Crystallographic and Spectroscopic Studies of d(CCGGTACCGG)

Abstract

The decanucleotide sequence d(CCGGTACCGG) crystallizes as a four-way junction at low cobalt ion concentrations (i.e., 1 mM). When the cobalt concentration in the crystallization solution is increased to 5 mM, the sequence crystallizes as resolved B-DNA duplexes. Gel retardation studies of the decamer show both a faint slow-moving band and a much thicker fast-moving band at low cobalt ion concentrations, and only the intense fast-moving band at higher ion concentration. Circular dichroism (CD) spectroscopy of the decamer indicates a structural transition as the cobalt ion concentration in the solution is increased, probably from B-type to A-type DNA. These studies revealed that the oligomer sequence has several conformations and structures accessible to it, in a manner dependent on sequence, ion concentration, and DNA concentration.

[Supplementary materials are available for this article. Go to the publisher's online edition of Nucleosides, Nucleotides & Nucleic Acids for the following free supplemental resources(s): Supplementary Figures 1, 2, and 3.]

Keywords:

• Holliday junction
• B-DNA duplex
• groove–backbone interaction
• gel electrophoresis
• circular dichroism

Acknowledgments

This work was financially supported by the following agencies of the Government of India: Department of Biotechnology (DBT) under a research grant and Department of Science and Technology (DST) under the Fund for Improvement of Science and Technology Infrastructure (FIST) program. S. Venkadesh and P. K. Mandal thank the Council of Scientific & Industrial Research (CSIR) for senior research fellowships. We gratefully acknowledge the use of the BM14 beam line at European Synchrotron Radiation Facility (ESRF), Grenoble, France, under the program of DBT, India.

Supplementary information for this article is available online.