DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides

Nucleic Acids Res. 2009 Feb;37(2):413-20. doi: 10.1093/nar/gkn930. Epub 2008 Dec 2.

Abstract

Single-stranded DNA molecules have the capacity to adopt catalytically active structures known as DNAzymes, although the fundamental limits of this ability have not been determined. Starting with a parent DNAzyme composed of all four types of standard nucleotides, we conducted a search of the surrounding sequence space to identify functional derivatives with catalytic cores composed of only three, and subsequently only two types of nucleotides. We provide the first report of a DNAzyme that contains only guanosine and cytidine deoxyribonucleotides in its catalytic domain, which consists of just 13 nucleotides. This DNAzyme catalyzes the Mn(2+)-dependent cleavage of an RNA phosphodiester bond approximately 5300-fold faster than the corresponding uncatalyzed reaction, but approximately 10,000-fold slower than the parent. The demonstration of a catalytic DNA molecule made from a binary nucleotide alphabet broadens our understanding of the fundamental limits of nucleic-acid-mediated catalysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biocatalysis
  • Cytosine Nucleotides / chemistry*
  • DNA, Catalytic / chemistry*
  • Guanine Nucleotides / chemistry*
  • Metals / chemistry
  • RNA / chemistry
  • RNA / metabolism

Substances

  • Cytosine Nucleotides
  • DNA, Catalytic
  • Guanine Nucleotides
  • Metals
  • RNA