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 A 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 width; 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.

A 6 bp Z‐DNA hairpin binds two Zα domains from the human RNA editing enzyme ADAR1

“…These data indicate that d(CG) 3 T 4 (CG) 3 exists in solution as a double-stranded d(CG) 3 stem connected through a T 4 hairpin loop. Such a hairpin has been previously found to crystallize in the Z-DNA conformation [20].…”

Energetics of the lattice: Packing elements in crystals of four-stranded intercalated cytosine-rich DNA molecules

“…and colleagues. 21 In that crystal, however, the first and the fourth thymine residues from the T 4 loop…”

Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

“…3A). Hydrogen bonds within dT•dT base pairs have been observed in single dT•dT mismatches with NMR spectroscopy (41) and predicted based on a X-ray crystal structure of two stemloop DNAs (42). Our results suggest that poly(dT)•poly(dT) forms a soft ladder-like structure with a slight left-handed helicity; interactions between the strands are disrupted under mild positive torques to form a second state that is even softer and presumably corresponds to strand-separated DNA.…”