Mechanism of oligonucleotide hybridization with the 3′-terminal region of the yeast tRNAPhe |
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Authors: | V A Petyuk R Giege V V Vlassov M A Zenkova |
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Institution: | (1) Novosibirsk Institute of Bioorganic Chemistry, Siberian Division, Russian Academy of Sciences, 630090 Novosibirsk, Russia;(2) Institut de Biologie Moleculaire et Cellulaire du CNRS, 67084 Strasbourg, France |
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Abstract: | Interaction of yeast phenylalanine tRNA with oligonucleotides complementary to its 3′-terminal nucleotide sequence was thoroughly
studied. Using the gel retardation technique, thermodynamic and kinetic parameters of the tRNA complexation in physiological
conditions were determined. Analysis of dependences of the complex formation on the oligonucleotide concentration and incubation
time showed that this process proceeds in two stages. At the first stage, a metastable complex of the oligonucleotide with
the open, single-stranded sequence ACCA at the 3′ end of tRNA rapidly forms. The second stage involves a slow intramolecular
rearrangement of the resulting metastable complex into a full-sized heteroduplex accompanied by the tRNAPhe unfolding. The data gained suggest that the RNA unfolding stage is limiting in the interaction of oligonucleotides with natural
RNAs. Principles of selection of optimal hybridization probes and antisense oligonucleotides are discussed. |
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Keywords: | antisense oligonucleotides hybridization tRNA unfolding of tRNA structure |
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