DSSR-derived G-quadruplex features in PDB entry 5o4d
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- G-quadruplex of human papillomavirus type 52
- Marusic, M., Plavec, J.: (2019) "Towards Understanding of Polymorphism of the G-rich Region of Human Papillomavirus Type 52." Molecules, 24
- 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.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-LwX+P), UD3(1+3), UDDD
1 glyco-bond=s--- groove=w--n planarity=0.324 type=other nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG13 2 glyco-bond=-ss- groove=w-n- planarity=0.525 type=bowl nts=4 GGGG A.DG2,A.DG6,A.DG20,A.DG12 3 glyco-bond=-s-- groove=wn-- planarity=0.398 type=other nts=4 GGGG A.DG8,A.DG11,A.DG14,A.DG22
In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.
Helix#1, 3 G-tetrad layers, INTRA-molecular, with 1 stem
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.
Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDDD, anti-parallel, 2(-LwX+P), UD3(1+3)
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=lateral helix=#1 nts=4 GCAG A.DG8,A.DC9,A.DA10,A.DG11 2 type=V-shaped helix=#1 nts=4 GGGG A.DG11,A.DG12,A.DG13,A.DG14