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Nucleic Acids Research, 1990, Vol. 18, No. 11 3185-3194
© 1990

CHEMISTRY

The structure and hydration of the A-DNA fragement d(GGGTACCC) at room temperature and low temperature

M. Eisenstein, F. Frolow, Z. Shakked and D. Rabinovich

Department of Structural Chemistry, The Weizmann Institute of Science Rehovot 76100, Israel

Received March 14, 1990. Accepted May 11, 1990.

The DNA fragment d(GGGTACCC) was crystallized as an A-DNA duplex in the hexagonal space group p61.The structure was analyzed at room temperature and low temperature (100K) at a esolution of 2.5 A. The helical conformations at the two temperatures are similar but the low-temperature structure is more economically hydrated than the room-temperature one. The structure of d(GGGTACCC) is compared to those of d(GGGTGCCC) and d(GGGCGCCC). This series of molecules, which consists of a mismatched duplex and its two Watson-Crick analogues, exhibits three conformational variants of the A-form of DNA, which are correlated with the specific intermolecular interactions observed In the various crystals. The largest differences in local conformation are displayed by the stacking geometries of the central pyrimldinepurfne and the flanking purine-pyrimidlne sites in each of the three duplexes. Stacking energy calculations performed on the crystal structures show that the mismatched duplex is destabilized with respect to each of the error-free duplexes, in accordance with helix-coil transition measurements.


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