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Nucleic Acids Research, 1978, Vol. 5, No. 1 127-137
© 1978

Articles

Helix geometry of single stranded DNA ‘A’ and ‘B’ forms from minimum energy conformations of dimeric subunits

B. Hingerty{dagger} and S. Broyde*

{dagger}MRC Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK *Biology Department New York University, Washington Square, New York, NY 10003, USA

Received September 30, 1977. Low energy conformations with dihedral angles similar to those occurring in fibers of the ‘A’and ‘B’ forms of DNAs have been calculated for the deoxydinucleoside phosphates dApdA, dCpdC, dTpdT, dGpdG and dGpdC (1–3). These conformers have been used as building blocks for generating larger single stranded polymers, whose helical parameters we have calculated. We find that single stranded ‘A’ and ‘B’ form helices tend to be narrower and more tightly wound than the duplexes obtained in fibers (4,5). This is consistent with experimental observations on single stranded fibers of poly (rC) (6). We also find that the different sequences have different helix geometries. In addition, it is observed that large variations in helix geometry for a given sequence are achievable at little energetic cost.


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