ArticleNucleic acids research2004
Substrate specificity and kinetic framework of a DNAzyme with an expanded chemical repertoire: a putative RNaseA mimic that catalyzes RNA hydrolysis independent of a divalent metal cation.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 60 citations in OpenAlex.
- Dynamism and evolvability in nucleic acid enzymes.Nature communications · 2026Article
- Polymerase Synthesis of Hypermodified DNA Displaying a Combination of Thiol, Hydroxyl, Carboxylate, and Imidazole Functional Groups in the Major Groove.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Nucleobase-modified nucleosides and nucleotides: Applications in biochemistry, synthetic biology, and drug discovery.Frontiers in chemistry · 2022Review
- How to Kinetically Dissect an RNA Machine.Biochemistry · 2021Article
- Human Recombinant DNase I (PulmozymeInternational journal of molecular sciences · 2021Article
- In vitro Selection of Chemically Modified DNAzymes.ChemistryOpen · 2020Review
- A densely modified MChemical science · 2018Article
- DNA Catalysis: The Chemical Repertoire of DNAzymes.Molecules (Basel, Switzerland) · 2015Review
- Synthesis and Enzymatic Incorporation of Modified Deoxyuridine Triphosphates.Molecules (Basel, Switzerland) · 2015Article
- Nucleoside triphosphates--building blocks for the modification of nucleic acids.Molecules (Basel, Switzerland) · 2012Review
- Merely two mutations switch a DNA-hydrolyzing deoxyribozyme from heterobimetallic (Zn2+/Mn2+) to monometallic (Zn2+-only) behavior.Chemical communications (Cambridge, England) · 2011Article
- DNA as a versatile chemical component for catalysis, encoding, and stereocontrol.Angewandte Chemie (International ed. in English) · 2010Review
- The structural diversity of deoxyribozymes.Molecules (Basel, Switzerland) · 2010Review
- Non-natural nucleotides as probes for the mechanism and fidelity of DNA polymerases.Biochimica et biophysica acta · 2010Review
- A role for hydrophobicity in a Diels-Alder reaction catalyzed by pyridyl-modified RNA.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
- RNase T1 mimicking artificial ribonuclease.Nucleic acids research · 2007Article
- Systematic characterization of 2'-deoxynucleoside- 5'-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA.Nucleic acids research · 2006Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This work addresses the binding, cleavage and dissociation rates for the substrate and products of a synthetic RNaseA mimic that was combinatorially selected using chemically modified nucleoside triphosphates. This trans-cleaving DNAzyme, 9(25)-11t, catalyzes sequence-specific ribophosphodiester hydrolysis in the total absence of a divalent metal cation, and in low ionic strength at pH 7.5 and in the presence of EDTA. It is the first such sequence capable of multiple turnover. 9(25)-11t consists of 31 bases, 18 of which form a catalytic domain containing 4 imidazole and 6 allylamino modified nucleotides. This sequence cleaves the 15 nt long substrate, S1, at one embedded ribocytosine at the eighth position to give a 5'-product terminating in a 2',3'-phosphodiester and a 3'-product terminating in a 5'-OH. Under single turnover conditions at 24 degrees C, 9(25)-11t displays a maximum first-order rate constant, k(cat), of 0.037 min(-1) and a catalytic efficiency, k(cat)/K(m), of 5.3 x 10(5) M(-1) min(-1). The measured value of k(cat) under catalyst excess conditions agrees with the value of k(cat) observed for steady-state multiple turnover, implying that slow product release is not rate limiting with respect to multiple turnover. The substrate specificity of 9(25)-11t was gauged in terms of k(cat) values for substrate sequence variants. Base substitutions on the scissile ribose and at the two bases immediately downstream decrease k(cat) values by a factor of 4 to 250, indicating that 9(25)-11t displays significant sequence specificity despite the lack of an apparent Watson-Crick base-pairing scheme for recognition.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.