ArticleNucleic acids research2008
Sequence-function relationships provide new insight into the cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme.
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 33 papers.
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Who cites it
33 citing papers in PubMed.
- 2'-O-methylation-dependent installation of NNature communications · 2026Article
- Advances in DNAzyme Selection, Molecular Engineering and Biomedical Applications.International journal of molecular sciences · 2026Review
- The Programmable Catalytic Core of 8-17 DNAzymes.Molecules (Basel, Switzerland) · 2024Article
- A high-fidelity DNAzyme-assisted CRISPR/Cas13a system with single-nucleotide resolved specificity.Chemical science · 2024Article
- Improving the Sensitivity of a Mn(II)-Specific DNAzyme for Cellular Imaging Sensor through Sequence Mutations.Analytical chemistry · 2024Article
- Development of 8-17 XNAzymes that are functional in cells.Chemical science · 2023Article
- Fluorescent detection of brown spot of tobacco caused byRSC advances · 2023Article
- DNA-based enzymatic systems and their applications.iScience · 2022Review
- An RNA-cleaving threose nucleic acid enzyme capable of single point mutation discrimination.Nature chemistry · 2022Article
- Biosensing with DNAzymes.Chemical Society reviews · 2021Review
- In vitro Selection of Chemically Modified DNAzymes.ChemistryOpen · 2020Review
- New Deoxyribozymes for the Native Ligation of RNA.Molecules (Basel, Switzerland) · 2020Article
- DNAzyme-Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells.Angewandte Chemie (International ed. in English) · 2020Article
- DNAzyme-Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells.Angewandte Chemie (Weinheim an der Bergstrasse, Germany) · 2020Article
- Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology.iScience · 2020Review
- High-resolution DNA quadruplex structure containing all the A-, G-, C-, T-tetrads.Nucleic acids research · 2018Article
- Evidence of a General Acid-Base Catalysis Mechanism in the 8-17 DNAzyme.Biochemistry · 2018Article
- Crystal structure of an RNA-cleaving DNAzyme.Nature communications · 2017Article
- Theranostic DNAzymes.Theranostics · 2017Review
- Sequence Mutation and Structural Alteration Transform a Noncatalytic DNA Sequence into an Efficient RNA-Cleaving DNAzyme.Journal of molecular evolution · 2015Article
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4 authors.
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Abstract
Many sequence variations of the 8-17 RNA-cleaving deoxyribozyme have been isolated through in vitro selection. In an effort to understand how these sequence variations affect cleavage site selectivity, we systematically mutated the catalytic core of 8-17 and measured the cleavage activity of each mutant deoxyribozyme against all 16 possible chimeric (RNA/DNA) dinucleotide junctions. We observed sequence-function relationships that suggest how the following non-conserved positions in the catalytic core influence selectivity at the dinucleotide (5' rN(18)-N(1.1) 3') cleavage site: (i) positions 2.1 and 12 represent a primary determinant of the selectivity at the 3' position (N(1.1)) of the cleavage site; (ii) positions 15 and 15.0 represent a primary determinant of the selectivity at the 5' position (rN(18)) of the cleavage site and (iii) the sequence of the 3-bp intramolecular stem has relatively little influence on cleavage site selectivity. Furthermore, we report for the first time that 8-17 variants have the collective ability to cleave all dinucleotide junctions with rate enhancements of at least 1000-fold over background. Three optimal 8-17 variants, identified from approximately 75 different sequences that were examined, can collectively cleave 10 of 16 junctions with useful rates of >/=0.1 min(-1), and exhibit an overall hierarchy of reactivity towards groups of related junctions according to the order NG > NA > NC > NT.
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