Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)₂ at 1.7 Å resolution

ABSTRACT

We present here a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG)₂ all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. However, in the presence of zinc, magnesium, and in the absence of any metal ion, it does not take up the junction structure, but forms an A-type double helix. This allowed us to study possible conformational changes in the double helix due to the presence of metal ions. Upon addition of the zinc ion, there is a change in the space group from P4₁2₁2 to P4₁. The overall conformation of the duplex remains the same. There are small changes in the interaction of the metal ions with the DNA. In the zinc-bound structure, there are two zinc ions that show direct interaction with the N7 atoms of terminal G₁₃ bases at either end of the molecule. There are small changes in the interhelical contacts. The consequence of these differences is to break some of the symmetry and change the space group.

KEYWORDS:

• A-DNA duplex
• X-ray crystallography
• two tetragonal space groups
• zinc interactions

Acknowledgments

We gratefully acknowledge Department of Biotechnology, Government of India for data collection facilities at BM14 beamline, ESRF, France. Also, we thank UGC for grants under the CAS program. S. Karthik thanks DST for INSPIRE fellowship and A. Thirugnanasambandam thanks UGC for a fellowship under the BSR scheme. We acknowledge with gratitude the comments of the referee who pointed out the correct interpretation of the space group ambiguity.