Pf1 filamentous phage as an alignment tool for generating local and globalstructural information in nucleic acids

Pf1 filamentous phage represent a simple versatile method for generating pa rtially ordered macromolecules in solution. The phage allow tunable degrees of alignment of macromolecules under a wide range of temperature and solve nt conditions. The negatively charged phage are ideal for aligning negative ly charged nucleic acids and these phage-nucleic acid solutions are stable indefinitely. We have used Pf1 phage to align various DNA and RNA molecules in solution for measurement of dipolar coupling interactions. These dipola r couplings can be used to improve the local structure of nucleic acids. Mo re importantly they also contain information on the global structure, such as DNA bending, which presently cannot be obtained by standard NMR methods. The principles involved in using Pfl phage to generate solutions of partia lly order macromolecules will be discussed. The use of H-1-H-1, H-1-C-13 an d H-1-N-15 dipolar couplings for generating angle constraints for structure refinement of nucleic acids will also be discussed.