Complementary oligonucleotide binding to transfer RNA

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Abstract

Association constants between Escherichia coli tRNATyr and oligoribonucleotides complementary to its sequence were determined by equilibrium dialysis. A tetramer was judged to bind to complementary single-stranded regions of the RNA molecule when its equilibrium constant was greater than twice the sum of the equilibrium constants of the constituent trimers. In the case of a tetramer binding to the anticodon loop, a study of the temperature dependence of the association constant revealed a much higher value of Tm than obtained with model compounds. A scan of the tRNATyr sequence with complementary trimers and tetramers identified four regions of the cloverleaf which were available for binding. These are: (1) the four 3′-terminal residues; (2) most of the anticodon loop; (3) a portion of the dihydrouracil loop and (4) some of the sequences in the variable-length region. In the latter two cases, the oligomers which bind may compete with the native tRNA structure. Nevertheless, oligomers which bind to one part of the tRNA molecule are generally found not to affect association constants of oligomers binding elsewhere on the tRNA. Similar equilibrium dialysis experiments with tRNAf Met reveal little difference in the regions of the cloverleaf available for oligomer binding.

Original languageEnglish (US)
Pages (from-to)25-41
Number of pages17
JournalJournal of Molecular Biology
Volume65
Issue number1
DOIs
StatePublished - Mar 14 1972

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RNA, Transfer, Tyr
Transfer RNA
Oligonucleotides
Anticodon
Dialysis
Oligoribonucleotides
RNA
Escherichia coli
Temperature

ASJC Scopus subject areas

  • Virology

Cite this

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abstract = "Association constants between Escherichia coli tRNATyr and oligoribonucleotides complementary to its sequence were determined by equilibrium dialysis. A tetramer was judged to bind to complementary single-stranded regions of the RNA molecule when its equilibrium constant was greater than twice the sum of the equilibrium constants of the constituent trimers. In the case of a tetramer binding to the anticodon loop, a study of the temperature dependence of the association constant revealed a much higher value of Tm than obtained with model compounds. A scan of the tRNATyr sequence with complementary trimers and tetramers identified four regions of the cloverleaf which were available for binding. These are: (1) the four 3′-terminal residues; (2) most of the anticodon loop; (3) a portion of the dihydrouracil loop and (4) some of the sequences in the variable-length region. In the latter two cases, the oligomers which bind may compete with the native tRNA structure. Nevertheless, oligomers which bind to one part of the tRNA molecule are generally found not to affect association constants of oligomers binding elsewhere on the tRNA. Similar equilibrium dialysis experiments with tRNAf Met reveal little difference in the regions of the cloverleaf available for oligomer binding.",
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Complementary oligonucleotide binding to transfer RNA. / Uhlenbeck, Olke C.

In: Journal of Molecular Biology, Vol. 65, No. 1, 14.03.1972, p. 25-41.

Research output: Contribution to journalArticle

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AB - Association constants between Escherichia coli tRNATyr and oligoribonucleotides complementary to its sequence were determined by equilibrium dialysis. A tetramer was judged to bind to complementary single-stranded regions of the RNA molecule when its equilibrium constant was greater than twice the sum of the equilibrium constants of the constituent trimers. In the case of a tetramer binding to the anticodon loop, a study of the temperature dependence of the association constant revealed a much higher value of Tm than obtained with model compounds. A scan of the tRNATyr sequence with complementary trimers and tetramers identified four regions of the cloverleaf which were available for binding. These are: (1) the four 3′-terminal residues; (2) most of the anticodon loop; (3) a portion of the dihydrouracil loop and (4) some of the sequences in the variable-length region. In the latter two cases, the oligomers which bind may compete with the native tRNA structure. Nevertheless, oligomers which bind to one part of the tRNA molecule are generally found not to affect association constants of oligomers binding elsewhere on the tRNA. Similar equilibrium dialysis experiments with tRNAf Met reveal little difference in the regions of the cloverleaf available for oligomer binding.

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