ArticleNucleic acids research2012
Establishing broad generality of DNA catalysts for site-specific hydrolysis of single-stranded DNA.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Cooperative Mismatch Discrimination by PNA and DNAzyme Enables High-Fidelity Cleavage of Plasmid DNA.Biochemistry · 2025Article
- PCR-Free Site-Directed Mutagenesis on Repetitive Sequences Using Single-Stranded DNA-Assisted Double-Stranded DNA Nicking by DNAzymes.Angewandte Chemie (International ed. in English) · 2025Article
- Site-specific N-alkylation of DNA oligonucleotide nucleobases by DNAzyme-catalyzed reductive amination.Nucleic acids research · 2024Article
- PNA-Assisted DNAzymes to Cleave Double-Stranded DNA for Genetic Engineering with High Sequence Fidelity.Journal of the American Chemical Society · 2021Article
- New DNA-hydrolyzing DNAs isolated from an ssDNA library carrying a terminal hybridization stem.Nucleic acids research · 2021Article
- Selective tumor cell death induced by irradiated riboflavin through recognizing DNA G-T mismatch.Nucleic acids research · 2017Article
- DNA-Catalyzed DNA Cleavage by a Radical Pathway with Well-Defined Products.Journal of the American Chemical Society · 2017Article
- DNA Oligonucleotide 3'-Phosphorylation by a DNA Enzyme.Biochemistry · 2016Article
- DNA Catalysis: The Chemical Repertoire of DNAzymes.Molecules (Basel, Switzerland) · 2015Review
- Pursuing DNA catalysts for protein modification.Accounts of chemical research · 2015Article
- In vitro selection of DNA-cleaving deoxyribozyme with site-specific thymidine excision activity.Nucleic acids research · 2014Article
- Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering.PloS one · 2014Article
- DNA-catalyzed hydrolysis of esters and aromatic amides.Journal of the American Chemical Society · 2013Article
- Small, highly active DNAs that hydrolyze DNA.Journal of the American Chemical Society · 2013Article
- DNA catalysis of a normally disfavored RNA hydrolysis reaction.Journal of the American Chemical Society · 2013Article
- Production of single-stranded DNAs by self-cleavage of rolling-circle amplification products.BioTechniques · 2013Article
- Catalytic DNA with phosphatase activity.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length.ACS combinatorial science · 2012Article
- Lanthanide ions as required cofactors for DNA catalysts.Chemical scienceArticle
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4 authors.
Funding
Abstract
We recently reported that a DNA catalyst (deoxyribozyme) can site-specifically hydrolyze DNA on the minutes time scale. Sequence specificity is provided by Watson-Crick base pairing between the DNA substrate and two oligonucleotide binding arms that flank the 40-nt catalytic region of the deoxyribozyme. The DNA catalyst from our recent in vitro selection effort, 10MD5, can cleave a single-stranded DNA substrate sequence with the aid of Zn(2+) and Mn(2+) cofactors, as long as the substrate cleavage site encompasses the four particular nucleotides ATG^T. Thus, 10MD5 can cleave only 1 out of every 256 (4(4)) arbitrarily chosen DNA sites, which is rather poor substrate sequence tolerance. In this study, we demonstrated substantially broader generality of deoxyribozymes for site-specific DNA hydrolysis. New selection experiments were performed, revealing the optimality of presenting only one or two unpaired DNA substrate nucleotides to the N(40) DNA catalytic region. Comprehensive selections were then performed, including in some cases a key selection pressure to cleave the substrate at a predetermined site. These efforts led to identification of numerous new DNA-hydrolyzing deoxyribozymes, many of which require merely two particular nucleotide identities at the cleavage site (e.g. T^G), while retaining Watson-Crick sequence generality beyond those nucleotides along with useful cleavage rates. These findings establish experimentally that broadly sequence-tolerant and site-specific deoxyribozymes are readily identified for hydrolysis of single-stranded DNA.
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