Towards Understanding of Polymorphism of the G-rich Region of Human Papillomavirus Type 52

Molecules. 2019 Apr 2;24(7):1294. doi: 10.3390/molecules24071294.


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(1-4) adopts a three G-quartet snap back (3 + 1) type scaffold with four syn 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.

Keywords: DNA; G-quadruplex; NMR; folding; human papillomaviruses; structure.

MeSH terms

  • DNA / chemistry
  • DNA / genetics*
  • G-Quadruplexes
  • Humans
  • Magnetic Resonance Spectroscopy
  • Nucleic Acid Conformation
  • Papillomaviridae / genetics*
  • Polymorphism, Single Nucleotide / genetics*
  • Structure-Activity Relationship


  • DNA