Nicole M. Nichols1

1 New England Biolabs, Inc., Ipswich, Massachusetts
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 3.12
DOI:  10.1002/0471142727.mb0312s93
Online Posting Date:  January, 2011
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library


Reaction conditions for a variety of endonucleases are detailed in this unit along with discussions of potential applications. Enzymes covered include BAL 31 nuclease, S1 nuclease, mung bean nuclease, micrococcal nuclease, and DNase I. A general discussion regarding the use of endonucleases to generate nonspecific breaks in dsDNA is also provided. For a detailed discussion of the endonucleases more typically associated with DNA damage repair (e.g., Endo III, IV, V and VIII of E. coli and human APE1), see UNIT 3.9. Curr. Protoc. Mol. Biol. 93:3.12.1‐3.12.7. © 2011 by John Wiley & Sons, Inc.

Keywords: DNase I; mung bean nuclease; DNA fragmentation; next‐generation DNA sequencing; micrococcal nuclease; MNase

PDF or HTML at Wiley Online Library

Table of Contents

  • Enzyme 1: Bal 31 Nuclease
  • Enzyme 2: S1 Nuclease
  • Enzyme 3: Mung Bean Nuclease
  • Enzyme 4: Micrococcal Nuclease
  • Enzyme 5: Deoxyribonuclease I (DNase I)
  • Literature Cited
  • Figures
PDF or HTML at Wiley Online Library


PDF or HTML at Wiley Online Library



Literature Cited

Literature Cited
   Alexander, M., Heppel, L.A., and Hurwitz, J. 1961. The purification and properties of micrococcal nuclease. J. Biol. Chem. 236:3014‐3019.
   Anderson, S. 1981. Shotgun DNA sequencing using cloned DNase I‐generated fragments. Nucleic Acids Res. 9:3015‐3027.
   Campbell, V.W. and Jackson, D.A. 1980. The effect of divalent cations on the mode of action of DNase I. The initial reaction products produced from covalently closed circular DNA. J. Biol. Chem. 255:3726‐3735.
   Gray, H.B., Ostrander, D.A., Hodnett, J.L., Legerski, R.J., and Robberson, D.L. 1975. Extracellular nucleases of Pseudomonas Bal 31. I. Characterization of single strand‐specific deoxyriboendonuclease and double‐strand deoxyriboexonuclease activites. Nucleic Acids Res. 2:1459‐1492.
   Gray, H.B., Winston, T.P., Hodnett, J.L., Legerski, R.J., Nees, D.W., Wei, C.‐F., and Robberson, D.L. 1981. The extracellular nuclease from Alteromonas espejiana: An enzyme highly specific for nonduplex structure in nominally duplex DNAs. In Gene Amplification and Analysis, Vol. 2: Structural Analysis of Nucleic Acids (J.G. Chirikjian and T.S. Papas, eds.) pp. 169‐203. Elsevier/North Holland, New York.
   Harismendy, O. and Frazer, K.A. 2009. Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR‐PCR using Illumina GA sequencing‐by‐synthesis technology. BioTechniques 46:229‐231.
   Kornberg, R.D. 1977. Structure of chromatin. Ann. Rev. Biochem. 46:931‐954.
   Kroeker, W.D., Kowalski, D., and Laskowski, M. 1976. Mung bean nuclease I. Terminally directed hydrolysis of native DNA. Biochemistry 15:4463‐4467.
   Lau, P.P. and Gray, H.B. 1979. Extracellular nucleases of Alteromonas espejiana Bal 31. IV. The single strand‐specific deoxyriboendonuclease activity as a probe for regions of staltered secondary structure in negatively and positively supercoiled closed circular DNA. Nucleic Acids Res. 6:331‐357.
   Legerski, R.J., Gray, H.B., and Robberson, D.L. 1977. A sensitive endonuclease probe for lesions in DNA helix structure produced by carcinogenic or mutagenic agents. J. Biol. Chem. 252:8740‐8746.
   Legerski, R.J., Hodnett, J.L., and Gray, H.B. 1978. Extracellular nucleases of Pseudomonas Bal 31. III. Use of the double‐strand deoxyriboexonuclease activity as a basis of a convenient method for the mapping of fragments of DNA produced by cleavage with restriction enzymes. Nucleic Acids Res. 5:1445‐1464.
   Moore, S. 1981. Pancreatic DNase. In The Enzymes, Vol. 14A (P.D. Boyer, ed.) pp. 281‐298. Academic Press, San Diego, California.
   O'Neill, L.P. and Turner, B.M. 2003. Immunoprecipitation of native chromatin: NChIP. Methods 31:76‐82.
   Pelham, H.R.B. and Jackson, R.J. 1976. An efficient mRNA‐dependent translation system from reticulocyte lysates. Eur. J. Biochem. 67:247‐256.
   Vogt, V.M. 1980. Purification and properties of S1 nuclease from Aspergillus. Methods Enzymol. 65:248‐254.
   Wei, C.‐F., Alianell, G.A., Bencen, G.H., and Gray, H.B. 1983. Isolation and comparison of two molecular species of the Bal 31 nuclease from Alteromonas espejiana with distinct kinetic properties. J. Biol. Chem. 258:13506‐13512.
PDF or HTML at Wiley Online Library