X-ray structure of a DNA hairpin molecule

Abstract

We have solved the crystal structure of a synthetic DNA hexadecanucleotide of sequence: C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G, at 2.1 Å resolution, and observed that it adopts a monomeric hairpin configuration with a Z-DNA hexamer stem. In the T4 loop the bases stack with one another and with neighbouring molecules of the crystal, and not with base pairs of their own hexamer stem. Two thymine T10 rings from different molecules stack between the C1–G16 ends of a third and a fourth hairpin helix, in a manner that suggests T–T base 'pairing' and simulates a long, 13-base-pair helix. Although such T–T interactions would not be present in solution, they illustrate a remarkable tendency of thymines for self-association. Purine–purine G–A base pairs are known to exist in the anti–anti conformation with an increase in local helix width1–4; it may be that more serious consideration should be given to the possible existence of pyrimidine–pyrimidine C–T base pairs with decreased local helix width, particularly where several such base pairs occur sequentially.