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Nucleic Acids Research, 1990, Vol. 18, No. 9 2759-2767
© 1990

Molecular Biology

Molecular structure of deoxycytidyl–3'– ethylphosphonate (RP) 5'–deoxyguanidine, d[Cp(CH3)G]. A neutral dinucleotide with Watson-Crick base pairing and a right handed helical twist

Fusen Han, William Watt, David J. Duchamp*, Larry Callahan+,1, Ferenc J. Kézdy§,1 and Kan Agarwal1

Physical and Analytical Chemistry Research, The Upjohn Company Kalamazoo Ml 49001 1Departments of Chemistry and Biochemistry and Molecular Biology, The University of Chicago, Chicago IL 60637, USA

*To whom correspondence should be addressed

Received November 20, 1989. Accepted February 21, 1990.

The crystal structure of d[Cp(CH3)G] has been determined as part of a project to study the mechanism of the B-Z transition in DNA. The asymmetric unit contains two dinucleotldes and the equivalent of 7.5 water molecules, partially disordered over 12 definable positions. The two symmetry-independent dinucleotides form a duplex with Watson-Crick basepairing and a right-handed helical sense. Comparison with previously determined structures of the B and A conformation showed that this duplex is closer to B than to A but significantly different from B. It corresponds to a stretched out helix with a 4 A rise per base pair and a helical twist of 32°. This structure may serve as a model for the bending of DNA in certain situations. The configuration at the methyl phosphonate is RP, and a mechanism, based on this assignment, is presented for the B–Z transition in DNA.

+Present address: Division of Cytolrine Biology, Center for Biologies, Food and Drug Administration, Bethesda, MD 20892, USA

§Present address. Biopolymer Chemistry Research, The Upjohn Company, Kalamazoo, MI 49001, USA


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