6JCD

G-quadruplex peripheral knot

• PDB DOI: https://doi.org/10.2210/pdb6JCD/pdb
• NAKB: 6JCD

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2019-01-28 Released: 2019-08-28 
• Deposition Author(s): Winnerdy, F.R., Truong, T.H.A., Phan, A.T.
• Funding Organization(s): National Research Foundation (Singapore)

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Experimental Data Snapshot

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

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 58: 13834-13839

• PubMed: 31317601 
• DOI: https://doi.org/10.1002/anie.201907740
• Primary Citation of Related Structures:  
  6JCD


• 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.

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Organizational Affiliation: 

School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.56 kDa 
• Atom Count: 501 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
24-mer DNA	A	24	synthetic construct

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Winnerdy, F.R., Truong, T.H.A., Phan, A.T.

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Funding Organization	Location	Grant Number
National Research Foundation (Singapore)	Singapore	NRF-NRFI2017-09

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2019-10-02
  Changes: Data collection, Database references
• Version 1.2: 2023-06-14
  Changes: Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references