DSSR-PyMOL cartoon-block schematics: PDB entry 6rnl

PDB-id

6rnl; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (1.88 Å)

Summary

L-[ru(tap)2(dppz)]2+ bound to the g-quadruplex forming sequence d(tagggtt)

Reference

McQuaid K, Hall JP, Baumgaertner L, Cardin DJ, Cardin CJ (2019): "Three thymine/adenine binding modes of the ruthenium complex Lambda-[Ru(TAP)2(dppz)]2+to the G-quadruplex forming sequence d(TAGGGTT) shown by X-ray crystallography." Chem.Commun.(Camb.), 55, 9116-9119. doi: 10.1039/c9cc04316k.

Abstract

Λ-[Ru(TAP)2(dppz)]2+ was crystallised with the G-quadruplex-forming heptamer d(TAGGGTT). Surprisingly, even though there are four unique binding sites, the complex is not in contact with any G-quartet surface. Two complexes stabilise cavities formed from terminal T·A and T·T mismatched pairs. A third shows kinking by a TAP ligand between T·T linkages, while the fourth shows sandwiching of a dppz ligand between a T·A/T·A quadruplex and a T·T mismatch, stabilised by an additional T·A base pair stacking interaction on a TAP surface. Overall, the structure shows an unexpected affinity for thymine, and suggests models for G-quadruplex loop binding.