Segregation of Partly Melted DNA Molecules

Segregation of partly melted DNA molecules is a convenient and efficient method to isolate DNA fragments associated with CpG islands. The method stands on the observation that the electrophoretic mobility of partly melted DNA fragments in a denaturing gradient gel is low and that they persist in the gel so long as the remaining helical part is sufficiently resistant to strand dissociation and dissociates slowly. Such features are observed in DNA fragments derived from CpG islands. These DNA fragments are preferentially retained in a denaturing gradient gel after prolonged electric field exposure, permitting the enrichment of DNA fragments derived from CpG islands. The principle and practical application of this method are reviewed.

Keywords:

• dCpG islands
• Denaturing gradient gel
• Electrophoresis
• Gene identification
• Strand dissociation kinetics

Acknowledgments

We thank L. Lerman for interesting us in DGGE. We also thank A. J. Oates, L. Xu, Y. H. Chuu, A. Sekiguchi, M. J. Terry, and Y. Miyamoto for the contribution to some of the work described in this article; and the Ministry of Health, Labour, and Welfare of Japan for support.

This article is dedicated to Professor Eiko Ohtsuka on the occasion of her 70th birthday.