In silico Simulations for DNA Shuffling Experiments
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In silico Simulations for DNA Shuffling Experiments

Authors: Luciana Montera

Abstract:

DNA shuffling is a powerful method used for in vitro evolute molecules with specific functions and has application in areas such as, for example, pharmaceutical, medical and agricultural research. The success of such experiments is dependent on a variety of parameters and conditions that, sometimes, can not be properly pre-established. Here, two computational models predicting DNA shuffling results is presented and their use and results are evaluated against an empirical experiment. The in silico and in vitro results show agreement indicating the importance of these two models and motivating the study and development of new models.

Keywords: Computer simulation, DNA shuffling, in silico andin vitro comparison.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1328632

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[1] Montera, L.; Nicoletti, M.C.; Silva, F.H. "Computer Assisted Parental Sequences Analysis as a Previous Step to DNA Shuffling Process". IEEE Congress on Evolutionary Computation, 8079-8086, 2006.
[2] Voigt, C.A., Mayo, S.L., Arnold, F.H. and Wang, ZG. "Computationally Focusing the Directed Evolution of Proteins". Journal of Cellular Biochemistry Supplement 37, 58-63, 2001.
[3] Cadwell, RC.; Joyce, G;F. "Randomization of genes by PCR mutagenesis". PCR Method Appl., 2, 28 33, 1992.
[4] Zhao, H., Giver, L., Shao, Z., Affholter, A., Arnold, F. H. "Molecular evolution by staggered extension process (StEP) in vitro recombination". Nature Biotechnol. 16, pp. 258-261, 1998.
[5] Shao, Z., Zhao, H., Giver, L., Arnold, F.H. "Random-priming in vitro recombination: an effective tool for directed evolution". Nucleic Acids Research 26, 681-683, 1998.
[6] Stemmer,W.P.C. "Rapid evolution of a protein in vitro by DNA shuffling". Nature 370, 389-391, 1994.
[7] Stemmer,W.P.C. "DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution". Proc. Natl. Acad. Sci. USA 91, 10747-10751, 1994.
[8] Patnaik, R.; Louie, S.; Gavrilovic, V.; Perry, K.; Stemmer, W.P.C.; Ryan, C.M.; Cardayré, S. "Genome shuffling of Lactobacillus for improve acid tolerance". Nature Biotechnology 20, 707-712, 2002.
[9] Christians, F.C.; Scapozza, L.; Crameri, A.; Folkers, G.; Stemmer, W.P.C. "Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling". Nature Biotechnology 17, 259-264, 1999.
[10] Chang, C.C.; Chen, T.T.; Cox, B.W.; Dawes, G.N.; Stemmer, W.P.C.; Punnonen, J.; Patten, P.A. "Evolution of a cytokine using DNA family shuffling". Nature Biotchnology 17(8), 793-797, 1999.
[11] Ness, J.E.; Welch, M.; Giver, L.; Bueno, M.; Cherry, J.R.; Borchert, T.V.; Stemmer, W.P.C.; Minshull, J. "DNA shuffling of DNA subgenomic sequences of subtilisin". Nature Biotechnology 17, 893- 896, 1999.
[12] Yanga, L.; Jianga, J.; Drouinb, L.M.; Agbandje-Mckennab, M.; Chena, C.; Qiaoa, C.; Pua, D.; Huc, X.; Wangc, D.; Lia, J.; Xiaoa, X. "A myocardium tropic adeno-associated virus (AAV) evolved by DNA shuffling and in vivo selection". PNAS 106(10), 3946-3951, 2009.
[13] Ryu, K.; Hwang, S.Y.; Kim, K.H.; Kang, J.H.; Lee, E.K. "Functionality improvement of fungal lignin peroxidase by DNA shuffling for 2,4- dichlorophenol degradability and H2O2 stability". Journal of Biotechnology 133(1), 110-115, 2008.
[14] Koerber, J.T.; , Jang, J.H; Schaffer, D.V. "DNA Shuffling of Adenoassociated Virus Yields Functionally Diverse Viral Progeny". Molecular Therapy 16(10), 1703-1709, 2008.
[15] Maheshri, N.; Koerber, J.T.; Kaspar, B.K.; Schaffer, D.V. "Directed evolution of adeno- associated virus yields enhanced gene delivery vectors". Nat. Biotech. 24, 198 -204, 2006.
[16] Volkov, A.A.; Arnold, F.H. "Methods for in vitro DNA Recombination and Random Chimeragenesis". Methods in Enzymology 328, 447-456, 2000.
[17] Moore, G.L.; Maranas, C.D.; Gutshall, K.R.; Brenchley, J.E. "Modeling and optimization of DNA recombination". Computers & Chemical Engineering 24, 693-699, 2000.
[18] Moore, G.L.; Maranas, C.D.; Lutz, S.; Benkovic, S.L. "Predicting crossover generation in DNA shuffling". PNAS 98, 3226-3231, 2001.
[19] Patrick, W.M.; Firth, A.E.; Blackburn, J.M. "User-friendly algorithms for estimating completeness and diversity in randomized proteinencoding libraries". Protein Engineering 16(6), 451-457, 2003.
[20] Raillard, S.; Krebber, A.; Chen, Y.; Ness, J.E.; Bermudez, E.; Trinidad, R.; Fullem, R.; Davis, C.; Welch, M.; Seffernick, J.; Wackett, L.P.; Stemmer, W.P.C.; Minshull, J. "Novel enzyme activities and functional plasticity revealed by recombining highly homologous enzymes". Chemistry & Biology 8, 891-898, 2001.
[21] Breslauer,K.J.; Frank,R.; Blocker, H.; Marky, L.A. "Predicting DNA duplex stability from the base sequence". Proc Natl Acad Sci USA 83(11), 3746-3750, 1986.
[22] Allawi, H.T. & SantaLucia, J.Jr. "Thermodynamics and NMR of Internal G-T Mismatches in DNA", Biochemistry 36, 10581-10594, 1997.
[23] Joern, J.M.; Meinhold, P.; Arnold, F.H. "Analysis of shuffled gene libraries". Journal of Molecular Biology, 316 (3), 643-56, 2002.