1FC8

NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC)D(TTCG)2'F-A(GTCC)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: RMSD FROM AVERAGE LOWER THAN 0.7 ANGSTROM 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes.

Trempe, J.F.Wilds, C.J.Denisov, A.Y.Pon, R.T.Damha, M.J.Gehring, K.

(2001) J.Am.Chem.Soc. 123: 4896-4903


  • PubMed Abstract: 
  • The first structure of a 2'-deoxy-2'-fluoro-D-arabinose nucleic acid (2'F-ANA)/RNA duplex is presented. We report the structural characterization by NMR spectroscopy of a small hybrid hairpin, r(GGAC)d(TTCG)2'F-a(GTCC), containing a 2'F-ANA/RNA stem ...

    The first structure of a 2'-deoxy-2'-fluoro-D-arabinose nucleic acid (2'F-ANA)/RNA duplex is presented. We report the structural characterization by NMR spectroscopy of a small hybrid hairpin, r(GGAC)d(TTCG)2'F-a(GTCC), containing a 2'F-ANA/RNA stem and a four-residue DNA loop. Complete (1)H, (13)C, (19)F, and (31)P resonance assignments, scalar coupling constants, and NOE constraints were obtained from homonuclear and heteronuclear 2D spectra. In the chimeric duplex, the RNA strand adopts a classic A-form structure having C3' endo sugar puckers. The 2'F-ANA strand is neither A-form nor B-form and contains O4' endo sugar puckers. This contrasts strongly with the dynamic sugar conformations previously observed in the DNA strands of DNA/RNA hybrid duplexes. Structural parameters for the duplex, such as minor groove width, x-displacement, and inclination, were intermediate between those of A-form and B-form duplexes and similar to those of DNA/RNA duplexes. These results rationalize the enhanced stability of 2'F-ANA/RNA duplexes and their ability to elicit RNase H activity. The results are relevant for the design of new antisense drugs based on sugar-modified nucleic acids.


    Organizational Affiliation

    Department of Biochemistry and Montreal Joint Center for Structural Biology, McGill University, Montreal, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*GP*AP*CP)D(*TP*TP*CP*GP*(GFL)P*(TAF)P*(CFL)P*(CFL))-3'A12N/A
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
GFL
Query on GFL
A
DNA LINKINGC10 H13 F N5 O7 PDG
CFL
Query on CFL
A
DNA LINKINGC9 H13 F N3 O7 PDC
TAF
Query on TAF
A
DNA LINKINGC10 H14 F N2 O8 PDT
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: RMSD FROM AVERAGE LOWER THAN 0.7 ANGSTROM 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance