5O4D

G-quadruplex of Human papillomavirus type 52

Summary for 5O4D

• Entry DOI: 10.2210/pdb5o4d/pdb
• NMR Information: BMRB: 34145
• Descriptor: DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3') (1 entity in total)
• Functional Keywords: g-quadruplex, dna, hpv52
• Biological source: Human papillomavirus type 52
• Total number of polymer chains: 1
• Total formula weight: 7276.68

Authors

Marusic, M.,Plavec, J. (deposition date: 2017-05-29, release date: 2018-06-13, Last modification date: 2024-05-15)

Primary citation

Marusic, M.,Plavec, J.
Towards Understanding of Polymorphism of the G-rich Region of Human Papillomavirus Type 52.
Molecules, 24:-, 2019

PubMed Abstract: The potential to affect gene expression via G-quadruplex stabilization has been extended to all domains of life, including viruses. Here, we investigate the polymorphism and structures of G-quadruplexes of the human papillomavirus type 52 with UV, CD and NMR spectroscopy and gel electrophoresis. We show that oligonucleotide with five G-tracts folds into several structures and that naturally occurring single nucleotide polymorphisms (SNPs) have profound effects on the structural polymorphism in the context of G-quadruplex forming propensity, conformational heterogeneity and folding stability. With help of SNP analysis, we were able to select one of the predominant forms, formed by G-rich sequence d(G₃TAG₃CAG₄ACACAG₃T). This oligonucleotide termed HPV52 adopts a three G-quartet snap back (3 + 1) type scaffold with four guanine residues, two edgewise loops spanning the same groove, a no-residue V loop and a propeller type loop. The first guanine residue is incorporated in the central G-quartet and all four-guanine residues from G4 stretch are included in the three quartet G-quadruplex core. Modification studies identified several structural elements that are important for stabilization of the described G-quadruplex fold. Our results expand set of G-rich targets in viral genomes and address the fundamental questions regarding folding of G-rich sequences.

PubMed: 30987050
DOI: 10.3390/molecules24071294

Experimental method

SOLUTION NMR