6KVB

Structure of an intra-locked G-quadruplex

Summary for 6KVB

• Entry DOI: 10.2210/pdb6kvb/pdb
• Descriptor: DNA (28-mer) (1 entity in total)
• Functional Keywords: dna g-quadruplex, intra-locked, irregular g-rich motif, nmr spectroscopy, dna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 8872.65

Authors

Maity, A.,Winnerdy, F.R.,Chang, W.D.,Chen, G.,Phan, A.T. (deposition date: 2019-09-03, release date: 2020-03-04, Last modification date: 2024-05-01)

Primary citation

Maity, A.,Winnerdy, F.R.,Chang, W.D.,Chen, G.,Phan, A.T.
Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs.
Nucleic Acids Res., 48:3315-3327, 2020

PubMed Abstract: G-rich DNA sequences with tracts of three or more continuous guanines (G≥3) are known to have high propensity to adopt stable G-quadruplex (G4) structures. Bioinformatic analyses suggest high prevalence of G-rich sequences with short G-tracts (G≤2) in the human genome. However, due to limited structural studies, the folding principles of such sequences remain largely unexplored and hence poorly understood. Here, we present the solution NMR structure of a sequence named AT26 consisting of irregularly spaced G2 tracts and two isolated single guanines. The structure is a four-layered G4 featuring two bi-layered blocks, locked between themselves in an unprecedented fashion making it a stable scaffold. In addition to edgewise and propeller-type loops, AT26 also harbors two V-shaped loops: a 2-nt V-shaped loop spanning two G-tetrad layers and a 0-nt V-shaped loop spanning three G-tetrad layers, which are named as VS- and VR-loop respectively, based on their distinct structural features. The intra-lock motif can be a basis for extending the G-tetrad core and a very stable intra-locked G4 can be formed by a sequence with G-tracts of various lengths including several G2 tracts. Findings from this study will aid in understanding the folding of G4 topologies from sequences containing irregularly spaced multiple short G-tracts.

PubMed: 32100003
DOI: 10.1093/nar/gkaa008

Experimental method

SOLUTION NMR