Predicting out-of-sequence reassembly in DNA shuffling

Journal of Theoretical Biology

Volumn 219, Issue 1, 2002, Pages 9-17

  Moore, Gregory L ^a   Maranas, Costas D ^a  

^a The Pennsylvania State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALGORITHM; ARTICLE; COMPUTER MODEL; CROSSING OVER; DNA SEQUENCE; DNA TEMPLATE; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; THERMODYNAMICS;

EID: 0036418698     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-5193(02)93102-4     Document Type: Article

References (11)

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2. Allawi, H. & SantaLucia Jr, J. (1998a). Nearest neighbor thermodynamic parameters for internal G·A mismatches in DNA. Biochemistry 37, 2170-2179.
3. Allawi, H. & SantaLucia Jr, J. (1998b). Nearest-neighbor thermodynamics of internal A·C mismatches in DNA: Sequence dependence and pH effects. Biochemistry 37, 9435-9444.
4. Allawi, H. & SantaLucia Jr, J. (1998c). Thermodynamics of internal C·T mismatches in DNA. Nucleic Acids Res. 26, 2694-2701.
5. Crameri, A., Raillard, S., Bermudez, E. & Stemmer, W. (1998). DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391, 288-291.
6. Moore, G. & Maranas, C. (2000). Modeling DNA mutation and recombination for directed evolution experiments. J. Theor. Biol. 205, 483-503, doi:10.1006/jtbi.2000.2082.
7. Moore, G., Maranas, C., Lutz, S. & Benkovic, S. (2001). Predicting crossover generation in DNA shuffling. Proc. Natl. Acad. Sci. U.S.A. 98, 3226-3231.
8. Nakano, S., Fujimoto, M. & Sugimoto, H. H. N. (1999). Nucleic acid duplex stability: Influence of base composition on cation effects. Nucleic Acids Res. 27, 2957-2965.
9. Ness, J., Welch, M., Giver, L., Bueno, M., Cherry, J., Borchert, T., Stemmer, W. & Minshull, L. (1999). DNA shuffling of subgenomic sequences of subtilisin. Nature Biotech. 17, 893-896.
10. SantaLucia Jr, J. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest neighbor thermodynamics. Proc. Natl. Acad. Sci. U.S.A. 95, 1460-1465.
11. Stemmer, W. (1994). DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. U.S.A. 91, 10747-10751.