ArticleNucleic acids research2008
In vitro selection of small RNA-cleaving deoxyribozymes that cleave pyrimidine-pyrimidine junctions.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 49 citations in OpenAlex.
- A DNA triangular prism scaffold-guided directionally-controlled derailment-free DNAzyme walker.Journal of advanced research · 2026Article
- A high-fidelity DNAzyme-assisted CRISPR/Cas13a system with single-nucleotide resolved specificity.Chemical science · 2024Article
- ZnCommunications biology · 2021Article
- In vitro Selection of Chemically Modified DNAzymes.ChemistryOpen · 2020Review
- A Novel Small RNA-Cleaving Deoxyribozyme with a Short Binding Arm.Scientific reports · 2019Article
- Identification of the Same Na(+)-Specific DNAzyme Motif from Two In Vitro Selections Under Different Conditions.Journal of molecular evolution · 2015Article
- Searching for a DNAzyme Version of the Leadzyme.Journal of molecular evolution · 2015Article
- DNA Catalysis: The Chemical Repertoire of DNAzymes.Molecules (Basel, Switzerland) · 2015Review
- An Efficient Catalytic DNA that Cleaves L-RNA.PloS one · 2015Article
- Overcoming EGFR T790M-based Tyrosine Kinase Inhibitor Resistance with an Allele-specific DNAzyme.Molecular therapy. Nucleic acids · 2014Article
- DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli.BMC biotechnology · 2010Article
- A highly selective lead sensor based on a classic lead DNAzyme.Chemical communications (Cambridge, England) · 2010Article
- DNA-catalyzed sequence-specific hydrolysis of DNA.Nature chemical biology · 2009Article
- A genotype-to-phenotype map of in vitro selected RNA-cleaving DNAzymes: implications for accessing the target phenotype.Nucleic acids research · 2009Article
- A self-cleaving DNA enzyme modified with amines, guanidines and imidazoles operates independently of divalent metal cations (M2+).Nucleic acids research · 2009Article
- DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides.Nucleic acids research · 2009Article
- Use of deoxyribozymes in RNA research.Methods in enzymology · 2009Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Herein, we sought new or improved endoribonucleases based on catalytic DNA molecules known as deoxyribozymes. The current repertoire of RNA-cleaving deoxyribozymes can cleave nearly all of the 16 possible dinucleotide junctions with rates of at least 0.1/min, with the exception of pyrimidine-pyrimidine (pyr-pyr) junctions, which are cleaved 1-3 orders of magnitude slower. We conducted four separate in vitro selection experiments to target each pyr-pyr dinucleotide combination (i.e. CC, UC, CT and UT) within a chimeric RNA/DNA substrate. We used a library of DNA molecules containing only 20 random-sequence nucleotides, so that all possible sequence permutations could be sampled in each experiment. From a total of 245 clones, we identified 22 different sequence families, of which 21 represented novel deoxyribozyme motifs. The fastest deoxyribozymes exhibited k(obs) values (single-turnover, intermolecular format) of 0.12/min, 0.04/min, 0.13/min and 0.15/min against CC, UC, CT and UT junctions, respectively. These values represent a 6- to 8-fold improvement for CC and UC junctions, and a 1000- to 1600-fold improvement for CT and UT junctions, compared to the best rates reported previously under identical reaction conditions. The same deoxyribozymes exhibited approximately 1000-fold lower activity against all RNA substrates, but could potentially be improved through further in vitro evolution and engineering.
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