2LSC

Solution structure of 2'F-ANA and ANA self-complementary duplex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion.

Martin-Pintado, N.Yahyaee-Anzahaee, M.Campos-Olivas, R.Noronha, A.M.Wilds, C.J.Damha, M.J.Gonzalez, C.

(2012) Nucleic Acids Res. 40: 9329-9339

  • DOI: 10.1093/nar/gks672

  • PubMed Abstract: 
  • We report here the first structure of double helical arabino nucleic acid (ANA), the C2'-stereoisomer of RNA, and the 2'-fluoro-ANA analogue (2'F-ANA). A chimeric dodecamer based on the Dickerson sequence, containing a contiguous central segment of a ...

    We report here the first structure of double helical arabino nucleic acid (ANA), the C2'-stereoisomer of RNA, and the 2'-fluoro-ANA analogue (2'F-ANA). A chimeric dodecamer based on the Dickerson sequence, containing a contiguous central segment of arabino nucleotides, flanked by two 2'-deoxy-2'F-ANA wings was studied. Our data show that this chimeric oligonucleotide can adopt two different structures of comparable thermal stabilities. One structure is a monomeric hairpin in which the stem is formed by base paired 2'F-ANA nucleotides and the loop by unpaired ANA nucleotides. The second structure is a bimolecular duplex, with all the nucleotides (2'F-ANA and ANA) forming Watson-Crick base pairs. The duplex structure is canonical B-form, with all arabinoses adopting a pure C2'-endo conformation. In the ANA:ANA segment, steric interactions involving the 2'-OH substituent provoke slight changes in the glycosidic angles and, therefore, in the ANA:ANA base pair geometry. These distortions are not present in the 2'F-ANA:2'F-ANA regions of the duplex, where the -OH substituent is replaced by a smaller fluorine atom. 2'F-ANA nucleotides adopt the C2'-endo sugar pucker and fit very well into the geometry of B-form duplex, allowing for favourable 2'F···H8 interactions. This interaction shares many features of pseudo-hydrogen bonds previously observed in 2'F-ANA:RNA hybrids and in single 2'F-ANA nucleotides.


    Organizational Affiliation

    Instituto de Química Física Rocasolano, CSIC, C/Serrano 119, 28006 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL)P*(A5O)P*(A5O)P*(UAR)P*(UAR)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3')A,B12N/A
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
GFL
Query on GFL
A, B
DNA LINKINGC10 H13 F N5 O7 PDG
CFL
Query on CFL
A, B
DNA LINKINGC9 H13 F N3 O7 PDC
UAR
Query on UAR
A, B
RNA LINKINGC9 H13 N2 O9 PU
A5O
Query on A5O
A, B
RNA LINKINGC10 H14 N5 O7 PA
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-10-24
    Type: Database references