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

Abstract

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 ofmolecules, 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 intermolecularinteractions 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 themismatched duplex is destabilized with respect to each of the error-free duplexes, in accordance with helix-coil transition measurements. © 1990 Oxford University Press.