THE J-COUPLING RESTRAINED MOLECULAR MECHANICS (JRMM) PROTOCOL - AN EFFICIENT ALTERNATIVE FOR DERIVING DNA ENDOCYCLIC TORSION ANGLE CONSTRAINTS .2. EXPERIMENTAL APPLICATION OF THE JRMM PROTOCOL

The J-coupling restrained molecular mechanics (JrMM) protocol, which c orrelates deoxyribose endocyclic torsion angles and vicinal proton-pro ton torsion angle phi(1'2') in Part I of this study, is demonstrated t o be a viable alternative to efficiently derive the endocyclic torsion angle constraints for the determination of the solution structures of DNA molecules. Extensive testing demonstrating the validity of the Jr MM-derived torsion angle constraints in the restrained molecular dynam ics and energy minimization structural refinement processes is perform ed theoretically using an energy-minimized B-DNA model and experimenta lly using a DNA hexamer d(CGTACG)(2). The results show that only a 0.2 Angstrom difference exists between the RMSD values of the refined str uctures using the ideal and the JrMM-derived endocyclic torsion angle constraints. The JrMM-derived torsion angles are also determined to be in good agreement with the torsion angles derived through the use of the vicinal J-derived torsion angles. These results show that through the use of reliably measured J(1'2') values and computer simulation me thod, the endocyclic torsion angle constraints can be derived reliably and efficiently. Thus the JrMM method serves as an alternative strate gy to generate endocyclic torsion angle constraints for the determinat ion of the solution structures of DNA molecules.