DSSR-PyMOL cartoon-block schematics: PDB entry 6r9k

PDB-id

6r9k; SNAP-derived features in text and JSON formats

Class

DNA

Method

NMR

Summary

A quadruplex hybrid structure with lpp loop orientation and 3 syn residues

Reference

Karg B, Mohr S, Weisz K (2019): "Duplex-Guided Refolding into Novel G-Quadruplex (3+1) Hybrid Conformations." Angew.Chem.Int.Ed.Engl., 58, 11068-11071. doi: 10.1002/anie.201905372.

Abstract

The oligomer d(GCGTG₃ TCAG₃ TG₃ TG₃ ACGC) with short complementary flanking sequences at the 5'- and 3'-ends was shown to fold into three different DNA G-quadruplex species. In contrast, a corresponding oligomer that lacks base complementarity between the two overhang sequences folds into a single parallel G-quadruplex. The three coexisting quadruplex structures were unambiguously identified and structurally characterized through detailed spectral comparisons with well-defined G-quadruplexes formed upon the deliberate incorporation of syn-favoring 8-bromoguanosine analogues into specific positions of the G-core. Two (3+1) hybrid structures coexist with the parallel fold and feature a novel lateral-propeller-propeller loop architecture that has not yet been confirmed experimentally. Both hybrid quadruplexes adopt the same topology and only differ in their pattern of anti→syn transitions and tetrad stackings.