Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (434K) Freely available
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 (41)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Kostenko, E.
Right arrow Articles by Zenkova, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kostenko, E.
Right arrow Articles by Zenkova, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2001, Vol. 29, No. 17 3611-3620
© 2001 Oxford University Press

5'-bis-pyrenylated oligonucleotides displaying excimer fluorescence provide sensitive probes of RNA sequence and structure

Elena Kostenko, Mikhail Dobrikov, Dmitrii Pyshnyi, Vladislav Petyuk, Nina Komarova, Valentin Vlassov and Marina Zenkova*

Novosibirsk Institute of Bioorganic Chemistry, Lavrentiev Avenue 8, Novosibirsk 630090, Russia

Oligonucleotide conjugates bearing two pyrene residues attached to 5'-phosphate through a phosphoramide bond were synthesised. Fluorescence spectra of the conjugates show a peak typical of monomer emission ({lambda}max 382 nm) and a broad emission peak with {lambda}max 476 nm, which indicates the excimer formation between the two pyrene residues. Conjugation of these two pyrene residues to the 5'-phosphate of oligonucleotides does not affect the stabilities of heteroduplexes formed by conjugates with the corresponding linear strands. A monomer fluorescence of the conjugates is considerably affected by the heteroduplex formation allowing the conjugates to be used as fluorescent hybridisation probes. The 5'-bis-pyrenylated oligonucleotides have been successfully used for investigation of affinity and kinetics of antisense oligonucleotides binding to the multidrug resistance gene 1 (PGY1/MDR1) mRNA. The changes of excimer fluorescence of the conjugates occurring during hybridisation depended on the structure of the binding sites: hybridisation to heavily structured parts of RNA resulted in quenching of the excimer fluorescence, while binding to RNA regions with a loose secondary structure was accompanied by an enhancement of the excimer fluorescence. Potentially, these conjugates may be considered as fluorescent probes for RNA structure investigation.

* To whom correspondence should be addressed. Tel: +7 3832 333761; Fax: +7 3832 333677; Email: marzen@niboch.nsc.ru


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
 Nucleic Acids ResHome page
A. A. Marti, X. Li, S. Jockusch, Z. Li, B. Raveendra, S. Kalachikov, J. J. Russo, I. Morozova, S. V. Puthanveettil, J. Ju, et al.
Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy
Nucleic Acids Res., June 12, 2006; 34(10): 3161 - 3168.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Nakamura, Y. Fukunaga, K. Sasa, Y. Ohtoshi, K. Kanaori, H. Hayashi, H. Nakano, and K. Yamana
Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference
Nucleic Acids Res., October 19, 2005; 33(18): 5887 - 5895.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. F. Blount and Y. Tor
Using pyrene-labeled HIV-1 TAR to measure RNA-small molecule binding
Nucleic Acids Res., October 1, 2003; 31(19): 5490 - 5500.
[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.