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Nucleic Acids Research, 1989, Vol. 17, No. 1 55-72
© 1989

CHEMISTRY

Refined crystal structure of an octanucleotide duplex with I.T. mismatched base pairs

W.B.T. Cruse, J. Aymani, Olga Kennard*, Tom Brown1,*, Audrey G.C. Jack1 and G.A. Leonard1

University Chemical Laboratory Lensfield Road, Cambridge CB2 1EW 1Department of Chemistry, University of Edinburgh West Mains Road, Edinburgh EH9 3JJ, UK

*To whom correspondence should be addressed

Received October 28, 1988. Revised December 5, 1988. Accepted December 5, 1988.

The structure of the synthetic deoxyoctamer d(GGIGCTCC) has been determined by single crystal X-ray diffraction techniques to a resolution of 1.7Å. The sequence crystallises in space group P61, with unit cell dimensions a = b = 45.07, c = 45.49Å. The refinement converged with a crystallographic residual R = 0.14 and the location of 81 solvent molecules. The octamer forms an A-DNA duplex with 6 Watson-Crick (G.C) base pairs and 2 inosine-thymine (I.T) pairs. Refinement of the structure shows it to be essentially isomorphous with that reported for d(GGGGCTCC) with the mispairs adopting a "wobble" conformation.

Conformational parameters and base stacking interactions are compared to those for the native duplex d(GGGGCCCC) and other similar sequences. A rationale for the apparent increased crystal packing efficiency and lattice stability of the I.T octamer is given.


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