7CLS

Solution structure of an intramolecular G-quadruplex containing a duplex bulge


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 2.1 of the entry. See complete history


Literature

Duplex formation in a G-quadruplex bulge.

Ngoc Nguyen, T.Q.Lim, K.W.Phan, A.T.

(2020) Nucleic Acids Res 48: 10567-10575

  • DOI: 10.1093/nar/gkaa738
  • Primary Citation of Related Structures:  
    7CLS

  • PubMed Abstract: 
  • Beyond the consensus definition of G-quadruplex-forming motifs with tracts of continuous guanines, G-quadruplexes harboring bulges in the G-tetrad core are prevalent in the human genome. Here, we study the incorporation of a duplex hairpin within a b ...

    Beyond the consensus definition of G-quadruplex-forming motifs with tracts of continuous guanines, G-quadruplexes harboring bulges in the G-tetrad core are prevalent in the human genome. Here, we study the incorporation of a duplex hairpin within a bulge of a G-quadruplex. The NMR solution structure of a G-quadruplex containing a duplex bulge was resolved, revealing the structural details of the junction between the duplex bulge and the G-quadruplex. Unexpectedly, instead of an orthogonal connection the duplex stem was observed to stack below the G-quadruplex forming a unique quadruplex-duplex junction. Breaking up of the immediate base pair step at the junction, coupled with a narrowing of the duplex groove within the context of the bulge, led to a progressive transition between the quadruplex and duplex segments. This study revealed that a duplex bulge can be formed at various positions of a G-quadruplex scaffold. In contrast to a non-structured bulge, the stability of a G-quadruplex slightly increases with an increase in the duplex bulge size. A G-quadruplex structure containing a duplex bulge of up to 33 nt in size was shown to form, which was much larger than the previously reported 7-nt bulge. With G-quadruplexes containing duplex bulges representing new structural motifs with potential biological significance, our findings would broaden the definition of potential G-quadruplex-forming sequences.


    Organizational Affiliation

    NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore.



Macromolecules
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (33-MER)A33synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 7CLS Olderado

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 2.0: 2020-10-14
    Changes: Advisory, Atomic model, Derived calculations, Refinement description
  • Version 2.1: 2020-10-21
    Changes: Database references