6ZRM

G-quadruplex with a G-A bulge

Summary for 6ZRM

• Entry DOI: 10.2210/pdb6zrm/pdb
• NMR Information: BMRB: 34529
• Descriptor: DNA (5'-D(*TP*GP*GP*GP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*TP*GP*GP*G)-3') (1 entity in total)
• Functional Keywords: g-quadruplex structure bulge osteoporosis, dna
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 6401.11

Authors

Lenarcic Zivkovic, M.,Plavec, J. (deposition date: 2020-07-13, release date: 2021-05-26, Last modification date: 2024-05-15)

Primary citation

Lenarcic Zivkovic, M.,Rozman, J.,Plavec, J.
Structure of a DNA G-Quadruplex Related to Osteoporosis with a G-A Bulge Forming a Pseudo-loop .
Molecules, 25:-, 2020

PubMed Abstract: Bone remodeling is a fine-tuned process principally regulated by a cascade triggered by interaction of receptor activator of NF-κB (RANK) and RANK ligand (RANKL). Excessive activity of the gene leads to increased bone resorption and can influence the incidence of osteoporosis. Although much has been learned about the intracellular signals activated by RANKL/RANK complex, significantly less is known about the molecular mechanisms of regulation of expression. Here, we report on the structure of an unprecedented DNA G-quadruplex, well-known secondary structure-mediated gene expression regulator, formed by a G-rich sequence found in the regulatory region of a gene. Solution-state NMR structural study reveals the formation of a three-layered parallel-type G-quadruplex characterized by an unique features, including a G-A bulge. Although a guanine within a G-tract occupies glycosidic conformation, bulge-forming residues arrange in a conformation to facilitate partial 5/6-ring stacking, typical of G-quadruplex structures with parallel G-tracts orientation. Such distinctive structural features protruding from the core of the structure can represent a novel platform for design of highly specific ligands with anti-osteoporotic function. Additionally, our study suggests that the expression of gene may be regulated by putative folding of its G-rich region into non-B-DNA structure(s).

PubMed: 33096904
DOI: 10.3390/molecules25204867

Experimental method

SOLUTION NMR