water structures, such as a double spine of water molecules against each side of the major groove, stabilizing the GC base pairs in an A-like conformation. The different hydration of GC and AT base pairs provides a physical basis for solvent-dependent facilitation of the A<-->B helix transition by GC base pairs. Crystal structures of CATGGGCCCATG and other A/B-DNA intermediates support a 'slide first, roll later' mechanism for the B-->A helix transition. In the distribution of helical parameters in protein-DNA crystal structures, GpG base steps show A-like properties, reflecting their innate predisposition for the A conformation.
Ng
Ho-Leung
HL
Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
Dickerson
Richard E
RE
D001483:Base Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry; D006860:Hydrogen Bonding; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry; D014867:Water / Q000737:chemistry
D009838:Oligodeoxyribonucleotides; D011506:Proteins; D014867:Water; D006147:Guanine; D004247:DNA