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Nucleic Acids Research, 2002, Vol. 30, No. 18 4061-4067
© 2002 Oxford University Press

Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG

Ho-Leung Ng and Richard E. Dickerson*

Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA

*To whom correspondence should be addressed. Tel: +1 310 825 5864; Fax: +1 310 267 1957; Email: red{at}mbi.ucla.edu

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{leftrightarrow}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.


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