Crystallographic Analysis of RNA Structure

Abstract

The bright light of X-ray crystallography has recently begun to illuminate the structural conformations available to RNA molecules. In this chapter, I describe the current state of the method emphasizing the recent advances, the structural information that has been gathered to date, and the directions and challenges that lie in the future of RNA structure determination by crystallography.

THE CRYSTALLOGRAPHIC METHOD
Although considered a complex and highly specialized field by many molecular biologists, in principle, X-ray crystallography is a straightforward and well-established endeavor. It requires a homogeneous sample, a systematic and meticulous search for crystallization conditions, knowledge of the theory and techniques in data collection, computer literacy, an understanding of phasing methods in structure determination and refinement as well as insight in structure analysis. Unfortunately, virtually every structure determination runs into unexpected problems, and that is when the experienced crystallographer needs all the tools he has available.

What Can We Learn from an X-ray Crystal Structure?
The crystallographic method of structure determination is complementary in many ways to its main alternative, multidimensional nuclear magnetic resonance (NMR) structure analysis. It is obviously restricted to providing the molecular structure in the solid state subject to possible deformation by crystal packing forces. The structure determined by crystallography is also averaged over the millions of molecules in the unit cells of the crystal. Overall, however, X-ray crystallography remains the most powerful technique of experimental structure determination. Molecular structures of virtually any size—from small molecules to viruses—can be determined by X-ray methods. Once...