Identification of the Same Na+-Specific DNAzyme Motif from Two In Vitro Selections Under Different Conditions

Seyed Fakhreddin Torabi, Yi Lu

Research output: Contribution to journalArticle

Abstract

We report an investigation of the functional relationship between two independently selected RNA-cleaving DNAzymes, NaA43, and Ce13, through in vitro selection. The NaA43 DNAzyme was obtained through a combination of gel-based and column-based in vitro selection in the presence of Na+ and reported to be highly selective for Na+ over other metal ions. The Ce13 DNAzyme was isolated via a gel-based method in the presence of Ce4+ and found to be active with trivalent lanthanides, Y3+ and Pb2+. Despite completely different activities reported for the two DNAzymes, they share a high level of sequence similarity (~60 % sequence identity). In this work, we systematically analyzed the activity of both DNAzymes to elucidate their potential functional relationship. We found that Na+ is an obligate cofactor of the Ce13 DNAzyme and lanthanides cannot initiate the cleavage reaction in the absence of Na+. Hence, we conclude that the Ce13 DNAzyme is a variant of the NaA43 DNAzyme that catalyzes reaction in the presence Na+ and also utilizes lanthanides in a potentially allosteric manner. These results have identified a new DNAzyme motif that is not only remarkably Na+-specific, but also allows for design of novel allosteric DNAzymes for different biotechnological applications.

Original languageEnglish (US)
Pages (from-to)225-234
Number of pages10
JournalJournal of Molecular Evolution
Volume81
Issue number5-6
DOIs
StatePublished - Dec 1 2015

Keywords

  • DNAzyme (deoxyribozyme)
  • Functional motif
  • In vitro selection
  • Lanthanides
  • Sodium

ASJC Scopus subject areas

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

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