1GV6

Solution structure of alfa-L-LNA:DNA duplex


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

Alfa-L-Lna (Alfa-L-Ribo Configured Locked Nucleic Acid) Recognition of DNA: An NMR Spectroscopic Study

Nielsen, K.M.E.Petersen, M.Haakansson, A.E.Wengel, J.Jacobsen, J.P.

(2002) Chemistry 8: 3001

  • DOI: 10.1002/1521-3765(20020703)8:13<3001::AID-CHEM3001>3.0.CO;2-1

  • PubMed Abstract: 
  • We have used NMR and CD spectroscopy to study and characterise two alpha-L-LNA:DNA duplexes, a nonamer that incorporates three alpha-L-LNA nucleotides and a decamer that incorporates four alpha-L-LNA nucleotides, in which alpha-L-LNA is alpha-L-ribo- ...

    We have used NMR and CD spectroscopy to study and characterise two alpha-L-LNA:DNA duplexes, a nonamer that incorporates three alpha-L-LNA nucleotides and a decamer that incorporates four alpha-L-LNA nucleotides, in which alpha-L-LNA is alpha-L-ribo-configured locked nucleic acid. Both duplexes adopt right-handed helical conformations and form normal Watson-Crick base pairing with all nucleobases in the anti conformation. Deoxyribose conformations were determined from measurements of scalar coupling constants in the sugar rings, and for the decamer duplex, distance information was derived from 1H-1H NOE measurements. In general, the deoxyriboses in both of the alpha-L-LNA:DNA duplexes adopt S-type (B-type structure) sugar puckers, that is the inclusion of the modified alpha-L-LNA nucleotides does not perturb the local native B-like double-stranded DNA (dsDNA) structure. The CD spectra of the duplexes confirm these findings, as these display B-type characteristic features that allow us to characterise the overall duplex type as B-like. The 1H-1H NOE distances which were determined for the decamer duplex were employed in a simulated annealing protocol to generate a model structure for this duplex, thus allowing a more detailed inspection of the impact of the alpha-L-ribo-configured nucleotides. In this structure, it is evident that the malleable DNA backbone rearranges in the vicinity of the modified nucleotides in order to accommodate them and present their nucleobases in a geometry suitable for Watson-Crick base pairing.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5- D(*CP*(ATL)P*GP*CP*(ATL)P*(ATL)P*CP*(ATL)P* GP*C) -3A10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5- D(*GP*CP*AP*GP*AP*AP*GP*CP*AP*G) -3B10N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ATL
Query on ATL
A
RNA LINKINGC11 H15 N2 O9 PDT
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: 2002-07-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance