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Nucleic Acids Research, 1994, Vol. 22, No. 6 920-928
© 1994

CHEMISTRY

Fluorescence energy transfer as a probe for nucleic acid structures and sequences

Jean-Louis Mergny, Alexandre S. Boutorine, Thérèse Garestier, Francis Belloc2, Michel Rougée, N.V. Bulychev1, A.A. Koshkin1, Jean Bourson3, Alexandre V. Lebedev1, Bernard Valeur3, Nguyen T. Thuong4 and Claude Hélène*

Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM U 201, CNRS UA 481 43 rue Cuvier, 75005 Paris, France 1Institute of Bioorganic Chemistry Novosibirsk 630090, Russia 2Laboratoire d'Hématologie Hôpital Haut-Lévêque 33604 Pessac 3Laboratoire de Chimie Génèrale, CNRS URA 1103, Conservatoire National des Arts et Métiers 292 rue Saint Martin, 75003 Paris 4Centre de Biophysique Moléculaire, Orléans la Source France

* To whom correspondence should be addressed

Received January 20, 1994. Accepted February 14, 1994.

The primary or secondary structure of single-stranded nucleic acids has been investigated with fluorescent oligonucleotides, i.e., oligonucleotides covalently linked to a fluorescent dye. Five different chromophores were used: 2-methoxy-6-chloro-9-amino-acridine, coumarin 500, fluorescein, rhodamine and ethldlum. The chemical synthesis of derivatized oligonucleotides is described. Hybridization of two fluorescent oligonucleotides to adjacent nucleic acid sequences led to fluorescence excitation energy transfer between the donor and the acceptor dyes. This phenomenom was used to probe primary and secondary structures of DNA fragments and the orientation of ollgodeoxynucleotides synthesized with the alpha-anomers of nucleoside units. Fluorescence energy transfer can be used to reveal the formation of hairpin structures and the translocation of genes between two chromosomes.


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