Geometries of Watson-Crick and Curtis (Hoogsteen) DNA Base Pairs

For further details, see New Scientist, May 16, 1998.

To view these models, install either (a) the Chime or (b) the Chem3D Net plug-in for your browser. Using the former, you will be able to highlight bonds using the button boxes below. Using the latter, you will be able to measure bond lengths, angles, etc. Calculations were performed using the PM3 Quantum mechanical method, with energies expressed in kcal mol-1. More accurate calculations (see below) give similar results.
Thymine-Adenine/Watson-CrickCytosine-Guanine/Watson-Crick
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DH -26.4. Note the weak C-H...O interaction in the WC structure DH -18.5. This has 3 strong hydrogen bonds
Thymine-Adenine/Hoogsteen-CurtisCytosine-Guanine/Curtis
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DH -27.4. The Curtis structure transforms to one with a weak C-H...O bond,
and two stronger conventional bonds (Hoogsteen) 		DH -14.4. This is the only geometry with no strong hydrogen bond to oxygen

For some examples of DNA base pairing as proven using x-ray/neutron diffraction crystallography, see this panel. An excellent article on the relative geometries and energies of Watson-Crick vs Hoogsteen pairing is to be found by I. R. Gould and P. A. Kollman, J. Am. Chem. Soc., 1994, 116, 2493. In this article, the Hoogsteen AT base pair is also predicted to be 1 kcal/mol more stable than the Watson-Crick pairing. It is thought however that the Watson-Crick model derives greater stabilisation from the base-base stacking energies than does the Hoogsteen model. The Curtis model differs from the Hoogsteen model in the (most unlikely) formation of a C-H..O hydrogen bond in preference to the N-H...O bond. The see-saw (pivoted about the central N-H...N bond) comes down firmly on the side of the N-H... bond!!
See also the Molecule-of-the-Month display on Viagra, where hydrogen bonding plays a key role in controlling the orientation of the molecule.
(c) H. S. Rzepa, 19 May, 1998.