Exponential growth by cross-catalytic cleavage of deoxyribozymogens

We have designed an autocatalytic cycle based on the highly efficient 10–23 RNA-cleaving deoxyribozyme that is capable of exponential amplification of catalysis. In this system, complementary 10–23 variants were inactivated by circularization, creating deoxyribozymogens. Upon linearization, the enzymes can act on their complements, creating a cascade in which linearized species accumulate exponentially. Seeding the system with a pool of linear catalysts resulted not only in amplification of function but in sequence selection and represents an in vitro selection experiment conducted in the absence of any protein enzymes.

[1]  E. Szathmáry,et al.  Selection versus Coexistence of Parabolic Replicators Spreading on Surfaces , 2001 .

[2]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[3]  A. Ellington,et al.  In vitro selection of nucleoprotein enzymes , 2001, Nature Biotechnology.

[4]  G. Kiedrowski,et al.  Surface-promoted replication and exponential amplification of DNA analogues , 1998, Nature.

[5]  K. Mann,et al.  A model for the tissue factor pathway to thrombin. II. A mathematical simulation. , 1994, Journal of Biological Chemistry.

[6]  L E Orgel,et al.  A nonenzymatic RNA polymerase model. , 1983, Science.

[7]  Günter von Kiedrowski,et al.  A Self‐Replicating System from Three Starting Materials , 1993 .

[8]  M. Matzen,et al.  Parabolic Growth of a Self‐Replicating Hexadeoxynucleotide Bearing a 3'‐5'‐Phosphoamidate Linkage , 1991 .

[9]  U. Landegren,et al.  Protein detection using proximity-dependent DNA ligation assays , 2002, Nature Biotechnology.

[10]  R. Breaker,et al.  Engineering precision RNA molecular switches. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[11]  A D Ellington,et al.  Design and optimization of effector-activated ribozyme ligases. , 2000, Nucleic acids research.

[12]  O. Uhlenbeck,et al.  In vitro selection of RNAs that undergo autolytic cleavage with Pb2+. , 1992, Biochemistry.

[13]  G. F. Joyce,et al.  Mechanism and utility of an RNA-cleaving DNA enzyme. , 1998, Biochemistry.

[14]  G. F. Joyce,et al.  A self-replicating ligase ribozyme , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Günter von Kiedrowski,et al.  Minimal Replicator Theory I: Parabolic Versus Exponential Growth , 1993 .

[16]  Günter von Kiedrowski,et al.  A Self‐Replicating Hexadeoxynucleotide , 1986 .

[17]  J. McCaskill,et al.  In vitro evolution of molecular cooperation in CATCH, a cooperatively coupled amplification system. , 1998, Chemistry & biology.

[18]  D. Sen,et al.  A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes. , 2002, Journal of molecular biology.

[19]  K. Taira,et al.  Effects of helical structures formed by the binding arms of DNAzymes and their substrates on catalytic activity. , 1998, Nucleic acids research.

[20]  D. Sievers,et al.  Self-replication of complementary nucleotide-based oligomers , 1994, Nature.

[21]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[22]  G. F. Joyce,et al.  A general purpose RNA-cleaving DNA enzyme. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[23]  L. Orgel,et al.  Template-directed synthesis on the pentanucleotide CpCpGpCpC. , 1984, Journal of molecular biology.

[24]  J. McCaskill,et al.  A molecular predator and its prey: coupled isothermal amplification of nucleic acids. , 1997, Chemistry & biology.

[25]  Günter von Kiedrowski,et al.  DNA nanotechnology: Chemical copying of connectivity , 2002, Nature.

[26]  N. Seeman.  DNA in a material world , 2003, Nature.

[27]  Andrew Ellington,et al.  In vitro selection of an allosteric ribozyme that transduces analytes to amplicons , 1999, Nature Biotechnology.

[28]  K. Nicolaou,et al.  Chemical self-replication of palindromic duplex DNA , 1994, Nature.

[29]  M. Mörl,et al.  A universal method to produce in vitro transcripts with homogeneous 3' ends. , 2002, Nucleic acids research.

[30]  M. Cairns,et al.  Target site selection for an RNA-cleaving catalytic DNA , 1999, Nature Biotechnology.

[31]  D. Green,et al.  The machinery of programmed cell death. , 2001, Pharmacology & therapeutics.

[32]  R R Breaker,et al.  Rational design of allosteric ribozymes. , 1997, Chemistry & biology.

[33]  D. Sen,et al.  A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate. , 2001, Journal of molecular biology.

[34]  L. Orgel,et al.  Autocatalytic synthesis of a tetranucleotide analogue , 1987, Nature.