Revised selection criteria for candidate restriction enzymes in genome walking

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Taheri, Ali ^a   Robinson, Stephen J ^a   Parkin, Isobel ^a   Gruber, Margaret Y ^a  

^a SASKATOON RESEARCH CENTRE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; GENOMIC DNA; PHOSPHATASE; PLANT DNA; PLASMID DNA; PROTEIN NDEL; PROTEIN NSIL; RESTRICTION ENDONUCLEASE; UNCLASSIFIED DRUG; BACTERIAL DNA; T DNA; T-DNA;

ANALYTIC METHOD; ARABIDOPSIS; ARTICLE; BRACHYPODIUM; COMPUTER MODEL; CONTROLLED STUDY; DNA DEGRADATION; DNA FLANKING REGION; DNA VECTOR; ENHANCER REGION; ENZYME ANALYSIS; GENE INSERTION; GENE LIBRARY; GENOME ANALYSIS; GENOME WALKING; ISOSCHIZOMER; NONHUMAN; PLANT CHROMOSOME; PLANT GENOME; PROTEIN METHYLATION; PROTEIN SECONDARY STRUCTURE; CHEMISTRY; CHROMOSOME WALKING; DNA METHYLATION; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ARABIDOPSIS; ARABIDOPSIS THALIANA; BRACHYPODIUM DISTACHYON;

ARABIDOPSIS; BASE SEQUENCE; CHROMOSOME WALKING; DNA METHYLATION; DNA RESTRICTION ENZYMES; DNA, BACTERIAL; GENOME, PLANT; MOLECULAR SEQUENCE DATA;

EID: 84859585718     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0035117     Document Type: Article

References (34)

1. Liu Y-G, Mitsukawa N, Oosumi T, Whittier RF, (1995) Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. The Plant Journal 8: 457-463.
2. Ochman H, Gerber AS, Hartl DL, (1988) Genetic Applications of an Inverse Polymerase Chain Reaction. Genetics 120: 621-623.
3. O'Kane CJ, Gehring WJ, (1987) Detection in situ of genomic regulatory elements in Drosophila. Proceedings of the National Academy of Sciences 84: 9123-9127.
4. Shyamala V, Ames GF-L, (1989) Genome walking by single-specific-primer polymerase chain reaction: SSP-PCR. Gene 84: 1-8.
5. Ji J, Braam J, (2010) Restriction Site Extension PCR: A Novel Method for High-Throughput Characterization of Tagged DNA Fragments and Genome Walking. PLoS ONE 5: e10577.
6. Robinson S, Tang L, Mooney B, McKay S, Clarke W, et al. (2009) An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches. BMC Plant Biology 9: 101.
7. Leung J, Giraudat J, (1998) Cloning genes of Arabidopsis thaliana by chromosome walking. Methods in Molecular Biology (Clifton, NJ) 82: 277-303.
8. Krysan PJ, Young JC, Jester PJ, Monson S, Copenhaver G, et al. (2002) Characterization of T-DNA insertion sites in Arabidopsis thaliana and the implications for saturation mutagenesis. OMICS: A Journal of Integrative Biology 6: 163-174.
9. Jung K-H, An G, Ronald PC, (2008) Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nature Review of Genetics 9: 91-101.
10. Thole V, Alves SC, Worland B, Bevan MW, Vain P, (2009) A protocol for efficiently retrieving and characterizing flanking sequence tags (FSTs) in Brachypodium distachyon T-DNA insertional mutants. Nat Protocols 4: 650-661.
11. Siebert PD, Chenchik A, Kellogg DE, Lukyanov KA, Lukyanov SA, (1995) An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Research 23: 1087-1088.
12. Padegimas LS, Reichert NA, (1998) Adaptor Ligation-Based Polymerase Chain Reaction-Mediated Walking. Analytical Biochemistry 260: 149-153.
13. Spertini D, Beliveau C, Bellemare G, (1999) Screening of transgenic plants by amplification of unknown genomic DNA flanking T-DNA. BioTechniques 27: 308-314.
14. Sterky F, Holmberg A, Alexandersson G, Lundeberg J, Uhlén M, (1998) Direct sequencing of bacterial artificial chromosomes (BACs) and prokaryotic genomes by biotin-capture PCR. Journal of Biotechnology 60: 119-129.
15. Korbie DJ, Mattick JS, (2008) Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nature Protocols 3: 1452-1456.
16. Hecker KH, Roux KH, (1996) High and low annealing temperatures increase both specificity and yield in touchdown and stepdown PCR. Biotechniques 20: 478-485.
17. Bae J-H, Sohn J-H, (2010) Template-blocking PCR: An advanced PCR technique for genome walking. Analytical Biochemistry 398: 112-116.
18. Zabarovsky ER, Allikmets RL, (1986) An improved technique for the efficient construction of gene libraries by partial filling-in of cohesive ends. Gene 42: 119-123.
19. Huang S, Liu H, He G, Yu F, (2007) An improved method to identify the T-DNA insertion site in transgenic Arabidopsis thaliana genome. Russian Journal of Plant Physiology 54: 822-826.
20. Ukai H, Ukai-Tadenuma M, Ogiu T, Tsuji H, (2002) A new technique to prevent self-ligation of DNA. Journal of Biotechnology 97: 233-242.
21. Sallaud C, Gay C, Larmande P, Bès M, Piffanelli P, et al. (2004) High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics. The Plant Journal 39: 450-464.
22. Dolye JJ, Doyle JL, (1990) Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
23. Rice P, Longden I, Bleasby A, (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 16: 276-277.
24. Tsuchiya T, Kameya N, Nakamura I, (2009) Straight Walk: A modified method of ligation-mediated genome walking for plant species with large genomes. Analytical Biochemistry 388: 158-160.
25. Kibbe WA, (2007) OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Research 35: W43-W46.
26. Maloy SR, Cronan JE, Freifelder D, (1996) Microbial Genetics: Jones and Bartlett Publishers (Boston).
27. Brown TA, (2010) Gene cloning and DNA analysis: an introduction Oxford;Hoboken Wiley-Blackwell pp. xvi-320.
28. Sambrook J, Fritsch EF, Maniatis T, (1989) Molecular cloning: a laboratory manual. Molecular cloning: a laboratory manual Ed. 2 xxxviii + 1546.
29. Sathees CR, Raman MJ, (1999) Mouse testicular extracts process DNA double-strand breaks efficiently by DNA end-to-end joining. Mutation Research/DNA Repair 433: 1-13.
30. Sgaramella V, Ehrlich SD, (1978) Use of the T4 Polynucleotide Ligase in The Joining of Flush-Ended DNA Segments Generated by Restriction Endonucleases. European Journal of Biochemistry 86: 531-537.
31. Martineau B, Voelker TA, Sanders RA, (1994) On Defining T-DNA. The Plant Cell Online 6: 1032-1033.
32. Weigel D, Ahn JH, Blazquez MA, Borevitz JO, Christensen SK, et al. (2000) Activation Tagging in Arabidopsis. Plant Physiol 122: 1003-1014.
33. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12: 499-510.
34. Tarasova G, Nayakshina T, Degtyarev S, (2008) Substrate specificity of new methyl-directed DNA endonuclease GlaI. BMC Molecular Biology 9: 7.