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A Universal Nested Deletion Method Using an Arbitrary Primer and Elimination of a Unique Restriction Site

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In Vitro Mutagenesis Protocols

Part of the book series: Methods In Molecular Medicineā„¢ ((MIMB,volume 57))

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Abstract

The generation of nested deletions within cloned fragments of DNA has important applications in molecular biology. For DNA sequencing, nested deletions provide a series of overlapping templates that can be used to generate a composite sequence with a single sequencing primer; in gene and protein functional studies, nested deletions allow researchers to locate and define a variety of functional domains based on regions of deletions.

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References

  1. Legerski, R. J., Hodnett, J. L., and Gray, H. B., Jr. (1978) Extracellular nucleases of Pseudomonas BAL 31 III. Use of the double-strand deoxyriboexonuclease activity as the basis of a convenient method for the mapping of fragments of DNA produced by cleavage with restriction enzymes. Nucleic Acids Res. 5, 1445.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  2. Henikoff, S. (1987) Unidirectional digestion with exonuclease III in DNA sequence analysis. Methods Enzymol. 155, 156ā€“165.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  3. Shen, W., and Waye, M. M. (1988) A novel method for generating a nested set of unidirectional deletion mutants using mixed oligodeoxynucleotides. Gene 70, 205ā€“211.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  4. Deng, W. P. and Nickoloff, J. A. (1992) Site-directed mutagenesis of virtually any plasmid by eliminating a unique site. Anal. Biochem. 200, 81ā€“88.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  5. Conley, E. C. and Saunders, J. R. (1984) Recombination-dependent recircularization of linearized pBR322 plasmid DNA following transformation of Escherichia coli. Mol. Gen. Genet. 194, 211ā€“218.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  6. Holmes, D. S. and Quigley, M. (1981) A rapid boiling method for the preparation of bacterial plasmids. Anal. Biochem. 114, 193ā€“197.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  7. Akada, R. (1994) Quick-check method to test the size of Escherichia coli plasmids. BioTechniques 17, 58.

    PubMedĀ  CASĀ  Google ScholarĀ 

  8. Zell, R. and Fritz, H. (1987) DNA mismatch repair in Escherichia coli counteracting the hydrolytic deamination of 5-methyl-cytosine residues. EMBO J. 6, 1809ā€“1815.

    PubMedĀ  CASĀ  Google ScholarĀ 

  9. Chung, C. T., Niemela, S. L., and Miller, R. H. (1989) One-step preparation of competent Escherichia coli: Transformation and storage of bacterial cells in the same solution. Proc. Natl. Acad. Sci. USA 86, 2172ā€“2175.

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  10. Protocol for Transformerā„¢ Site-Directed Mutagenesis Kit. (1994) Clontech Laboratories, Inc, PT1130-1, Palo Alto, CA.

    Google ScholarĀ 

  11. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

    Google ScholarĀ 

  12. Zhu, L. (1992) Highly efficient site-directed mutagenesis of dsDNA plasmids. CLONTECHniques VII(1), 1ā€“5.

    Google ScholarĀ 

  13. Masumune, Y. and Richardson, C. A. (1971) Strand displacement during deoxyribonucleic acid synthesis at single-strand breaks. J. Biol. Chem. 246. 2692ā€“2701.

    Google ScholarĀ 

  14. Nossal, N. G. (1974) DNA synthesis on a double-stranded DNA template by the T4 bacteriophage DNA polymerase and the T4 gene 32 DNA unwinding protein. J. Biol. Chem. 249, 5668ā€“5676.

    PubMedĀ  CASĀ  Google ScholarĀ 

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Ā© 1996 Humana Press Inc.

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Zhu, L., Holtz, A.E. (1996). A Universal Nested Deletion Method Using an Arbitrary Primer and Elimination of a Unique Restriction Site. In: Trower, M.K. (eds) In Vitro Mutagenesis Protocols. Methods In Molecular Medicineā„¢, vol 57. Humana Press. https://doi.org/10.1385/0-89603-332-5:119

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  • DOI: https://doi.org/10.1385/0-89603-332-5:119

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-332-0

  • Online ISBN: 978-1-59259-544-0

  • eBook Packages: Springer Protocols

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