1HHX

Solution structure of LNA3:RNA hybrid


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 34 
  • Selection Criteria: LOWEST ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Locked Nucleic Acid (Lna) Recognition of RNA: NMR Solution Structures of Lna:RNA Hybrids

Petersen, M.Bondensgaard, K.Wengel, J.Jacobsen, J.P.

(2002) J.Am.Chem.Soc. 124: 5974

  • Primary Citation of Related Structures:  
  • Also Cited By: 1HG9

  • PubMed Abstract: 
  • Locked nucleic acids (LNAs) containing one or more 2'-O,4'-C-methylene-linked bicyclic ribonucleoside monomers possess a number of the prerequisites of an effective antisense oligonucleotide, e.g. unprecedented helical thermostability when hybridized ...

    Locked nucleic acids (LNAs) containing one or more 2'-O,4'-C-methylene-linked bicyclic ribonucleoside monomers possess a number of the prerequisites of an effective antisense oligonucleotide, e.g. unprecedented helical thermostability when hybridized with cognate RNA and DNA. To acquire a detailed understanding of the structural features of LNA giving rise to its remarkable properties, we have conducted structural studies by use of NMR spectroscopy and now report high-resolution structures of two LNA:RNA hybrids, the LNA strands being d(5'-CTGAT(L)ATGC-3') and d(5'-CT(L)GAT(L)AT(L)GC-3'), respectively, T(L) denoting a modified LNA monomer with a thymine base, along with the unmodified DNA:RNA hybrid. In the structures, the LNA nucleotides are positioned as to partake in base stacking and Watson-Crick base pairing, and with the inclusion of LNA nucleotides, we observe a progressive change in duplex geometry toward an A-like duplex structure. As such, with the inclusion of three LNA nucleotides, the hybrid adopts an almost canonical A-type duplex geometry, and thus it appears that the number of modifications has reached a saturation level with respect to structural changes, and that further incorporations would furnish only minute changes in the duplex structure. We attempt to rationalize the conformational steering induced by the LNA nucleotides by suggesting that the change in electronic density at the brim of the minor groove, introduced by the LNA modification, is causing an alteration of the pseudorotational profile of the 3'-flanking nucleotide, thus shifting this sugar equilibrium toward N-type conformation.


    Related Citations: 
    • Structural Studies of Lna:RNA Duplexes by NMR: Conformations and Implications for Rnase H Activity.
      Bondensgaard, K.,Petersen, M.,Singh, S.K.,Rajwanshi, V.K.,Kumar, R.,Wengel, J.,Jacobsen, J.P.
      (2000) Chemistry 6: 2687


    Organizational Affiliation

    Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Odense University, DK-5230 Odense M, Denmark. mip@chem.sdu.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5- D(*CP*+TP*GP*AP*+TP*AP*+TP*GP*C) -3A9N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3B9N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TLN
Query on TLN
A
RNA LINKINGC11 H15 N2 O9 PDU
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 34 
  • Selection Criteria: LOWEST ENERGY 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance