A modified universal fast walking method for single-tube transposon mapping

Nature Protocols

Volumn 2, Issue 6, 2007, Pages 1556-1563

  Myrick, Kyl V ^a   Gelbart, William M ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BUFFER; COMPLEMENTARY DNA; LIGASE; RESTRICTION ENDONUCLEASE;

AMPLICON; ARTICLE; AUTOMATION; CONTAINER; DNA FINGERPRINTING; DNA TEMPLATE; GENE INSERTION; GENE MAPPING; GENETIC PROCEDURES; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUALITY CONTROL; REACTION ANALYSIS; SYNTHESIS; TRANSPOSON; VIRAL GENETICS;

ANIMALS; CHROMOSOME WALKING; DNA TRANSPOSABLE ELEMENTS; DROSOPHILA MELANOGASTER; TIME FACTORS;

EID: 34250782173     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2007.223     Document Type: Article

References (21)

1. Myrick, K.V. & Gelbart, W.M. Universal fast walking for direct and versatile determination of flanking sequence. Gene 284, 125-131 (2002).
2. Huet, F. et al. A deletion-generator compound element allows deletion saturation analysis for genomewide phenotypic annotation. Proc. Natl. Acad Sci. USA 99, 9948-9953 (2002).
3. Park, D.J., Renfree, M.B. & Marshall Graves, J.A. Universal last walking applied to cDNA. Prep. Biochem. Biotechnol. 34, 123-133 (2004).
4. Arkhipova, I.R. & Meselson, M. Diverse DNA transposons in rotifers of the class Bdelloidea. Proc. Natl Acad. Sci. USA 102, 11781-11786 (2005).
5. Schon, I. & Arkhipova, I.R. Two families of non-LTR rebrotransposons, Syrinx and Daphne, from the Darwinulid ostracod, Darwinula stevensoni. Gene 371, 296-307 (2006).
6. Kuo, S., Chang, W.J. & Landweber, L.F. Complex germline architecture: two genes intertwined on two Loci. Mol. Biol. Evol. 23, 4-6 (2006).
7. Chang, W.J., Kuo, S. & Landweber, L.F. A new scrambled gene in the ciliate Uroleptus. Gene 368, 72-77 (2006).
8. Walser, J.C., Chen, B. & Feder, M.E. Heat-shock promoters: Targets for evolution by P transposable elements in Drosophila. PLoS Genet. 2, e165 (2006).
9. Ochman, H., Gerber, A.S. & Hart, D.L. Genetic applications of an inverse polymerase chain reaction. Genetics 120, 621-623 (1988).
10. Triglia, T., Peterson, M.G. & Kemp, D.J. A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acids Res. 16, 8186 (1988).
11. Mueller, P.R. & Wold, B. In vivo footprinting of a muscle specific enhancer by Ligation mediated PCR. Science 246, 780-786 (1989).
12. Riley, J. et al. A novel, rapid method for the isolation of terminat sequences from yeast artificial chromosome (YAC) clones. Nucleic Acids Res. 18, 2887-2890 (1990).
13. Jones, D.H. & Winistorfer, S.C. Sequence specific generation of a DNA panhandle permits PCR amplification of unknown Ranking DNA. Nucleic Acids Res. 20, 595-600 (1992).
14. Megonigal, M.D. et al. Panhandle PCR for cDNA: A rapid method for isolation of MLL fusion transcripts involving unknown partner genes. Proc. Natl Acad. Sci. USA 97, 9597-9602 (2000).
15. Puskas, L.G., Fartmann, B. & Bottka, S. Restricted PCR: Amplification of an individual sequence flanked by a highly repetitive element from total human DNA. Nucleic Acids Res. 22, 3251-3252 (1994).
16. Liu, Y.G. & Whittier, R.F. Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 25, 674-681 (1995).
17. Schmidt, M. et al. Detection and direct genomic sequencing of multiple rare unknown flanking DNA in highly complex samples. Hum. Gene Ther. 12, 743 (2001).
18. Walser, J.C., Evgen'ev, M.B. & Feder, M.E. A genomic walking method for screening sequence length polymorphism. Mol. Ecol. Notes 6, 563-567 (2006).
19. Huang, A.M., Rehm, E.J. & Rubin, G.M. in Drosophila Protocols (eds. Sullivan, W., Ashburner, M. & Hawley, R.S.) 429-437 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2000).
20. Maniatis, T., Fritsch, E.F. & Sambrook, J. Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1982).
21. Altschul, S.F., Gish, Wi, Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).