Parallel selections in vitro reveal a preference for 2′-5′ RNA ligation upon deoxyribozyme-mediated opening of a 2′,3′-cyclic phosphate

Daniel R. Semlow, Scott K Silverman

Research output: Contribution to journalArticle

Abstract

We previously used in vitro selection to identify Mg2+-dependent deoxyribozymes that mediate the ligation reaction of an RNA 5′-hydroxyl group with a 2′,3′-cyclic phosphate. In these efforts, all of the deoxyribozymes were identified via a common in vitro selection strategy, and all of the newly formed RNA linkages were non-native 2′-5′ phosphodiester bonds rather than native 3′-5′ linkages. Here we performed several new selections in which the relative arrangements of RNA and DNA were different as compared with the earlier studies. In all cases, we again find deoxyribozymes that create only 2′-5′ linkages. This includes deoxyribozymes with an arrangement that favors 3′-5′ linkages for a different chemical reaction, that of a 2′,3′-diol plus 5′-triphosphate. These data indicate a strong and context-independent chemical preference for creating 2′-5′ RNA linkages upon opening of a 2′,3′-cyclic phosphate with a 5′-hydroxyl group. Preliminary assays show that some of the newly identified deoxyribozymes have promise for ligating RNA in a sequence-general fashion. Because 2′,3′-cyclic phosphates are the products of uncatalyzed RNA backbone cleavage, their ligation reactions may be of direct relevance to the RNA World hypothesis.

Original languageEnglish (US)
Pages (from-to)207-215
Number of pages9
JournalJournal of Molecular Evolution
Volume61
Issue number2
DOIs
StatePublished - Aug 1 2005

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Catalytic DNA
Ligation
RNA
Phosphates
linkage (genetics)
phosphate
phosphates
Hydroxyl Radical
RNA Cleavage
glycols
chemical reactions
In Vitro Techniques
chemical reaction
cleavage
nucleotide sequences
assay
DNA
assays

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

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abstract = "We previously used in vitro selection to identify Mg2+-dependent deoxyribozymes that mediate the ligation reaction of an RNA 5′-hydroxyl group with a 2′,3′-cyclic phosphate. In these efforts, all of the deoxyribozymes were identified via a common in vitro selection strategy, and all of the newly formed RNA linkages were non-native 2′-5′ phosphodiester bonds rather than native 3′-5′ linkages. Here we performed several new selections in which the relative arrangements of RNA and DNA were different as compared with the earlier studies. In all cases, we again find deoxyribozymes that create only 2′-5′ linkages. This includes deoxyribozymes with an arrangement that favors 3′-5′ linkages for a different chemical reaction, that of a 2′,3′-diol plus 5′-triphosphate. These data indicate a strong and context-independent chemical preference for creating 2′-5′ RNA linkages upon opening of a 2′,3′-cyclic phosphate with a 5′-hydroxyl group. Preliminary assays show that some of the newly identified deoxyribozymes have promise for ligating RNA in a sequence-general fashion. Because 2′,3′-cyclic phosphates are the products of uncatalyzed RNA backbone cleavage, their ligation reactions may be of direct relevance to the RNA World hypothesis.",
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