6JCD

G-quadruplex peripheral knot

Summary for 6JCD

• Entry DOI: 10.2210/pdb6jcd/pdb
• Descriptor: 24-mer DNA (1 entity in total)
• Functional Keywords: g-quadruplex, diagonal loop, knot, triad, dna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 7555.83

Authors

Winnerdy, F.R.,Truong, T.H.A.,Phan, A.T. (deposition date: 2019-01-28, release date: 2019-08-28, Last modification date: 2024-05-15)

Primary citation

Truong, T.H.A.,Winnerdy, F.R.,Phan, A.T.
An Unprecedented Knot-like G-Quadruplex Peripheral Motif.
Angew.Chem.Int.Ed.Engl., 58:13834-13839, 2019

PubMed Abstract: A knot-like G-quadruplex peripheral structure is formed by a 7-nt DNA sequence DL7 (TGTTGGT), in which six out of its seven nucleobases participate in compact base-pairing interactions. Here, the solution NMR structure of a 24-nt DNA oligonucleotide containing the DL7 sequence shows the interaction between a two-layer anti-parallel G-quadruplex core and the peripheral knot-like structure, including the construction of two sharp turns in the DNA backbone. The formation of this novel structural element highlights the intricate properties of single-stranded DNA folding in presence of G-quadruplex-forming motifs. We demonstrated the compatibility of the DL7 knot-like structure with various G-quadruplexes, which could have implications in drug design and DNA engineering.

PubMed: 31317601
DOI: 10.1002/anie.201907740

Experimental method

SOLUTION NMR