Structural Property of DNA That Migrates Faster in Gel Electrophoresis, as Deduced by CD Spectroscopy

Bent DNAs are known to migrate slower than ordinary DNA in non-denaturing polyacrylamide gel electrophoresis. In contrast, several satellite DNAs have been shown to migrate fast. The structural property that causes the fast migration, however, is not clarified so far on molecular basis. We have investigated the structural property of a satellite DNA, which contains consecutive purine sequences and migrates faster in gel, by CD spectroscopy. Partial formation of an A-form–like structure has been suggested. Reduction in DNA length due to the formation of the A-form–like structure may be responsible for the fast migration. The pronounced rigidity of DNA may also contribute to the behavior.

Keywords:

• Bent DNA
• CD
• Satellite DNA
• A-Form

Acknowledgments

We thank Dr. Hideki Tagashira for technical assistance. M.K. was supported by Grants-in-Aid for Scientific Research (Nos. 17026011, 17048009, 18011008, and 18370046) and the Protein 3000 Project of MEXT and by a PRESTO grant of JST. T.O. was supported by MEXT (No. 17050022). A.M. is supported by a postdoctoral fellow program of JSPS.

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