The J-coupling Restrained Molecular Mechanics (JrMM) Protocol - An Efficient Alternative for Deriving DNA Endocyclic Torsion Angle Constraints Part II: Experimental Application of the JrMM Protocol

Abstract

The J-coupling restrained molecular mechanics (JrMM) protocol, which correlates deoxyribose endocyclic torsion angles and vicinal proton-proton torsion angle phi 1'2' in Part I of this study, is demonstrated to 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 JrMM-derived torsion angle constraints in the restrained molecular dynamics and energy minimization structural refinement processes is performed theoretically using an energy-minimized B-DNA model and experimentally using a DNA hexamer d(CGTACG)2. The results show that only a 0.2 A difference exists between the RMSD values of the refined structures 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 J1'2' values and computer simulation method, the endocyclic torsion angle constraints can be derived reliably and efficiently. Thus the JrMM method serves as an alternative strategy to generate endocyclic torsion angle constraints for the determination of the solution structures of DNA molecules.