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

PDB-id

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

Class

DNA

Method

NMR

Summary

Adenine-driven structural switch from two- to three-quartet DNA g-quadruplex

Reference

Lenarcic Zivkovic M, Rozman J, Plavec J (2018): "Adenine-Driven Structural Switch from a Two- to Three-Quartet DNA G-Quadruplex." Angew. Chem. Int. Ed. Engl., 57, 15395-15399. doi: 10.1002/anie.201809328.

Abstract

G-rich sequence found in the regulatory region of RANKL gene associated with homeostasis of bone metabolism folds into a two-quartet basket-type G-quadruplex stabilized by A•G•A and G•G•G base-triads. Perusal of local structural features together with G/A-to-T modifications uncovered critical role of A5 for formation of distinct antiparallel two-quartet and not three-quartet topology that would be expected based on sequence with four GGG-tracts alone. Structural changes induced by A5-to-T5 modification include a switch in orientation and relative positions of G-strands that together with anti to syn reorientation of G12 provide insights into complexity of intricate interactions that influence folding process of G-rich DNA. Understanding the impact of loop residues for overall stability and formation of G-quadruplexes advances our knowledge and ability to predict structures adopted by G-rich sequences which are involved in regulatory mechanisms in cell and may also facilitate drug design driven by structural insights.