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

Abstract

The DNA tetramer d(^ICpCpGpG) 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 four 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 Å resolution. The ^ICCGG helix has a twist corresponding to 10.7 bp per turn, a 19° base tilt and a 2.3 Å rise per base pair along the helix axis. The mean propeller twist of 18° 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.