Computer Assisted Parental Sequences Analysis as a Previous Step to DNA Shuffling Process

Experiments of directed evolution have been successfully used to improve specific biological functions. DNA shuffling is a directed evolution process which generates genetic diversity through the recombination of parental sequences. It is expected that the sequences resulting from a Shuffling process be a mixture of the parental sequences. In order to evaluate which pair of sequences could potentially produce the best result, this paper analyses, using information given by a software, the adequacy of three pairs of parental sequences as candidates for undergoing a DNA shuffling process.

[1]  Wayne M Patrick,et al.  User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. , 2003, Protein engineering.

[2]  W. Stemmer,et al.  Evolution of a cytokine using DNA family shuffling , 1999, Nature Biotechnology.

[3]  Narendra Maheshri,et al.  Computational and experimental analysis of DNA shuffling , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[4]  W. Stemmer.  Rapid evolution of a protein in vitro by DNA shuffling , 1994, Nature.

[5]  Frances H. Arnold,et al.  Molecular evolution by staggered extension process (StEP) in vitro recombination , 1998, Nature Biotechnology.

[6]  J. Joern.  Engineering dioxygenases by laboratory evolution: a comparison of evolutionary search strategies , 2003 .

[7]  W. Stemmer.  DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[8]  David W. Russell,et al.  Genetic engineering with PCR. , 2006, Cold Spring Harbor Protocols.

[9]  Fengzhu Sun,et al.  Modeling DNA shuffling , 1998, RECOMB '98.

[10]  Fengzhu Sun,et al.  The Polymerase Chain Reaction and Branching Processes , 1995, J. Comput. Biol..

[11]  F. Arnold,et al.  Methods for in vitro DNA recombination and random chimeragenesis. , 2000, Methods in enzymology.

[12]  F. Arnold,et al.  Random chimeragenesis by heteroduplex recombination. , 2000, Methods in enzymology.

[13]  Costas D. Maranas,et al.  Modeling and optimization of DNA recombination , 2000 .

[14]  R. Horton,et al.  Genetic Engineering with PCR , 1998 .

[15]  Fengzhu Sun.  Stochastic Modeling of Polymerase Chain Reaction and Related Biotechnologies , 2001 .

[16]  Arjang Hassibi,et al.  A STOCHASTIC MODEL AND SIMULATION ALGORITHM FOR POLYMERASE CHAIN REACTION ( PCR ) SYSTEMS , 2004 .

[17]  F. Arnold,et al.  Optimization of DNA shuffling for high fidelity recombination. , 1997, Nucleic acids research.

[18]  Jon E. Ness,et al.  DNA shuffling of subgenomic sequences of subtilisin , 1999, Nature Biotechnology.

[19]  R. Howard,et al.  Applications of DNA shuffling to pharmaceuticals and vaccines. , 1997, Current opinion in biotechnology.

[20]  F. Brühlmann,et al.  Tuning biphenyl dioxygenase for extended substrate specificity. , 1999, Biotechnology and bioengineering.

[21]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[22]  Gerd Folkers,et al.  Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling , 1999, Nature Biotechnology.

[23]  S. Harayama,et al.  Novel family shuffling methods for the in vitro evolution of enzymes. , 1999, Gene.

[24]  F. Arnold,et al.  Engineering new functions and altering existing functions. , 1996, Current opinion in structural biology.

[25]  C D Maranas,et al.  Predicting crossover generation in DNA shuffling , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[26]  F. Arnold,et al.  Optimizing industrial enzymes by directed evolution. , 1997, Advances in biochemical engineering/biotechnology.