2K97

Dimeric solution structure of the cyclic octamer d(pCGCTCCGT)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 

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This is version 1.2 of the entry. See complete history


Literature

Self-association of short DNA loops through minor groove C:G:G:C tetrads.

Viladoms, J.Escaja, N.Frieden, M.Gomez-Pinto, I.Pedroso, E.Gonzalez, C.

(2009) Nucleic Acids Res 37: 3264-3275

  • DOI: 10.1093/nar/gkp191
  • Primary Citation of Related Structures:  
    2K8Z, 2K90, 2K97

  • PubMed Abstract: 
  • In addition to the better known guanine-quadruplex, four-stranded nucleic acid structures can be formed by tetrads resulting from the association of Watson-Crick base pairs. When such association occurs through the minor groove side of the base pairs, the resulting structure presents distinctive features, clearly different from quadruplex structures containing planar G-tetrads ...

    In addition to the better known guanine-quadruplex, four-stranded nucleic acid structures can be formed by tetrads resulting from the association of Watson-Crick base pairs. When such association occurs through the minor groove side of the base pairs, the resulting structure presents distinctive features, clearly different from quadruplex structures containing planar G-tetrads. Although we have found this unusual DNA motif in a number of cyclic oligonucleotides, this is the first time that this DNA motif is found in linear oligonucleotides in solution, demonstrating that cyclization is not required to stabilize minor groove tetrads in solution. In this article, we have determined the solution structure of two linear octamers of sequence d(TGCTTCGT) and d(TCGTTGCT), and their cyclic analogue d, utilizing 2D NMR spectroscopy and restrained molecular dynamics. These three molecules self-associate forming symmetric dimers stabilized by a novel kind of minor groove C:G:G:C tetrad, in which the pattern of hydrogen bonds differs from previously reported ones. We hypothesize that these quadruplex structures can be formed by many different DNA sequences, but its observation in linear oligonucleotides is usually hampered by competing Watson-Crick duplexes.


    Organizational Affiliation

    Departament de Química Orgànica and IBUB, Universitat de Barcelona, C/. Martí i Franquès 1-11, 08028 Barcelona, Spain.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(P*CP*GP*CP*TP*CP*CP*GP*T)-3'A, B 8N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 
  • OLDERADO: 2K97 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations, Other