THE J-COUPLING RESTRAINED MOLECULAR MECHANICS (JRMM) PROTOCOL - AN EFFICIENT ALTERNATIVE FOR DERIVING DNA ENDOCYCLIC TORSION ANGLE CONSTRAINTS .1. CORRELATION OF ENDOCYCLIC TORSION ANGLES AND VICINAL TORSION ANGLE PHI(1'2')

An efficient alternative which makes use of the reliable 3J(1) (2) val ue to derive the endocyclic torsion angle constraints is proposed in t his study. Based on the information embedded in the two plots, (i) the vicinal proton-proton J-couplings, 3J(1'2'), 3J(1'2 ''), 3J(2'3'), 3J (2 '' 3') and 3J(3'4') against the pseudorotation phase angle, and (ii ) 3J(1'2 ''), 3J(2'3'), 3J(2 '' 3') and 3J(3'4') against 3J(1'2'); usi ng the calculated J-couplings obtained for a range of sugar geometries of deoxyribose ring in nucleosides and nucleotides encountered along the pseudorotation itinerary [J. van Wijk, B.D. Huckriede, J.H. Ippel and C. Altona, Methods Enzymol. 211, 286-306 (1992)], it is suggested that the vicinal 3J(1'2') possesses structural information other than the vicinal torsion angle phi(1'2'). This study is divided into two pa rts. In Part I, a correlation diagram between the endocyclic torsion a ngles nu(i), (i=0,1,2,3,4) and the restrained vicinal torsion angle ph i(1'2') is obtained through the use of the J-coupling restrained molec ular mechanics (JrMM) protocol. The established phi(1'2')-nu(i) correl ation shows nu(i) can be deduced from the reliable 3J(1'2') value and it forms the basis for developing an alternative protocol to derive en docyclic torsion angle constraints. In Part II of this series, extensi ve testing demonstrating the validity of the JrMM protocol to derive n u(i) for defining the sugar geometry of solution DNA molecules is pres ented.