2N89

Tetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC at acidic pH


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Stabilization of i-motif structures by 2'-beta-fluorination of DNA.

Assi, H.A.Harkness, R.W.Martin-Pintado, N.Wilds, C.J.Campos-Olivas, R.Mittermaier, A.K.Gonzalez, C.Damha, M.J.

(2016) Nucleic Acids Res 44: 4998-5009

  • DOI: 10.1093/nar/gkw402
  • Primary Citation of Related Structures:  
    2N89

  • PubMed Abstract: 
  • i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH(+)). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies ...

    i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH(+)). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2'-endo conformation, instead of the C3'-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology.


    Organizational Affiliation

    Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada masad.damha@mcgill.ca.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')A, B, C, D6synthetic construct
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 20 
    • Conformers Submitted: 10 
    • Selection Criteria: structures with the lowest energy 
    • OLDERADO: 2N89 Olderado

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2016-08-17
      Type: Initial release