5M1W

Structure of a stable G-hairpin


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 1.2 of the entry. See complete history


Literature

Structure of a Stable G-Hairpin.

Gajarsky, M.Zivkovic, M.L.Stadlbauer, P.Pagano, B.Fiala, R.Amato, J.Tomaska, L.Sponer, J.Plavec, J.Trantirek, L.

(2017) J Am Chem Soc 139: 3591-3594

  • DOI: 10.1021/jacs.6b10786
  • Primary Citation of Related Structures:  
    5M1W

  • PubMed Abstract: 
  • In this study, we report the first atomic resolution structure of a stable G-hairpin formed by a natively occurring DNA sequence. An 11-nt long G-rich DNA oligonucleotide, 5'-d(GTGTGGGTGTG)-3', corresponding to the most abundant sequence motif in irregular telomeric DNA from Saccharomyces cerevisiae (yeast), is demonstrated to adopt a novel type of mixed parallel/antiparallel fold-back DNA structure, which is stabilized by dynamic G:G base pairs that transit between N1-carbonyl symmetric and N1-carbonyl, N7-amino base-pairing arrangements ...

    In this study, we report the first atomic resolution structure of a stable G-hairpin formed by a natively occurring DNA sequence. An 11-nt long G-rich DNA oligonucleotide, 5'-d(GTGTGGGTGTG)-3', corresponding to the most abundant sequence motif in irregular telomeric DNA from Saccharomyces cerevisiae (yeast), is demonstrated to adopt a novel type of mixed parallel/antiparallel fold-back DNA structure, which is stabilized by dynamic G:G base pairs that transit between N1-carbonyl symmetric and N1-carbonyl, N7-amino base-pairing arrangements. Although the studied sequence first appears to possess a low capacity for base pairing, it forms a thermodynamically stable structure with a rather complex topology that includes a chain reversal arrangement of the backbone in the center of the continuous G-tract and 3'-to-5' stacking of the terminal residues. The structure reveals previously unknown principles of the folding of G-rich oligonucleotides that could be applied to the prediction of natural and/or the design of artificial recognition DNA elements. The structure also demonstrates that the folding landscapes of short DNA single strands is much more complex than previously assumed.


    Organizational Affiliation

    Central European Institute of Technology, Masaryk University , Kamenice 753/5, 62500 Brno, Czech Republic.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G)-3')A11Saccharomyces cerevisiae
    Protein Feature View
    Expand
    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 100 
    • Conformers Submitted: 10 
    • Selection Criteria: structures with the lowest energy 
    • OLDERADO: 5M1W Olderado

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Czech Science FoundationCzech Republic13-28310S
    Czech Science FoundationCzech Republic16-13721S
    CEITEC 2020, Ministry of Education, Youth and Sports and National Programme for Sustainability IICzech RepublicLQ1601
    European Organization for Molecular BiologyCzech RepublicIG2535
    Marie-Curie grantCzech RepublicECOPOD
    Slovenian Research AgencySloveniaP1-242
    Slovenian Research AgencySloveniaJ1-6733
    Programma STAR 2014 of University of Naples Federico IIItaly14-CSP3-C03-141

    Revision History  (Full details and data files)

    • Version 1.0: 2017-03-01
      Type: Initial release
    • Version 1.1: 2017-03-29
      Changes: Database references
    • Version 1.2: 2019-05-08
      Changes: Data collection