Oligonucleotide binding to the native and denatured conformers of yeast transfer RNA3Leu

Olke C. Uhlenbeck*, Jack G. Chirikjian, Jacques R. Fresco

*Corresponding author for this work

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

The equilibrium binding patterns of complementary oligonucleotides to the native and denatured conformers of yeast transfer RNA3Leu have been determined. The pattern of binding to the native conformer follows that observed previously with other tRNAs. The results indicate that the anticodon loop and 3′ terminus are free in solution, and that all stems of the cloverleaf appear intact, although the dihydrouracil and "extra arm" stems are sufficiently weak to be subject to competitive binding by the probe oligomers. The T ΨC loop is also inaccessible to oligomer binding, while the dihydrouracil loop shows a low level of binding suggestive of oligomer competition with existing RNA structure. By contrast, in the denatured conformer the dihydrouracil loop and stem show strong oligomer binding characteristics of random RNA segments, whereas the anticodon loop no longer binds complementary oligomers. Binding to other regions remains unchanged, suggesting that the three major cloverleaf stems are intact. These observations are used as a basis for consideration of models for the two conformers.

Original languageEnglish (US)
Pages (from-to)495-504
Number of pages10
JournalJournal of Molecular Biology
Volume89
Issue number3
DOIs
StatePublished - Nov 5 1974

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Oligonucleotides
Anticodon
Yeasts
RNA
Competitive Binding
Transfer RNA
dihydrouracil

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

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title = "Oligonucleotide binding to the native and denatured conformers of yeast transfer RNA3Leu",
abstract = "The equilibrium binding patterns of complementary oligonucleotides to the native and denatured conformers of yeast transfer RNA3Leu have been determined. The pattern of binding to the native conformer follows that observed previously with other tRNAs. The results indicate that the anticodon loop and 3′ terminus are free in solution, and that all stems of the cloverleaf appear intact, although the dihydrouracil and {"}extra arm{"} stems are sufficiently weak to be subject to competitive binding by the probe oligomers. The T ΨC loop is also inaccessible to oligomer binding, while the dihydrouracil loop shows a low level of binding suggestive of oligomer competition with existing RNA structure. By contrast, in the denatured conformer the dihydrouracil loop and stem show strong oligomer binding characteristics of random RNA segments, whereas the anticodon loop no longer binds complementary oligomers. Binding to other regions remains unchanged, suggesting that the three major cloverleaf stems are intact. These observations are used as a basis for consideration of models for the two conformers.",
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Oligonucleotide binding to the native and denatured conformers of yeast transfer RNA3Leu. / Uhlenbeck, Olke C.; Chirikjian, Jack G.; Fresco, Jacques R.

In: Journal of Molecular Biology, Vol. 89, No. 3, 05.11.1974, p. 495-504.

Research output: Contribution to journalArticle

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N2 - The equilibrium binding patterns of complementary oligonucleotides to the native and denatured conformers of yeast transfer RNA3Leu have been determined. The pattern of binding to the native conformer follows that observed previously with other tRNAs. The results indicate that the anticodon loop and 3′ terminus are free in solution, and that all stems of the cloverleaf appear intact, although the dihydrouracil and "extra arm" stems are sufficiently weak to be subject to competitive binding by the probe oligomers. The T ΨC loop is also inaccessible to oligomer binding, while the dihydrouracil loop shows a low level of binding suggestive of oligomer competition with existing RNA structure. By contrast, in the denatured conformer the dihydrouracil loop and stem show strong oligomer binding characteristics of random RNA segments, whereas the anticodon loop no longer binds complementary oligomers. Binding to other regions remains unchanged, suggesting that the three major cloverleaf stems are intact. These observations are used as a basis for consideration of models for the two conformers.

AB - The equilibrium binding patterns of complementary oligonucleotides to the native and denatured conformers of yeast transfer RNA3Leu have been determined. The pattern of binding to the native conformer follows that observed previously with other tRNAs. The results indicate that the anticodon loop and 3′ terminus are free in solution, and that all stems of the cloverleaf appear intact, although the dihydrouracil and "extra arm" stems are sufficiently weak to be subject to competitive binding by the probe oligomers. The T ΨC loop is also inaccessible to oligomer binding, while the dihydrouracil loop shows a low level of binding suggestive of oligomer competition with existing RNA structure. By contrast, in the denatured conformer the dihydrouracil loop and stem show strong oligomer binding characteristics of random RNA segments, whereas the anticodon loop no longer binds complementary oligomers. Binding to other regions remains unchanged, suggesting that the three major cloverleaf stems are intact. These observations are used as a basis for consideration of models for the two conformers.

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