The molecular structure of d(ICpCpGpG), a fragment of right-handed double helical A-DNA

Abstract

The DNA tetramer d(Iodo-CpCpGpG) or ICCGG crystallizes as a double-stranded 4-base pair (bp) segment of an A helix. Two such tetramer helices are packed together in the crystal with local helix axes nearly coincident, simulating an 8-bp helix, and 4 such octamers make up the tetragonal unit cell. Restrained energy and reciprocal space refinement has led to an R factor of 20.5% at 2.1 .ANG. resolution. The ICCGG helix has a twist corresponding to 10.7 bp/turn, a 19.degree. base tilt and a 2.3 .ANG. rise/base pair along the helix axis. The mean propeller twist of 18.degree. is comparable with, and has the same rotational sense as that observed in the B-DNA dodecamer CGCGAATTCGCG at similarly high alcohol concentration. Backbone phosphate groups in A-DNA are extensively hydrated, including a network across the opening of the major groove, whereas base edge N and O groups in major and minor grooves are less hydrated than in B-DNA. The minor groove spine of hydration observed in B-DNA is totally absent. These observations of relative hydration confirm and extend the model for the B-to-A helix transition proposed earlier on the basis of the B helix structure.