6A7Y

Solution structure of an intermolecular leaped V-shape G-quadruplex

Summary for 6A7Y

• Entry DOI: 10.2210/pdb6a7y/pdb
• Descriptor: DNA (5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'), DNA (5'-D(*TP*GP*GP*GP*GP*A)-3') (2 entities in total)
• Functional Keywords: g-quadruplex, v-shape, dna
• Biological source: Sterkiella nova; More
• Total number of polymer chains: 2
• Total formula weight: 7569.91

Authors

Wan, C.J.,Zhang, N. (deposition date: 2018-07-05, release date: 2018-12-12, Last modification date: 2024-05-15)

Primary citation

Wan, C.,Fu, W.,Jing, H.,Zhang, N.
NMR solution structure of an asymmetric intermolecular leaped V-shape G-quadruplex: selective recognition of the d(G2NG3NG4) sequence motif by a short linear G-rich DNA probe.
Nucleic Acids Res., 47:1544-1556, 2019

PubMed Abstract: Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itself distinctive and thus an essentially more accessible target. As an alternative to the conventional antisense method using a complementary chain, forming an intermolecular G-quadruplex from two different oligomers, in which the longer one as the target is captured by a short G-rich fragment, could be helpful for recognizing G-rich sequences and structural motifs. However, such an intermolecular leaped V-shape G-quadruplex consisting of DNA oligomers of quite different lengths has not been evaluated. Here, we present the first nuclear magnetic resonance (NMR) study of an asymmetric intermolecular leaped V-shape G-quadruplex assembled between an Oxytricha nova telomeric sequence d(G2T4G4T4G4) and a single G-tract fragment d(TG4A). Furthermore, we explored the selectivity of this short fragment as a potential probe, examined the kinetic discrimination for probing a specific mutant, and proposed the key sequence motif d(G2NG3NG4) essential for building the leaped V-shape G-quadruplexes.

PubMed: 30445650
DOI: 10.1093/nar/gky1167

Experimental method

SOLUTION NMR