1H0Q

NMR solution structure of a fully modified locked nucleic acid (LNA) hybridized to RNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NMR Studies of Fully Modified Locked Nucleic Acid (Lna) Hybrids: Solution Structure of an Lna:RNA Hybrid and Characterization of an Lna:RNA Hybrid

Nielsen, K.E.Rasmussen, J.Kumar, R.Wengel, J.Jacobsen, J.P.Petersen, M.

(2004) Bioconjug.Chem. 15: 449

  • DOI: 10.1021/bc034145h

  • PubMed Abstract: 
  • LNA is a bicyclic nucleic acid analogue that contains one or more 2'-O,4'-C methylene linkage(s), which effectively locks the furanose ring in a C3'-endo conformation. We report here the NMR solution structure of a nonamer LNA:RNA hybrid and a struct ...

    LNA is a bicyclic nucleic acid analogue that contains one or more 2'-O,4'-C methylene linkage(s), which effectively locks the furanose ring in a C3'-endo conformation. We report here the NMR solution structure of a nonamer LNA:RNA hybrid and a structural characterization of a nonamer LNA:DNA hybrid, where the LNA strands are composed entirely of LNA nucleotides. This is the first structural characterization of fully modified LNA oligonucleotides. The high-resolution structure reveals that the LNA:RNA hybrid adopts an almost canonical A-type duplex morphology. The helix axis is almost straight and the duplex geometry is regular. This shows that fully modified LNA oligomers can hybridize with complementary RNA and form duplexes within the Watson-Crick framework. The LNA:DNA hybrid structurally resembles an RNA:DNA hybrid as shown by determination of deoxyribose sugar puckers and analysis of NOESY NMR spectra.


    Organizational Affiliation

    Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, 5230 Odense M, Denmark.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
5-D(*(LKC)P*(TLN)P*(LCG)P*(LCA)P*(TLN)P*(LCA)P* (TLN)P*(LCG)P*(LCC))-3A9N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5-R(*GP*CP*AP*UP*AP*UP*CP*AP*G)-3B9N/A
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
TLN
Query on TLN
A
RNA LINKINGC11 H15 N2 O9 PDU
LCA
Query on LCA
A
RNA LINKINGC11 H14 N5 O7 PA
LCG
Query on LCG
A
RNA LINKINGC11 H14 N5 O8 PDG
LKC
Query on LKC
A
RNA LINKINGC11 H15 N3 O5

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LCC
Query on LCC
A
RNA LINKINGC11 H16 N3 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance