DNA catalysis of a normally disfavored RNA hydrolysis reaction

Darren J. Parker, Ying Xiao, John M. Aguilar, Scott K Silverman

Research output: Contribution to journalArticle

Abstract

We recently used in vitro selection to identify many deoxyribozymes that catalyze DNA phosphodiester bond hydrolysis and create 5′-phosphate and 3′-hydroxyl termini. Alternatively, numerous deoxyribozymes have been identified for catalysis of RNA cleavage by 2′-hydroxyl transesterification, forming 2′,3′-cyclic phosphate and 5′-hydroxyl termini. In this study, we investigated the ability of DNA to catalyze RNA cleavage by hydrolysis rather than transesterification, although normally the hydrolysis reaction is substantially disfavored relative to transesterification. Via a series of in vitro selection experiments, we found that reselection of a DNA-hydrolyzing deoxyribozyme leads either to transesterification or hydrolysis, depending on exclusion or inclusion of a stringent selection pressure for hydrolysis. An entirely new selection starting from a random DNA pool, using an all-RNA substrate and imposing the same selection pressure, also leads to RNA hydrolysis. Collectively, these results establish experimentally that small DNA sequences have the catalytic ability to direct a chemical reaction down a disfavored pathway, even when a more favorable mechanism is readily available. Our view of DNA catalysis is therefore expanded beyond merely increasing the rates of reactions that would have occurred more slowly without the catalyst.

Original languageEnglish (US)
Pages (from-to)8472-8475
Number of pages4
JournalJournal of the American Chemical Society
Volume135
Issue number23
DOIs
StatePublished - Jun 12 2013

Fingerprint

catalysis
RNA
Catalysis
hydrolysis
Hydrolysis
DNA
Transesterification
Catalytic DNA
RNA Cleavage
Hydroxyl Radical
cleavage
Phosphates
phosphate
Pressure
DNA sequences
chemical reaction
Chemical reactions
catalyst
substrate
Catalysts

ASJC Scopus subject areas

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

Cite this

DNA catalysis of a normally disfavored RNA hydrolysis reaction. / Parker, Darren J.; Xiao, Ying; Aguilar, John M.; Silverman, Scott K.

In: Journal of the American Chemical Society, Vol. 135, No. 23, 12.06.2013, p. 8472-8475.

Research output: Contribution to journalArticle

Parker, Darren J. ; Xiao, Ying ; Aguilar, John M. ; Silverman, Scott K. / DNA catalysis of a normally disfavored RNA hydrolysis reaction. In: Journal of the American Chemical Society. 2013 ; Vol. 135, No. 23. pp. 8472-8475.
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