Kinked Model of a DNA Tridecamer with an Unpaired Adenosine: Energy Minimization and X-ray Structural Studies

摘要

X-ray crystallographic studies have been carried out on the DNA tridecamer d(CGCAGAATTCGCG). Previous NMR studies predict that this tridecamer forms a duplex similar to the B-DNA dodecamer, except for an extra adenosine residue that is stacked within the helix but remains unpaired. Initially we collected only low resolution X-ray diffraction data as crystals of this tridecamer decayed in the X-ray beam in a few hours, even when cooled to 4 C. By cooling the crystals to approx. -150 C, it was possible to preserve their lifetime practically indefinitely, thus permitting accurate X ray data collection to high resolution. We have employed methods of energy minimization and molecular dynamics, resulting in a symmetrically kinked model of this tridecamer. Reprints. (AW)