6JCD

G-quadruplex peripheral knot


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

An Unprecedented Knot-like G-Quadruplex Peripheral Motif.

Truong, T.H.A.Winnerdy, F.R.Phan, A.T.

(2019) Angew.Chem.Int.Ed.Engl. --: --

  • DOI: 10.1002/anie.201907740

  • 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 ...

    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.


    Organizational Affiliation

    School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
24-mer DNAA24synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Singapore)SingaporeNRF-NRFI2017-09

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release