Model-guided ligation strategy for optimal assembly of DNA libraries

Protein Engineering, Design and Selection

Volumn 25, Issue 10, 2012, Pages 669-678

  Ng, Daphne T W ^a   Sarkar, Casim A ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

DNA ligation; thermodynamic model; Type IIS restriction endonucleases

Indexed keywords

DIRECTED EVOLUTION; DNA CONCENTRATION; DNA LIBRARY; DNA LIGATION; IN-VITRO; IN-VIVO; LIGATION REACTIONS; PARAMETERIZED; PRODUCT DISTRIBUTIONS; RELATIVE ABUNDANCE; RESTRICTION ENDONUCLEASES; RIBOSOME DISPLAY; THERMODYNAMIC MODEL; TRIAL AND ERROR;

DNA; GENETIC ENGINEERING; LINEAR TRANSFORMATIONS; MOLECULAR BIOLOGY; OPTIMIZATION; THERMODYNAMIC PROPERTIES;

SURGICAL EQUIPMENT;

DNA; DNA FRAGMENT; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

ARTICLE; BACTERIUM COLONY; BASE PAIRING; BIOENGINEERING; CLONING; DNA LIBRARY; DNA LIGATION; DNA SEQUENCE; HYDROGEN BOND; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR WEIGHT; PRIORITY JOURNAL; RESTRICTION SITE; RIBOSOME; SIMULATION; STOICHIOMETRY; THERMODYNAMICS;

BACTERIOPHAGE T4; BASE SEQUENCE; CLONING, MOLECULAR; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DIRECTED MOLECULAR EVOLUTION; DNA; DNA LIGASES; GENE LIBRARY; GENETIC VECTORS; MODELS, BIOLOGICAL; MODELS, CHEMICAL; THERMODYNAMICS;

EID: 84867019099     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzs019     Document Type: Article

References (27)

1. Barendt, P.A., Shah, N.A., Barendt, G.A. and Sarkar, C.A. (2012) PLoS Genet., 8, e1002598.
2. Bath, A.J., Milsom, S.E., Gormley, N.A. and Halford, S.E. (2002) J. Biol. Chem., 277, 4024-4033.
3. Binz, H.K., Amstutz, P., Kohl, A., Stumpp, M.T., Briand, C., Forrer, P., Grütter, M.G. and Plückthun, A. (2004) Nat. Biotechnol., 22, 575-582.
4. Burton, Z.F. and Kaguni, J.M. (1997) Experiments in Molecular Biology: Biochemical Applications. Academic Press, San Diego, CA, pp. 62-65.
5. Cherepanov, A.V. and De Vries, S. (2003) Eur. J. Biochem., 270, 4315-4325.
6. Dardel, F. (1988) Nucleic Acids Res., 16, 1767-1778.
7. Dickson, K.S., Burns, C.M. and Richardson, J.P. (2000) J. Biol. Chem., 275, 15828-15831.
8. Dugaiczyk, A., Boyer, H.W. and Goodman, H.M. (1975) J. Mol. Biol., 96, 171-184.
9. Ferretti, L. and Sgaramella, V. (1981) Nucleic Acids Res., 9, 85-93.
10. Hanes, J. and Plückthun, A. (1997) Proc. Natl. Acad. Sci. U.S.A., 94, 4937-4942.
11. Harada, K. and Orgel, L.E. (1993) Nucleic Acids Res., 21, 2287-2291.
12. Inoue, H. and Nojima, H. (1990) Gene, 96, 23-28.
13. Jacobson, H. and Stockmayer, W.H. (1950) J. Chem. Phys., 18, 1600-1606.
14. Landegren, U., Kaiser, R., Sanders, J. and Hood, L. (1988) Science, 241, 1077-1080.
15. Legerski, R.J. and Robberson, D.L. (1985) J. Mol. Biol., 181, 297-312.
16. Protozanova, E., Yakovchuk, P. and Frank-Kamenetskii, M.D. (2004) J. Mol. Biol., 342, 775-785.
17. Revie, D., Smith, D.W. and Yee, T.W. (1988) Nucleic Acids Res., 16, 10301-10321.
18. Roberts, R.J. (2003) Nucleic Acids Res., 31, 1805-1812.
19. Roberts, R.J., Vincze, T., Posfai, J. and Macelis, D. (2010) Nucleic Acids Res., 38, D234-D236.
20. Sambrook, J. and Russell, D.W. (2001) In Irwin, N. and Janssen, K.A. (eds), Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 1.157-1.159.
21. SantaLucia, J. (1998) Proc. Natl. Acad. Sci. U.S.A., 95, 1460-1465.
22. SantaLucia, J., Allawi, H.T. and Ananda Seneviratne, P. (1996) Biochemistry, 35, 3555-3562.
23. Sugino, A., Goodman, H.M., Heyneker, H.L., Shine, J., Boyer, H.W. and Cozzarelli, N.R. (1977) J. Biol. Chem., 252, 3987-3994.
24. Szybalski, W., Kim, S.C., Hasan, N. and Podhajska, A.J. (1991) Gene, 100, 13-26.
25. Tobias, A.V. (2003) In Arnold, F.H. and Georgiou, G. (eds), Directed Evolution Library Creation: Methods and Protocols. Humana Press, Totowa, NJ, pp. 11-16.
26. Yakovchuk, P., Protozanova, E. and Frank-Kamenetskii, M.D. (2006) Nucleic Acids Res., 34, 564-574.
27. Zahnd, C., Amstutz, P. and Plückthun, A. (2007) Nat. Methods, 4, 269-279.