7XH9

Crystal structure of a dimeric interlocked parallel G-quadruplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A.G.G.G.G pentad in an interlocked G-quadruplex.

Ngo, K.H.Liew, C.W.Lattmann, S.Winnerdy, F.R.Phan, A.T.

(2022) Biochem Biophys Res Commun 613: 153-158

  • DOI: https://doi.org/10.1016/j.bbrc.2022.04.020
  • Primary Citation of Related Structures:  
    7X7G, 7XDH, 7XH9, 7XHD, 7XIE

  • PubMed Abstract: 

    93del is a 16-nucleotide G-quadruplex-forming aptamer which can inhibit the activity of the HIV-1 integrase enzyme at nanomolar concentration. Previous structural analyses of 93del using NMR spectroscopy have shown that the aptamer forms an interlocked G-quadruplex structure in K + solution. Due to its exceptional stability and unique topology, 93del has been used in many different studies involving DNA G-quadruplexes, such as DNA aptamer and multimer design, as well as DNA fluorescence research. To gain further insights on the structure of this unique aptamer, we have determined several high-resolution crystal structures of 93del and its variants. While confirming the overall dimeric interlocked G-quadruplex folding topology previously determined by NMR, our results reveal important detailed structural information, particularly the formation of a water-mediated A•G•G•G•G pentad. These insights allow us to better understand the formation of various structural elements in G-quadruplexes and should be useful for designing and manipulating G-quadruplex scaffolds with desired properties.


  • Organizational Affiliation

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


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*CP*GP*GP*TP*GP*GP*GP*T)-3')
A, B
16synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.436α = 62.147
b = 30.341β = 79.962
c = 30.35γ = 79.967
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)SingaporeNRF-NRFI2017-09
Ministry of Education (MoE, Singapore)SingaporeMOE2018-T2-2-029

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description