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Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference

Through binding and fluorescence studies of oligonucleotides covalently attached to a pyrene group via one carbon linker at the sugar residue, we previously found that pyrene-modified RNA oligonucleotides do not emit well in the single-stranded form, yet the attached pyrene emits with a significantl...

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Autores principales: Nakamura, Mitsunobu, Fukunaga, Yudai, Sasa, Kazuhiro, Ohtoshi, Yukinori, Kanaori, Kenji, Hayashi, Haruhisa, Nakano, Hidehiko, Yamana, Kazushige
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1258169/
https://www.ncbi.nlm.nih.gov/pubmed/16237124
http://dx.doi.org/10.1093/nar/gki889
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author Nakamura, Mitsunobu
Fukunaga, Yudai
Sasa, Kazuhiro
Ohtoshi, Yukinori
Kanaori, Kenji
Hayashi, Haruhisa
Nakano, Hidehiko
Yamana, Kazushige
author_facet Nakamura, Mitsunobu
Fukunaga, Yudai
Sasa, Kazuhiro
Ohtoshi, Yukinori
Kanaori, Kenji
Hayashi, Haruhisa
Nakano, Hidehiko
Yamana, Kazushige
author_sort Nakamura, Mitsunobu
collection PubMed
description Through binding and fluorescence studies of oligonucleotides covalently attached to a pyrene group via one carbon linker at the sugar residue, we previously found that pyrene-modified RNA oligonucleotides do not emit well in the single-stranded form, yet the attached pyrene emits with a significantly high quantum yield upon binding to a complementary RNA strand. In sharp contrast, similarly modified pyrene–DNA probes exhibit very weak fluorescence both in the double-stranded and single-stranded forms. The pyrene-modified RNA oligonucleotides therefore provide a useful tool for monitoring RNA hybridization. The purpose of this paper is to present the structural basis for the different fluorescence properties of pyrene-modified RNA/RNA and pyrene-modified DNA/DNA duplexes. The results of absorption, fluorescence anisotropy and circular dichroism studies all consistently indicated that the pyrene attached to the RNA duplex is located outside of the duplex, whereas the pyrene incorporated into the DNA duplex intercalates into the double helix. (1)H NMR measurements unambiguously confirmed that the pyrene attached to the DNA duplex indeed intercalates between the base pairs of the duplex. Molecular dynamics simulations support these differences in the local structural elements around the pyrene between the pyrene–RNA/RNA and the pyrene–DNA/DNA duplexes.
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spelling pubmed-12581692005-10-24 Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference Nakamura, Mitsunobu Fukunaga, Yudai Sasa, Kazuhiro Ohtoshi, Yukinori Kanaori, Kenji Hayashi, Haruhisa Nakano, Hidehiko Yamana, Kazushige Nucleic Acids Res Article Through binding and fluorescence studies of oligonucleotides covalently attached to a pyrene group via one carbon linker at the sugar residue, we previously found that pyrene-modified RNA oligonucleotides do not emit well in the single-stranded form, yet the attached pyrene emits with a significantly high quantum yield upon binding to a complementary RNA strand. In sharp contrast, similarly modified pyrene–DNA probes exhibit very weak fluorescence both in the double-stranded and single-stranded forms. The pyrene-modified RNA oligonucleotides therefore provide a useful tool for monitoring RNA hybridization. The purpose of this paper is to present the structural basis for the different fluorescence properties of pyrene-modified RNA/RNA and pyrene-modified DNA/DNA duplexes. The results of absorption, fluorescence anisotropy and circular dichroism studies all consistently indicated that the pyrene attached to the RNA duplex is located outside of the duplex, whereas the pyrene incorporated into the DNA duplex intercalates into the double helix. (1)H NMR measurements unambiguously confirmed that the pyrene attached to the DNA duplex indeed intercalates between the base pairs of the duplex. Molecular dynamics simulations support these differences in the local structural elements around the pyrene between the pyrene–RNA/RNA and the pyrene–DNA/DNA duplexes. Oxford University Press 2005 2005-10-19 /pmc/articles/PMC1258169/ /pubmed/16237124 http://dx.doi.org/10.1093/nar/gki889 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
spellingShingle Article
Nakamura, Mitsunobu
Fukunaga, Yudai
Sasa, Kazuhiro
Ohtoshi, Yukinori
Kanaori, Kenji
Hayashi, Haruhisa
Nakano, Hidehiko
Yamana, Kazushige
Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference
title Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference
title_full Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference
title_fullStr Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference
title_full_unstemmed Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference
title_short Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference
title_sort pyrene is highly emissive when attached to the rna duplex but not to the dna duplex: the structural basis of this difference
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1258169/
https://www.ncbi.nlm.nih.gov/pubmed/16237124
http://dx.doi.org/10.1093/nar/gki889
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