1HG9

Solution structure of DNA:RNA hybrid


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 40 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • Also Cited By: 1HHX, 1HHW

  • PubMed Abstract: 
  • We have used NMR and CD spectroscopy to study the conformations of modified oligonucleotides (locked nucleic acid, LNA) containing a conformationally restricted nucleotide (T(L)) with a 2'-O,4'-C-methylene bridge. We have investigated two LNA:RNA dup ...

    We have used NMR and CD spectroscopy to study the conformations of modified oligonucleotides (locked nucleic acid, LNA) containing a conformationally restricted nucleotide (T(L)) with a 2'-O,4'-C-methylene bridge. We have investigated two LNA:RNA duplexes, d(CTGAT(L)ATGC):r(GCAUAUCAG) and d(CT(L)GAT(L)AT(L)GC):r(GCAUAUCAG), along with the unmodified DNA:RNA reference duplex. Increases in the melting temperatures of +9.6 degrees C and +8.1 degrees C per modification relative to the unmodified duplex were observed for these two LNA:RNA sequences. The three duplexes all adopt right-handed helix conformations and form normal Watson-Crick base pairs with all the bases in the anti conformation. Sugar conformations were determined from measurements of scalar coupling constants in the sugar rings and distance information derived from 1H-1H NOE measurements; all the sugars in the RNA strands of the three duplexes adopt an N-type conformation (A-type structure), whereas the sugars in the DNA strands change from an equilibrium between S- and N-type conformations in the unmodified duplex towards more of the N-type conformation when modified nucleotides are introduced. The presence of three modified T(L) nucleotides induces drastic conformational shifts of the remaining unmodified nucleotides of the DNA strand, changing all the sugar conformations except those of the terminal sugars to the N type. The CD spectra of the three duplexes confirm the structural changes described above. On the basis of the results reported herein, we suggest that the observed conformational changes can be used to tune LNA:RNA duplexes into substrates for RNase H: Partly modified LNA:RNA duplexes may adopt a duplex structure between the standard A and B types, thereby making the RNA strand amenable to RNase H-mediated degradation.


    Related Citations: 
    • 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
    • The Conformations of Locked Nucleic Acids (Lna)
      Petersen, M.,Nielsen, C.B.,Nielsen, K.E.,Jensen, G.A.,Bondensgaard, K.,Singh, S.K.,Rajwanshi, V.K.,Koshkin, A.A.,Dahl, B.M.,Wengel, J.,Jacobsen, J.P.
      (2000) J.Mol.Recognit. 13: 44


    Organizational Affiliation

    Department of Chemistry, University of Southern Denmark Odense University.




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
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 40 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance