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Nucleic Acids Research, 1989, Vol. 17, No. 8 3229-3245
© 1989

MOLECULAR BIOLOGY

The propeller DNA conformation of poly(dA).poly(dT)

Joan Aymami, Miquel Coll, Christin A. Frederick, Andrew H.-J. Wang+ and Alexander Rich*

Department of Biology, Massachusetts Institute of Technology Cambridge, MA 02139, USA

*To whom correspondence should be addressed

Received October 26, 1988. Revised March 17, 1989. Accepted March 17, 1989.

Physical properties of the DNA duplex, poly(dA).poly(dT) differ considerably from the alternating copolymer poly(dAT). A number of molecular models have been used to describe these structures obtained from fiber X-ray diffraction data. The recent solutions of single crystal DNA dodecamer structures with segments of oligo-A.oligo-T have revealed the presence of a high propeller twist in the AT regions which is stabilized by the formation of bifurcated (three-center) hydrogen bonds on the floor of the major groove, involving the N6 amino group of adenine hydrogen bonding to two 04 atoms of adjacent thymine residues on the opposite strand. Here we show that it is possible to incorporate the features of the single crystal analysis, specifically high propeller twist, bifurcated hydrogen bonds, and a narrow minor groove, as well as the close interstrand N signal between adenine HC2 and ribose HC1' of the opposite strand, into a model that is fully compatible with the diffraction data obtained from poly(dA) poly(dT).

*Present address: Department of Physiology and Biophysics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA


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