title: DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides.
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.
authors.affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5.
authors.forename: Kenny
authors.initials: K
authors.lastname: Schlosser
authors.forename: Yingfu
authors.initials: Y
authors.lastname: Li
mesh_terms: D055162:Biocatalysis; D003597:Cytosine Nucleotides / Q000737:chemistry*; D021881:DNA, Catalytic / Q000737:chemistry*; D006150:Guanine Nucleotides / Q000737:chemistry*; D008670:Metals / Q000737:chemistry; D012313:RNA / Q000737:chemistry / Q000378:metabolism
chemical_list: D003597:Cytosine Nucleotides; D021881:DNA, Catalytic; D006150:Guanine Nucleotides; D008670:Metals; D012313:RNA