Literature DB >> 27236301

Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes.

Scott K Silverman1.   

Abstract

The discovery of natural RNA enzymes (ribozymes) prompted the pursuit of artificial DNA enzymes (deoxyribozymes) by in vitro selection methods. A key motivation is the conceptual and practical advantages of DNA relative to proteins and RNA. Early studies focused on RNA-cleaving deoxyribozymes, and more recent experiments have expanded the breadth of catalytic DNA to many other reactions. Including modified nucleotides has the potential to widen the scope of DNA enzymes even further. Practical applications of deoxyribozymes include their use as sensors for metal ions and small molecules. Structural studies of deoxyribozymes are only now beginning; mechanistic experiments will surely follow. Following the first report 21 years ago, the field of deoxyribozymes has promise for both fundamental and applied advances in chemistry, biology, and other disciplines.
Copyright © 2016 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  DNA catalyst; DNA enzyme; DNAzyme; catalytic DNA; deoxyribozyme

Mesh:

Substances:

Year:  2016        PMID: 27236301      PMCID: PMC4930396          DOI: 10.1016/j.tibs.2016.04.010

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  122 in total

1.  A DNA enzyme with N-glycosylase activity.

Authors:  T L Sheppard; P Ordoukhanian; G F Joyce
Journal:  Proc Natl Acad Sci U S A       Date:  2000-07-05       Impact factor: 11.205

2.  Characterization of a DNA-cleaving deoxyribozyme.

Authors:  N Carmi; R R Breaker
Journal:  Bioorg Med Chem       Date:  2001-10       Impact factor: 3.641

3.  RNA cleavage by a DNA enzyme with extended chemical functionality.

Authors:  S W Santoro; G F Joyce; K Sakthivel; S Gramatikova
Journal:  J Am Chem Soc       Date:  2000-03-22       Impact factor: 15.419

Review 4.  How RNA folds.

Authors:  I Tinoco; C Bustamante
Journal:  J Mol Biol       Date:  1999-10-22       Impact factor: 5.469

5.  Crystal structure of an 82-nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme.

Authors:  J Nowakowski; P J Shim; G S Prasad; C D Stout; G F Joyce
Journal:  Nat Struct Biol       Date:  1999-02

6.  Capping DNA with DNA.

Authors:  Y Li; Y Liu; R R Breaker
Journal:  Biochemistry       Date:  2000-03-21       Impact factor: 3.162

7.  Phosphorylating DNA with DNA.

Authors:  Y Li; R R Breaker
Journal:  Proc Natl Acad Sci U S A       Date:  1999-03-16       Impact factor: 11.205

8.  In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme.

Authors:  J Li; W Zheng; A H Kwon; Y Lu
Journal:  Nucleic Acids Res       Date:  2000-01-15       Impact factor: 16.971

9.  Improving metal ion specificity during in vitro selection of catalytic DNA.

Authors:  Peter J Bruesehoff; Jing Li; Anthony J Augustine; Yi Lu
Journal:  Comb Chem High Throughput Screen       Date:  2002-06       Impact factor: 1.339

10.  Functional proteins from a random-sequence library.

Authors:  A D Keefe; J W Szostak
Journal:  Nature       Date:  2001-04-05       Impact factor: 49.962

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  53 in total

Review 1.  Metal-Dependent DNAzymes for the Quantitative Detection of Metal Ions in Living Cells: Recent Progress, Current Challenges, and Latest Results on FRET Ratiometric Sensors.

Authors:  Kevin Hwang; Quanbing Mou; Ryan J Lake; Mengyi Xiong; Brandalynn Holland; Yi Lu
Journal:  Inorg Chem       Date:  2019-07-31       Impact factor: 5.165

Review 2.  Designed and Evolved Nucleic Acid Nanotechnology: Contrast and Complementarity.

Authors:  Tulsi Ram Damase; Peter B Allen
Journal:  Bioconjug Chem       Date:  2019-01-03       Impact factor: 4.774

Review 3.  Beyond DNA and RNA: The Expanding Toolbox of Synthetic Genetics.

Authors:  Alexander I Taylor; Gillian Houlihan; Philipp Holliger
Journal:  Cold Spring Harb Perspect Biol       Date:  2019-06-03       Impact factor: 10.005

4.  Inability of DNAzymes to cleave RNA in vivo is due to limited Mg[Formula: see text] concentration in cells.

Authors:  Julian Victor; Gerhard Steger; Detlev Riesner
Journal:  Eur Biophys J       Date:  2017-12-16       Impact factor: 1.733

5.  DNA nanotechnology for nucleic acid analysis: multifunctional molecular DNA machine for RNA detection.

Authors:  A J Cox; H N Bengtson; K H Rohde; D M Kolpashchikov
Journal:  Chem Commun (Camb)       Date:  2016-12-06       Impact factor: 6.222

Review 6.  Building machines with DNA molecules.

Authors:  Hamid Ramezani; Hendrik Dietz
Journal:  Nat Rev Genet       Date:  2019-10-21       Impact factor: 53.242

Review 7.  DNAzymes as Activity-Based Sensors for Metal Ions: Recent Applications, Demonstrated Advantages, Current Challenges, and Future Directions.

Authors:  Ryan J Lake; Zhenglin Yang; JingJing Zhang; Yi Lu
Journal:  Acc Chem Res       Date:  2019-11-13       Impact factor: 22.384

8.  DNA Antenna Tile-Associated Deoxyribozyme Sensor with Improved Sensitivity.

Authors:  Amanda J Cox; Hillary N Bengtson; Yulia V Gerasimova; Kyle H Rohde; Dmitry M Kolpashchikov
Journal:  Chembiochem       Date:  2016-09-13       Impact factor: 3.164

9.  Divide and Control: Comparison of Split and Switch Hybridization Sensors.

Authors:  Alexandra L Smith; Dmitry M Kolpashchikov
Journal:  ChemistrySelect       Date:  2017-07-04       Impact factor: 2.109

10.  A highly specific sodium aptamer probed by 2-aminopurine for robust Na+ sensing.

Authors:  Wenhu Zhou; Jinsong Ding; Juewen Liu
Journal:  Nucleic Acids Res       Date:  2016-09-20       Impact factor: 16.971

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