ArticleACS combinatorial science2012
Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length.
Article in ACS combinatorial science, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Sequence-Dependent Acylation of Peptide Lysine Residues by DNAzymes.Chembiochem : a European journal of chemical biology · 2024Article
- DNA Catalysis: Design, Function, and Optimization.Molecules (Basel, Switzerland) · 2024Review
- Pushing the Limits of Nucleic Acid Function.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Review
- Generation of single stranded DNA with selective affinity to bovine spermatozoa.Animal bioscience · 2021Article
- New DNA-hydrolyzing DNAs isolated from an ssDNA library carrying a terminal hybridization stem.Nucleic acids research · 2021Article
- Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors.Pharmaceuticals (Basel, Switzerland) · 2021Review
- DNAmoreDB, a database of DNAzymes.Nucleic acids research · 2021Article
- Random-sequence genetic oligomer pools display an innate potential for ligation and recombination.eLife · 2018Article
- Aptamer-field-effect transistors overcome Debye length limitations for small-molecule sensing.Science (New York, N.Y.) · 2018Article
- Characterization of Highly Efficient RNA-Cleaving DNAzymes that Function at Acidic pH with No Divalent Metal-Ion Cofactors.ChemistryOpen · 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
- Analysis of In Vitro Aptamer Selection Parameters.Journal of molecular evolution · 2015Review
- Identification of Sequence-Selective Tyrosine Kinase Deoxyribozymes.Journal of molecular evolution · 2015Article
- DNA Catalysis: The Chemical Repertoire of DNAzymes.Molecules (Basel, Switzerland) · 2015Review
- Pursuing DNA catalysts for protein modification.Accounts of chemical research · 2015Article
- A generalizable DNA-catalyzed approach to peptide-nucleic acid conjugation.Chembiochem : a European journal of chemical biology · 2014Article
- In vitro selection of DNA-cleaving deoxyribozyme with site-specific thymidine excision activity.Nucleic acids research · 2014Article
- DNA-catalyzed hydrolysis of esters and aromatic amides.Journal of the American Chemical Society · 2013Article
- DNA catalysts with tyrosine kinase activity.Journal of the American Chemical Society · 2013Article
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8 authors.
Funding
Abstract
Functional nucleic acids are DNA and RNA aptamers that bind targets, or they are deoxyribozymes and ribozymes that have catalytic activity. These functional DNA and RNA sequences can be identified from random-sequence pools by in vitro selection, which requires choosing the length of the random region. Shorter random regions allow more complete coverage of sequence space but may not permit the structural complexity necessary for binding or catalysis. In contrast, longer random regions are sampled incompletely but may allow adoption of more complicated structures that enable function. In this study, we systematically examined random region length (N(20) through N(60)) for two particular deoxyribozyme catalytic activities, DNA cleavage and tyrosine-RNA nucleopeptide linkage formation. For both activities, we previously identified deoxyribozymes using only N(40) regions. In the case of DNA cleavage, here we found that shorter N(20) and N(30) regions allowed robust catalytic function, either by DNA hydrolysis or by DNA deglycosylation and strand scission via β-elimination, whereas longer N(50) and N(60) regions did not lead to catalytically active DNA sequences. Follow-up selections with N(20), N(30), and N(40) regions revealed an interesting interplay of metal ion cofactors and random region length. Separately, for Tyr-RNA linkage formation, N(30) and N(60) regions provided catalytically active sequences, whereas N(20) was unsuccessful, and the N(40) deoxyribozymes were functionally superior (in terms of rate and yield) to N(30) and N(60). Collectively, the results indicate that with future in vitro selection experiments for DNA and RNA catalysts, and by extension for aptamers, random region length should be an important experimental variable.
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