In vitro evolution of an RNA-cleaving DNA enzyme into an RNA ligase switches the selectivity from 3′-5′ to 2′-5′

Amber Flynn-Charlebois, Tracey K. Prior, Kelly A. Hoadley, Scott K Silverman

Research output: Contribution to journalArticle

Abstract

Deoxyribozymes that ligate RNA expand the scope of nucleic acid catalysis and allow preparation of site-specifically modified RNAs. Previously, deoxyribozymes that join a 5′-hydroxyl and a 2′,3′-cyclic phosphate were identified by in vitro selection from random DNA pools. Here, the alternative strategy of in vitro evolution was used to transform the 8-17 deoxyribozyme that cleaves RNA into a family of DNA enzymes that ligate RNA. The parent 8-17 DNA enzyme cleaves native 3′-5′ phosphodiester linkages but not 2′-5′ bonds. Surprisingly, the new deoxyribozymes evolved from 8-17 create only 2′-5′ linkages. Thus, reversing the direction of the DNA-mediated process from ligation to cleavage also switches the selectivity in forming the new phosphodiester bond. The same change in selectivity was observed upon evolution of the 10-23 RNA-cleaving deoxyribozyme into an RNA ligase. The DNA enzymes previously isolated from random pools also create 2′-5′ linkages. Therefore, deoxyribozyme-mediated formation of a non-native 2′-5′ phosphodiester linkage from a 5′-hydroxyl and a 2′,3′-cyclic phosphate is strongly favored in many different contexts.

Original languageEnglish (US)
Pages (from-to)5346-5350
Number of pages5
JournalJournal of the American Chemical Society
Volume125
Issue number18
DOIs
StatePublished - May 7 2003

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Catalytic DNA
Catalyst selectivity
Ligases
RNA
DNA
Enzymes
Switches
enzyme
Hydroxyl Radical
Phosphates
phosphate
Nucleic acids
catalysis
nucleic acid
Catalysis
Nucleic Acids
cleavage
Ligation
In Vitro Techniques
transform

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

In vitro evolution of an RNA-cleaving DNA enzyme into an RNA ligase switches the selectivity from 3′-5′ to 2′-5′. / Flynn-Charlebois, Amber; Prior, Tracey K.; Hoadley, Kelly A.; Silverman, Scott K.

In: Journal of the American Chemical Society, Vol. 125, No. 18, 07.05.2003, p. 5346-5350.

Research output: Contribution to journalArticle

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