In vitro evolution of phi29 DNA polymerase using isothermal compartmentalized self replication technique

Protein Engineering, Design and Selection

Volumn 29, Issue 12, 2016, Pages 617-628

  Povilaitis, Tadas ^a   Alzbutas, Gediminas ^a   Sukackaite, Rasa ^a   Siurkus, Juozas ^a   Skirgaila, Remigijus ^a  

^a Thermo Fisher Scientific   (United States)

Author keywords

Amplification bias; ICSR; In vitro evolution; Phi29 DNA polymerase; WGA

Indexed keywords

BIOMOLECULES; CELL MEMBRANES; DNA; EMULSIFICATION; ENZYMES; ISOTHERMS;

ELEVATED TEMPERATURE; FREEZING THAWING CYCLES; ICSR; IN-VITRO; PHI29 DNA POLYMERASE; SELECTION PRESSURES; THERMOPHILIC ENZYMES; WHOLE GENOME AMPLIFICATIONS;

POLYMERASE CHAIN REACTION;

DNA POLYMERASE; PLASMID DNA; DNA; DNA DIRECTED DNA POLYMERASE;

ARTICLE; BACILLUS PHAGE PHI29; BACTERIAL CELL; BACTERIAL CELL WALL; CONTROLLED STUDY; DNA DENATURATION; DNA REPLICATION; EMULSION; ESCHERICHIA COLI; FREEZE THAWING; GENE AMPLIFICATION; GENE MUTATION; GENETIC VARIABILITY; HIGH TEMPERATURE; IN VITRO STUDY; ISOTHERMAL COMPARTMENTALIZED SELF REPLICATION; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; AMINO ACID SEQUENCE; BACILLUS PHAGE; CHEMISTRY; ENZYMOLOGY; GENETICS; GENOMICS; HALF LIFE TIME; METABOLISM; MUTATION; NUCLEIC ACID AMPLIFICATION; PROCEDURES; TEMPERATURE;

AMINO ACID SEQUENCE; BACILLUS PHAGES; DNA; DNA-DIRECTED DNA POLYMERASE; GENOMICS; HALF-LIFE; MUTATION; NUCLEIC ACID AMPLIFICATION TECHNIQUES; TEMPERATURE;

EID: 85018460526     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzw052     Document Type: Article

References (45)

1. Alsmadi,O., Alkayal,F., Monies,D. and Meyer,B.F. (2009) BMC Res. Notes, 2, 48.
2. Baar,C., d'Abbadie,M., Vaisman,A., Arana,M.E., Hofreiter,M., Woodgate,R., Kunkel,T.A. and Holliger,P. (2011) Nucleic Acids Res., 39, e51.
3. Barik,S. (1995) Mol. Biotechnol., 3, 1-7.
4. Berman,A.J., Kamtekar,S., Goodman,J.L., Lázaro,J.M., de Vega,M., Blanco, L., Salas,M. and Steitz,T.A. (2007) EMBO J, 26, 3494-3505.
5. Beyer,S., Nickels,P. and Simmel,F.C. (2005) Nano Lett., 5, 719-722.
6. Bibillo,A., Hanzel,D., Peluso,P., Rank,D. and Wegener,J. (2009) European Patent Application EP2089517A2.
7. Bjornson,K., Clark,S., Park,I. and Christians,F. (2010) US Patent Application, US2010/0093555A1.
8. Blanco,L. and Salas,M. (1995) Methods Enzymol., 262, 283-294.
9. Blanco,L., Bernad,A., Lázaro,J.M., Martín,G., Garmendia,C. and Salas,M. (1989) J. Biol. Chem., 264, 8935-8940.
10. Clark,S., Bibillo,A., Peluso,P., Christians,F., He,M., Park,I., Lee,H., Bjornson,K., Jia,L. and Emig,R. (2010) US Patent Application, US20100112645A1.
11. Dean,F.B., Hosono,S., Fang,L. et al (2002) Proc. Natl. Acad. Sci. U. S. A., 99, 5261-5266.
12. del Prado,A., Lázaro,J.M., Villar,L., Salas,M. and de Vega,M. (2013) PLoS One, 8, e72765.
13. de Vega,M., Lázaro,J.M., Mencía,M., Blanco,L. and Salas,M. (2010) Proc. Natl. Acad. Sci. U. S. A., 107, 16506-16511.
14. de Vega,M., Lázaro,J.M., Salas,M. and Blanco,L. (1998) J. Mol. Biol., 279, 807-822.
15. Dufour,E., Méndez,J., Lázaro,J., de Vega,M., Blanco,L. and Salas,M. (2000) J. Mol. Biol., 304, 289-300.
16. d'Abbadie,M., Hofreiter,M., Vaisman,A., Loakes,D., Gasparutto,D., Cadet,J., Woodgate,R., Pääbo,S. and Holliger,P. (2007) Nat. Biotechnol., 25, 939-943.
17. Ellefson,J.W., Meyer,A.J., Hughes,R.A., Cannon,J.R., Brodbelt,J.S. and Ellington,A.D. (2014) Nat. Biotechnol., 32, 97-101.
18. Esteban,J.A., Salas,M. and Blanco,L. (1993) J. Biol. Chem., 268, 2719-2726.
19. Facchiano,A.M., Colonna,G. and Ragone,R. (1998) Protein Eng., 11, 753-760.
20. Ghadessy,F.J., Ong,J.L. and Holliger,P. (2001) Proc. Natl. Acad. Sci. U.S.A., 98, 4552-4557.
21. Ghadessy,F.J., Ramsay,N., Boudsocq,F., Loakes,D., Brown,A., Iwai,S., Vaisman,A., Woodgate,R. and Holliger,P. (2004) Nat. Biotechnol., 22, 755-759.
22. Henry,A.A. and Romesberg,F.E. (2005) Curr. Opin. Biotechnol., 16, 370-377.
23. Houlihan,G., Gatti-Lafranconi,P., Kaltenbach,M., Lowe,D. and Hollfelder,F. (2014) J. Immunol. Methods, 405, 47-56.
24. Hutchison,C.A.III, Smith,H.O., Pfannkoch,C. and Venter,J.C. (2005) Proc. Natl. Acad. Sci. U. S. A., 102, 17332-17336.
25. Johne,R., Müller,H., Rector,A., van Ranst,M. and Stevens,H. (2009) Trends Microbiol., 17, 205-211.
26. Kamtekar,S., Berman,A.J., Wang,J., Lázaro,J.M., de Vega,M., Blanco,L., Salas,M. and Steitz,T.A. (2004) Mol. Cell, 16, 609-618.
27. Loakes,D., Gallego,J., Pinheiro,V.B., Kool,E.T. and Holliger,P. (2009) J. Am. Chem. Soc., 131, 14827-14837.
28. Marine,R., McCarren,C., Vorrasane,V., Nasko,D., Crowgey,E., Polson,S.W. and Wommack,K.E. (2014) Microbiome, 2, 3.
29. Merkiene,E., Gaidamaviciute,E., Riauba,L., Janulaitis,A. and Lagunavicius,A. (2010) RNA, 16, 1508-1515.
30. Mokry,M., Feitsma,H., Nijman,I.J., de Bruijn,E., van der Zaag,P.J., Guryev, V. and Cuppen,E. (2010) Nucleic Acids Res., 38, e116.
31. Ong,J.L., Loakes,D., Jaroslawski,S., Too,K. and Holliger,P. (2006) J. Mol. Biol., 361, 537-550.
32. Pace,C.N. and Scholtz,J.M. (1998) Biophys. J., 75, 422-427.
33. Pan,X., Urban,A.E., Palejev,D., Schulz,V., Grubert,F., Hu,Y., Snyder,M. and Weissman,S.M. (2008) Proc. Natl. Acad. Sci. U. S. A., 105, 15499-15504.
34. Pinheiro,V.B., Arangundy-Franklin,S. and Holliger,P. (2014) Curr. Protoc. Nucleic Acid Chem., 57, 9.9.1-18.
35. Ramsay,N., Jemth,A., Brown,A., Crampton,N., Dear,P. and Holliger,P. (2010) J. Am. Chem. Soc., 132, 5096-5104.
36. Rosenthal,A. and Jones,D.S. (1990) Nucleic Acids Res., 18, 3095-3096.
37. Sakaguchi,M., Matsuzaki,M., Niimiya,K., Seino,J., Sugahara,Y. and Kawakita,M. (2007) J. Biochem., 141, 213-220.
38. Silander,K. and Saarela,J. (2008) Methods Mol. Biol., 439, 1-18.
39. Telenius,H., Carter,N.P., Bebb,C.E., Nordenskjöld,M., Ponder,B.A. and Tunnacliffe,A. (1992) Genomics, 13, 718-725.
40. Tubeleviciute,A. and Skirgaila,R. (2010) Protein Eng. Des. Sel., 23, 589-597.
41. Vieille,C. and Zeikus,G.J. (2001) Microbiol. Mol. Biol. Rev., 65, 1-43.
42. Williams,R., Peisajovich,S.G., Miller,O.J., Magdassi,S., Tawfik,D.S. and Griffiths,A.D. (2006) Nat. Methods, 3, 545-550.
43. Zaccolo,M., Williams,D.M., Brown,D.M. and Gherardi,E. (1996) J. Mol. Biol., 255, 589-603.
44. Zhang,L., Cui,X., Schmitt,K., Hubert,R., Navidi,W. and Arnheim,N. (1992) Proc. Natl. Acad. Sci. U. S. A., 89, 5847-5851.
45. Zinchenko,A., Devenish,S.R.A., Kintses,B., Colin,P., Fischlechner,M. and Hollfelder,F. (2014) Anal. Chem., 86, 2526-2533.