Primer extension mutagenesis powered by selective rolling circle amplification

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Huovinen, Tuomas ^a   Brockmann, Eeva Christine ^a   Akter, Sultana ^a   Perez Gamarra, Susan ^a   Ylä Pelto, Jani ^a   Liu, Yuan ^a,b   Lamminmäki, Urpo ^a  

^a UNIVERSITY OF TURKU   (Finland)

^b INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DNA; DNA POLYMERASE; HETERODUPLEX; SINGLE STRANDED DNA; URACIL; URACIL DNA GLYCOSIDASE; DNA DIRECTED DNA POLYMERASE;

ARTICLE; CELL TRANSFORMATION; CONTROLLED STUDY; DNA STRAND; ESCHERICHIA COLI; GENE AMPLIFICATION; GENE MUTATION; MUTAGENESIS; NONHUMAN; NUCLEIC ACID ANALYSIS; PRIMER EXTENSION MUTAGENESIS; SELECTIVE ROLLING CIRCLE AMPLIFICATION; WILD TYPE; DNA TEMPLATE; GENE LIBRARY; GENETICS; METABOLISM; MUTATION; NUCLEIC ACID AMPLIFICATION;

DNA, CIRCULAR; DNA, SINGLE-STRANDED; DNA-DIRECTED DNA POLYMERASE; GENE LIBRARY; MUTAGENESIS; MUTATION; NUCLEIC ACID AMPLIFICATION TECHNIQUES; TEMPLATES, GENETIC; URACIL; URACIL-DNA GLYCOSIDASE;

EID: 84857066178     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031817     Document Type: Article

References (27)

1. Kunkel T, (1985) Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A 82: 488-492.
2. Jung R, Scott M, Oliveira L, Nielsen N, (1992) A simple and efficient method for the oligodeoxyribonucleotide-directed mutagenesis of double-stranded plasmid DNA. Gene 121: 17-24.
3. Markvardsen P, Lassen S, Borchert V, Clausen I, (1995) Uracil-USE, an improved method for site-directed mutagenesis on double-stranded plasmid DNA. Biotechniques 18: 370-372.
4. Li F, Liu S, Mullins J, (1999) Site-directed mutagenesis using uracil-containing double-stranded DNA templates and DpnI digestion. Biotechniques 27: 734-738.
5. Sidhu S, Li B, Chen Y, Fellouse F, Eigenbrot C, et al. (2004) Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions. J Mol Biol 338: 299-310.
6. Sidhu S, Lowman H, Cunningham B, Wells J, (2000) Phage display for selection of novel binding peptides. Methods Enzymol 328: 333-363.
7. Hutchison CA, Smith HO, Pfannkoch C, Venter JC, (2005) Cell-free cloning using phi29 DNA polymerase. Proc Natl Acad Sci U S A 102: 17332-17336.
8. Dean F, Hosono S, Fang L, Wu X, Faruqi A, et al. (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A 99: 5261-5266.
9. Larsson C, Koch J, Nygren A, Janssen G, Raap AK, et al. (2004) In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes. Nat Methods 1: 227-232.
10. Blanco L, Bernad A, Lázaro JM, Martín G, Garmendia C, et al. (1989) Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J Biol Chem 264: 8935-8940.
11. Dean F, Nelson J, Giesler T, Lasken R, (2001) Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 11: 1095-1099.
12. Sagher D, Strauss B, (1985) Abasic sites from cytosine as termination signals for DNA synthesis. Nucleic Acids Res 13: 4285-4298.
13. Tye B, Lehman I, (1977) Excision repair of uracil incorporated in DNA as a result of a defect in dUTPase. J Mol Biol 117: 293-306.
14. Warner H, Duncan B, Garrett C, Neuhard J, (1981) Synthesis and metabolism of uracil-containing deoxyribonucleic acid in Escherichia coli. J Bacteriol 145: 687-695.
15. Lari S, Chen C, Vertéssy B, Morré J, Bennett S, (2006) Quantitative determination of uracil residues in Escherichia coli DNA: Contribution of ung, dug, and dut genes to uracil avoidance. DNA Repair (Amst) 5: 1407-1420.
16. Brockmann EC, Akter S, Savukoski T, Huovinen T, Lehmusvuori A, et al. (2011) Synthetic single-framework antibody library integrated with rapid affinity maturation by VL shuffling. Protein Eng Des Sel.
17. Schaaper RM, Loeb LA, (1981) Depurination causes mutations in SOS-induced cells. Proc Natl Acad Sci U S A 78: 1773-1777.
18. Baas PD, van Teeffelen HA, Teertstra WR, Jansz HS, Veeneman GH, et al. (1980) Restoration of the biological activity of in vitro synthesized phi X DNA by transfection of ung- spheroplasts or dUTPase treatment. FEBS Lett 110: 15-20.
19. Kunkel TA, (1984) Mutational specificity of depurination. Proc Natl Acad Sci U S A 81: 1494-1498.
20. Dianov G, Lindahl T, (1994) Reconstitution of the DNA base excision-repair pathway. Curr Biol 4: 1069-1076.
21. Sandigursky M, Freyer GA, Franklin WA, (1998) The post-incision steps of the DNA base excision repair pathway in Escherichia coli: studies with a closed circular DNA substrate containing a single U:G base pair. Nucleic Acids Res 26: 1282-1287.
22. Glickman BW, Radman M, (1980) Escherichia coli mutator mutants deficient in methylation-instructed DNA mismatch correction. Proc Natl Acad Sci U S A 77: 1063-1067.
23. Dower WJ, Miller JF, Ragsdale CW, (1988) High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res 16: 6127-6145.
24. Serrano-Heras G, Bravo A, Salas M, (2008) Phage phi29 protein p56 prevents viral DNA replication impairment caused by uracil excision activity of uracil-DNA glycosylase. Proc Natl Acad Sci U S A 105: 19044-19049.
25. Huovinen T, Julin M, Sanmark H, Lamminmäki U, (2011) Enhanced error-prone RCA mutagenesis by concatemer resolution. Plasmid 66: 47-51.
26. Fujii R, Kitaoka M, Hayashi K, (2004) One-step random mutagenesis by error-prone rolling circle amplification. Nucleic Acids Res 32: e145.
27. Yagodkin A, Azhayev A, Roivainen J, Antopolsky M, Kayushin A, et al. (2007) Improved synthesis of trinucleotide phosphoramidites and generation of randomized oligonucleotide libraries. Nucleosides Nucleotides Nucleic Acids 26: 473-497.