DSSR-PyMOL cartoon-block schematics: PDB entry 4ltk

PDB-id

4ltk; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (1.45 Å)

Summary

Dehydration-rehydration of a nucleic acid system containing a polypyridyl ruthenium complex at 74% relative humidity (6-7)

Reference

Hall JP, Sanchez-Weatherby J, Alberti C, Quimper CH, O'Sullivan K, Brazier JA, Winter G, Sorensen T, Kelly JM, Cardin DJ, Cardin CJ (2014): "Controlled Dehydration of a Ruthenium Complex-DNA Crystal Induces Reversible DNA Kinking." J.Am.Chem.Soc., 136, 17505-17512. doi: 10.1021/ja508745x.

Abstract

Hydration-dependent DNA deformation has been known since Rosalind Franklin recognized that the relative humidity of the sample had to be maintained to observe a single conformation in DNA fiber diffraction. We now report for the first time the crystal structure, at the atomic level, of a dehydrated form of a DNA duplex and demonstrate the reversible interconversion to the hydrated form at room temperature. This system, containing d(TCGGCGCCGA) in the presence of Λ-[Ru(TAP)2(dppz)](2+) (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine), undergoes a partial transition from an A/B hybrid to the A-DNA conformation, at 84-79% relative humidity. This is accompanied by an increase in kink at the central step from 22° to 51°, with a large movement of the terminal bases forming the intercalation site. This transition is reversible on rehydration. Seven data sets, collected from one crystal at room temperature, show the consequences of dehydration at near-atomic resolution. This result highlights that crystals, traditionally thought of as static systems, are still dynamic and therefore can be the subject of further experimentation.