UNIT 2.7 Separation of Small DNA Fragments by Conventional Gel Electrophoresis

  1. Joanne Chory1,
  2. Jack D. Pollard Jr.2

Published Online: 1 MAY 2001

DOI: 10.1002/0471142727.mb0207s47

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Chory, J. and Pollard, J. D. 2001. Separation of Small DNA Fragments by Conventional Gel Electrophoresis. Current Protocols in Molecular Biology. 47:III:2.7:2.7.1–2.7.8.

Author Information

  1. 1

    The Salk Institute for Biological Studies, La Jolla, California

  2. 2

    Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts

Publication History

  1. Published Online: 1 MAY 2001
  2. Published Print: JUL 1999


Large amounts of small (<1000-bp) DNA fragments can be separated by conventional electrophoretic means. The purified fragments can then be used for cloning, sequencing, and labeling. In this unit, the techniques of DNA separation via both nondenaturing polyacrylamide and sieving agarose electrophoresis are discussed. Methods are detailed for the pouring and electrophoresis of nondenaturing polyacrylamide gels, followed by elution of the labeled or unlabeled separated DNA fragments from the gels by either passive diffusion or electroelution. A method is also provided for the use of sieving agarose, a specially treated type of agarose designed to be used at high concentrations. Poured and run like conventional agarose gels, this matrix can resolve small DNA fragments much like a nondenaturing polyacrylamide gel.