A DNA enzyme that cleaves RNA
TL;DR: Using in vitro selection techniques, a DNA enzyme is obtained that catalyzes the Pb(2+)-dependent cleavage of an RNA phosphoester in a reaction that proceeds with rapid turnover, and compares favorably to that of known RNA enzymes.
About: This article is published in Chemistry & Biology.The article was published on 1994-12-01. It has received 1225 citations till now. The article focuses on the topics: Base pair & Primase.
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TL;DR: This review discusses various nanomaterials that have been explored to mimic different kinds of enzymes and covers their kinetics, mechanisms and applications in numerous fields, from biosensing and immunoassays, to stem cell growth and pollutant removal.
Abstract: Over the past few decades, researchers have established artificial enzymes as highly stable and low-cost alternatives to natural enzymes in a wide range of applications. A variety of materials including cyclodextrins, metal complexes, porphyrins, polymers, dendrimers and biomolecules have been extensively explored to mimic the structures and functions of naturally occurring enzymes. Recently, some nanomaterials have been found to exhibit unexpected enzyme-like activities, and great advances have been made in this area due to the tremendous progress in nano-research and the unique characteristics of nanomaterials. To highlight the progress in the field of nanomaterial-based artificial enzymes (nanozymes), this review discusses various nanomaterials that have been explored to mimic different kinds of enzymes. We cover their kinetics, mechanisms and applications in numerous fields, from biosensing and immunoassays, to stem cell growth and pollutant removal. We also summarize several approaches to tune the activities of nanozymes. Finally, we make comparisons between nanozymes and other catalytic materials (other artificial enzymes, natural enzymes, organic catalysts and nanomaterial-based catalysts) and address the current challenges and future directions (302 references).
2,951 citations
TL;DR: The design and observation of two-dimensional crystalline forms of DNA that self-assemble from synthetic DNA double-crossover molecules that create specific periodic patterns on the nanometre scale are reported.
Abstract: Molecular self-assembly presents a `bottom-up' approach to the fabrication of objects specified with nanometre precision. DNA
molecular structures and intermolecular interactions are particularly
amenable to the design and synthesis of complex molecular objects. We
report the design and observation of two-dimensional crystalline forms
of DNA that self-assemble from synthetic DNA double-crossover
molecules. Intermolecular interactions between the structural units are
programmed by the design of `sticky ends' that associate according to
Watson-Crick complementarity, enabling us to create specific periodic
patterns on the nanometre scale. The patterned crystals have been
visualized by atomic force microscopy.
2,713 citations
1,915 citations
TL;DR: An in vitro selection procedure was used to develop a DNA enzyme that can be made to cleave almost any targeted RNA substrate under simulated physiological conditions, and its activity is dependent on the presence of Mg2+ ion.
Abstract: An in vitro selection procedure was used to develop a DNA enzyme that can be made to cleave almost any targeted RNA substrate under simulated physiological conditions. The enzyme is comprised of a catalytic domain of 15 deoxynucleotides, flanked by two substrate-recognition domains of seven to eight deoxynucleotides each. The RNA substrate is bound through Watson–Crick base pairing and is cleaved at a particular phosphodiester located between an unpaired purine and a paired pyrimidine residue. Despite its small size, the DNA enzyme has a catalytic efficiency (kcat/Km) of ≈109 M−1⋅min−1 under multiple turnover conditions, exceeding that of any other known nucleic acid enzyme. Its activity is dependent on the presence of Mg2+ ion. By changing the sequence of the substrate-recognition domains, the DNA enzyme can be made to target different RNA substrates. In this study, for example, it was directed to cleave synthetic RNAs corresponding to the start codon region of HIV-1 gag/pol, env, vpr, tat, and nef mRNAs.
1,411 citations
TL;DR: This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.
Abstract: DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.
1,249 citations
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TL;DR: The RNA moieties of ribonuclease P purified from both E. coli and B. subtilis can cleave tRNA precursor molecules in buffers containing either 60 mM Mg2+ or 10 mM MG2+ plus 1 mM spermidine, and in vitro, the RNA and protein subunits from one species can complement sub units from the other species in reconstitution experiments.
2,524 citations
TL;DR: The isolation of single-stranded DNA aptamers to the protease thrombin of the blood coagulation cascade is described and binding affinities in the range 25–200 nM are reported.
Abstract: Aptamers are double-stranded DNA or single-stranded RNA molecules that bind specific molecular targets. Large randomly generated populations can be enriched in aptamers by in vitro selection and polymerase chain reaction. But so far single-stranded DNA has not been investigated for aptamer properties, nor has a target protein been considered that does not interact physiologically with nucleic acid. Here we describe the isolation of single-stranded DNA aptamers to the protease thrombin of the blood coagulation cascade and report binding affinities in the range 25-200 nM. Sequence data from 32 thrombin aptamers, selected from a pool of DNA containing 60 nucleotides of random sequence, displayed a highly conserved 14-17-base region. Several of these aptamers at nanomolar concentrations inhibited thrombin-catalysed fibrin-clot formation in vitro using either purified fibrinogen or human plasma.
2,358 citations
TL;DR: It is proposed that the IVS portion of the RNA has several enzyme-like properties that enable it to break and reform phosphodiester bonds and that enzymes, small nuclear RNAs and folding of the pre-rRNA into an RNP are unnecessary for these reactions.
2,077 citations
TL;DR: A 19-nucleotide RNA fragment can cause rapid, highly specific cleavage of a 24-nuclear RNA fragment under physiological conditions.
Abstract: A 19-nucleotide RNA fragment can cause rapid, highly specific cleavage of a 24-nucleotide RNA fragment under physiological conditions. Because each 19-mer can participate in many cleavage reactions, this molecule has all the properties associated with an RNA enzyme.
900 citations
TL;DR: This aptamer structure was determined by NMR and illustrates that this molecule forms a specific folded structure, which may be used in the further development of oligonucleotide-based thrombin inhibitors.
Abstract: We have used two-dimensional 1H NMR spectroscopy to study the conformation of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG) in solution This is one of a series of thrombin-binding DNA aptamers with a consensus 15-base sequence that was recently isolated and shown to inhibit thrombin-catalyzed fibrin clot formation in vitro [Bock, L C, Griffin, L C, Latham, J A, Vermaas, E H & Toole, J J (1992) Nature (London) 355, 564-566] The oligonucleotide forms a unimolecular DNA quadruplex consisting of two G-quartets connected by two TT loops and one TGT loop A potential TT bp is formed between the two TT loops across the diagonal of the top G-quartet Thus, all of the invariant bases in the consensus sequence are base-paired This aptamer structure was determined by NMR and illustrates that this molecule forms a specific folded structure Knowledge of this structure may be used in the further development of oligonucleotide-based thrombin inhibitors
845 citations