Molecular evolution of RNA in vitro.

Experimental studies of RNA evolution in vitro are reviewed in the context of Eigen's 1971 theory and its subsequent extensions. Current research activity and future prospects for using automated molecular biology techniques for in vitro evolution experiments are surveyed.

[1]  Manfred Eigen,et al.  Template-free RNA synthesis by Qβ replicase , 1986, Nature.

[2]  M. Eigen,et al.  The hypercycle. Coupling of RNA and protein biosynthesis in the infection cycle of an RNA bacteriophage. , 1991, Biochemistry.

[3]  R. Symons,et al.  Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites , 1987, Cell.

[4]  F. Kramer,et al.  Complete nucleotide sequence of a replicating RNA molecule. , 1973, Science.

[5]  Jack W. Szostak,et al.  In vitro evolution of a self-alkylatlng ribozyme , 1995, Nature.

[6]  F. Oehlenschläger,et al.  Comparison of self-sustained sequence-replication reaction systems. , 1996, European journal of biochemistry.

[7]  C. Biebricher,et al.  The mutant distribution of an RNA species replicated by Q beta replicase. , 1995, Journal of molecular biology.

[8]  A. Chetverin,et al.  An in vivo recombinant RNA capable of autocatalytic synthesis by Qβ replicase , 1988, Nature.

[9]  L. Gold,et al.  In vitro selection of RNA ligands to substance P. , 1995, Biochemistry.

[10]  M. Eigen,et al.  Template-directed and template-free RNA synthesis by Q beta replicase. , 1993, Journal of molecular biology.

[11]  G. P. Smith,et al.  Libraries of peptides and proteins displayed on filamentous phage. , 1993, Methods in enzymology.

[12]  T. Cech,et al.  The intervening sequence RNA of Tetrahymena is an enzyme. , 1986, Science.

[13]  G. F. Joyce,et al.  Cleavage of an amide bond by a ribozyme , 1995, Science.

[14]  S. Diekmann,et al.  Structural analysis of self-replicating RNA synthesized by Qbeta replicase. , 1982, Journal of molecular biology.

[15]  G. F. Joyce,et al.  Directed evolution of an RNA enzyme. , 1992, Science.

[16]  M Eigen,et al.  Multichannel PCR and serial transfer machine as a future tool in evolutionary biotechnology. , 1995, BioTechniques.

[17]  R. Luce,et al.  In vitro recombination and terminal elongation of RNA by Q beta replicase. , 1992, The EMBO journal.

[18]  Alan R. Fersht,et al.  Analysis of Enzyme Structure and Activity by Protein Engineering , 1984 .

[19]  K. Mullis,et al.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. , 1988, Science.

[20]  Steven A. Benner,et al.  Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet , 1990, Nature.

[21]  R. Lerner,et al.  Antibody catalysis of difficult chemical transformations , 1993 .

[22]  D. Patel,et al.  Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. , 1997, Chemistry & biology.

[23]  Fred Russell Kramer,et al.  Template-determined, variable rate of RNA chain elongation , 1978, Cell.

[24]  M. Eigen,et al.  Kinetics of RNA replication: competition and selection among self-replicating RNA species. , 1985, Biochemistry.

[25]  L. Orgel,et al.  Oligomerization of (guanosine 5'-phosphor)-2-methylimidazolide on poly(C). An RNA polymerase model. , 1982, Journal of molecular biology.

[26]  C. Biebricher,et al.  Sequence analysis of RNA species synthesized by Q beta replicase without template. , 1993, Biochemistry.

[27]  Charles Weissmann,et al.  Nucleotide sequence heterogeneity of an RNA phage population , 1978, Cell.

[28]  Phillip A. Sharp,et al.  Structure of RNAs replicated by the DNA-dependent T7 RNA polymerase , 1990, Cell.

[29]  N. Pace,et al.  The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme , 1983, Cell.

[30]  C. Biebricher,et al.  Design of artificial short-chained RNA species that are replicated by Q beta replicase. , 1995, Biochemistry.

[31]  M. Illangasekare,et al.  Aminoacyl-RNA synthesis catalyzed by an RNA , 1995, Science.

[32]  J. Szostak,et al.  Isolation of a ribozyme with 5'-5' ligase activity. , 1995, Chemistry & biology.

[33]  Manfred Eigen,et al.  Kinetics of ribonucleic acid replication. , 1983 .

[34]  G. P. Smith,et al.  Antibody-selectable filamentous fd phage vectors: affinity purification of target genes. , 1988, Gene.

[35]  F. Crick.  Origin of the Genetic Code , 1967, Nature.

[36]  R. Liskamp.  Opportunities for New Chemical Libraries: Unnatural Biopolymers and Diversomers , 1994 .

[37]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[38]  T. Blumenthal,et al.  Does Qβ replicase synthesize RNA in the absence of template? , 1983, Nature.

[39]  L. Gold,et al.  Selection and characterization of RNAs replicated by Q beta replicase. , 1995, Biochemistry.

[40]  Jennifer A. Doudna,et al.  RNA-catalysed synthesis of complementary-strand RNA , 1989, Nature.

[41]  F. Kramer,et al.  Evolution in vitro: sequence and phenotype of a mutant RNA resistant to ethidium bromide. , 1974, Journal of molecular biology.

[42]  L. Gold,et al.  Template recognition by an RNA-dependent RNA polymerase: identification and characterization of two RNA binding sites on Q beta replicase. , 1995, Biochemistry.

[43]  A. Ellington,et al.  In vitro selection of RNA lectins: using combinatorial chemistry to interpret ribozyme evolution. , 1995, Chemistry & biology.

[44]  L. Gold,et al.  In vitro selection of a novel catalytic RNA: characterization of a sulfur alkylation reaction and interaction with a small peptide. , 1996, RNA.

[45]  F. Kramer,et al.  RNA replication: required intermediates and the dissociation of template, product, and Q beta replicase. , 1979, Biochemistry.

[46]  Manfred Eigen,et al.  Evolutionary molecular engineering based on RNA replication , 1984 .

[47]  Manfred Eigen,et al.  Product analysis of RNA generated de novo by Qβ replicase , 1981 .

[48]  L. Orgel,et al.  Prebiotic chemistry and nucleic acid replication , 1974 .

[49]  Kinetic analysis of pausing and fidelity of human immunodeficiency virus type 1 reverse transcription. , 1996, Biochemistry.

[50]  M. Eigen,et al.  Kinetics of RNA replication: plus-minus asymmetry and double-strand formation. , 1984, Biochemistry.

[51]  L. Loeb,et al.  DNA sequences of random origin as probes of Escherichia coli promoter architecture. , 1988, The Journal of biological chemistry.

[52]  J. Szostak,et al.  Ribozyme-catalysed amino-acid transfer reactions , 1996, Nature.

[53]  K. Lieberman,et al.  Genetic probes of ribosomal RNA function. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[54]  J. Scott,et al.  Searching for peptide ligands with an epitope library. , 1990, Science.

[55]  A. E. Dahlberg.  The functional role of ribosomal RNA in protein synthesis , 1989, Cell.

[56]  J. Szostak,et al.  A DNA metalloenzyme with DNA ligase activity , 1995, Nature.

[57]  H. Noller,et al.  Unusual resistance of peptidyl transferase to protein extraction procedures. , 1992, Science.

[58]  M. Eigen,et al.  Kinetic analysis of template-instructed and de novo RNA synthesis by Q beta replicase. , 1981, Journal of molecular biology.

[59]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[60]  C. Biebricher,et al.  Template‐free generation of RNA species that replicate with bacteriophage T7 RNA polymerase. , 1996, The EMBO journal.

[61]  J W Szostak,et al.  Structurally complex and highly active RNA ligases derived from random RNA sequences. , 1995, Science.

[62]  S. Kauffman,et al.  Applied molecular evolution. , 1992, Journal of theoretical biology.

[63]  S Forrest,et al.  Genetic algorithms , 1996, CSUR.

[64]  A. Nero.  Controlling Indoor Air Pollution. , 1988 .