1F3S

Solution Structure of DNA Sequence GGGTTCAGG Forms GGGG Tetrade and G(C-A) Triad.


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 18 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A two-stranded template-based approach to G.(C-A) triad formation: designing novel structural elements into an existing DNA framework.

Kettani, A.Basu, G.Gorin, A.Majumdar, A.Skripkin, E.Patel, D.J.

(2000) J Mol Biol 301: 129-146

  • DOI: 10.1006/jmbi.2000.3932
  • Primary Citation of Related Structures:  
    1F3S

  • PubMed Abstract: 
  • We have designed a DNA sequence, d(G-G-G-T-T-C-A-G-G), which dimerizes to form a 2-fold symmetric G-quadruplex in which G(syn). G(anti).G(syn).G(anti) tetrads are sandwiched between all trans G. (C-A) triads. The NMR-based solution structural analysis was greatly aided by monitoring hydrogen bond alignments across N-H ...

    We have designed a DNA sequence, d(G-G-G-T-T-C-A-G-G), which dimerizes to form a 2-fold symmetric G-quadruplex in which G(syn). G(anti).G(syn).G(anti) tetrads are sandwiched between all trans G. (C-A) triads. The NMR-based solution structural analysis was greatly aided by monitoring hydrogen bond alignments across N-H...N and N-H...O==C hydrogen bonds within the triad and tetrad, in a uniformly ((13)C,(15)N)-labeled sample of the d(G-G-G-T-T-C-A-G-G) sequence. The solution structure establishes that the guanine base-pairs with the cytosine through Watson-Crick G.C pair formation and with adenine through sheared G.A mismatch formation within the G.(C-A) triad. A model of triad DNA was constructed that contains the experimentally determined G.(C-A) triad alignment as the repeating stacked unit.


    Organizational Affiliation

    Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*GP*TP*TP*CP*AP*GP*G)-3')A, B9N/A
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 18 
    • Conformers Submitted: 10 
    • Selection Criteria: structures with the lowest energy 
    • OLDERADO: 1F3S Olderado

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2000-11-13
      Type: Initial release
    • Version 1.1: 2007-10-21
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance