Skip Navigation

Nucleic Acids Research 2004 32(20):6078-6085; doi:10.1093/nar/gkh942
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (476K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (5)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Sørensen, J. J.
Right arrow Articles by Petersen, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sørensen, J. J.
Right arrow Articles by Petersen, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 18 November 2004

Nucleic Acids Research, Vol. 32 No. 20 © Oxford University Press 2004; all rights reserved

Solution structure of a dsDNA:LNA triplex

Jesper J. Sørensen, Jakob T. Nielsen and Michael Petersen*

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

* To whom correspondence should be addressed. Tel: +45 6550 2530; Fax: +45 6615 8780; Email: mip{at}chem.sdu.dk

Received July 18, 2004; Revised and Accepted October 27, 2004

We have determined the NMR structure of an intramolecular dsDNA:LNA triplex, where the LNA strand is composed of alternating LNA and DNA nucleotides. The LNA oligonucleotide binds to the dsDNA duplex in the major groove by formation of Hoogsteen hydrogen bonds to the purine strand of the duplex. The structure of the dsDNA duplex is changed to accommodate the LNA strand, and it adopts a geometry intermediate between A- and B-type. There is a substantial propeller twist between base-paired nucleobases. This propeller twist and a concomitant large propeller twist between the purine and LNA strands allows the pyrimidines of the LNA strand to interact with the 5'-flanking duplex pyrimidines. Altogether, the triplex has a regular global geometry as shown by a straight helix axis. This shows that even though the third strand is composed of alternating DNA and LNA monomers with different sugar puckers, it forms a seamless triplex. The thermostability of the triplex is increased by 19°C relative to the unmodified DNA triplex at acidic pH. Using NMR spectroscopy, we show that the dsDNA:LNA triplex is stable at pH 8, and that the triplex structure is identical to the structure determined at pH 5.1.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Biol. Chem.Home page
M. C. de Almagro, S. Coma, V. Noe, and C. J. Ciudad
Polypurine Hairpins Directed against the Template Strand of DNA Knock Down the Expression of Mammalian Genes
J. Biol. Chem., April 24, 2009; 284(17): 11579 - 11589.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. Pande and L. Nilsson
Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations
Nucleic Acids Res., March 1, 2008; 36(5): 1508 - 1516.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
E. Brunet, P. Alberti, L. Perrouault, R. Babu, J. Wengel, and C. Giovannangeli
Exploring Cellular Activity of Locked Nucleic Acid-modified Triplex-forming Oligonucleotides and Defining Its Molecular Basis
J. Biol. Chem., May 20, 2005; 280(20): 20076 - 20085.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.