1HO6

CHIMERIC ARABINONUCLEIC ACID (ANA) HAIRPIN WITH ANA/RNA HYBRID STEM


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids.

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

(2001) Nucleic Acids Res. 29: 4284-4293

  • Primary Citation of Related Structures:  1HOQ

  • PubMed Abstract: 
  • Hybrids of RNA and arabinonucleic acid (ANA) as well as the 2'-fluoro-ANA analog (2'F-ANA) were recently shown to be substrates of the enzyme RNase H. Although RNase H binds to double-stranded RNA, no cleavage occurs with such duplexes. Therefore, kn ...

    Hybrids of RNA and arabinonucleic acid (ANA) as well as the 2'-fluoro-ANA analog (2'F-ANA) were recently shown to be substrates of the enzyme RNase H. Although RNase H binds to double-stranded RNA, no cleavage occurs with such duplexes. Therefore, knowledge of the structure of ANA/RNA hybrids may prove helpful in the design of future antisense oligonucleotide analogs. In this study, we have determined the NMR solution structures of ANA/RNA and DNA/RNA hairpin duplexes and compared them to the recently published structure of a 2'F-ANA/RNA hairpin duplex. We demonstrate here that the sugars of RNA nucleotides of the ANA/RNA hairpin stem adopt the C3'-endo (north, A-form) conformation, whereas those of the ANA strand adopt a 'rigid' O4'-endo (east) sugar pucker. The DNA strand of the DNA/RNA hairpin stem is flexible, but the average DNA/RNA hairpin structural parameters are close to the ANA/RNA and 2'F-ANA/RNA hairpin parameters. The minor groove width of ANA/RNA, 2'F-ANA/RNA and DNA/RNA helices is 9.0 +/- 0.5 A, a value that is intermediate between that of A- and B-form duplexes. These results rationalize the ability of ANA/RNA and 2'F-ANA/RNA hybrids to elicit RNase H activity.


    Related Citations: 
    • Properties of Arabinonucleic Acids (ANA & 2'F-ANA): Implications for the Design of Antisense Therapeutics that Invoke RNase H Cleavage of RNA
      Damha, M.J.,Noronha, A.M.,Wilds, C.J.,Trempe, J.F.,Denisov, A.Y.,Pon, R.T.,Gehring, K.
      (2001) Nucleosides and Nucleotides 20: 429


    Organizational Affiliation

    Department of Biochemistry and Montreal Joint Centre for Structural Biology, McGill University, Montreal, QC H3G 1Y6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA/RNA (5'-R(*GP*GP*AP*C)-D(P*TP*TP*CP*G)-(P*(GAO)P*(UAR)P*(CAR)P*(CAR)-3')A12N/A
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
CAR
Query on CAR
A
RNA LINKINGC9 H14 N3 O8 PDC
GAO
Query on GAO
A
RNA LINKINGC10 H14 N5 O8 PG
UAR
Query on UAR
A
RNA LINKINGC9 H13 N2 O9 PU
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance