Sequence dependence of base-pair stacking in right-handed DNA in solution: proton nuclear Overhauser effect NMR measurements.

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Abstract
Single-crystal X-ray studies of d(C-G-C-G-A-A-T-T-C-G-C-G) exhibit base-pair propellar twisting (Dickerson, R.E. and Drew, H. R., 1981) that results in close contacts between adjacent purines in the minor groove in pyrimidine (3''-5'')-purine steps and in the major groove in purine (3''-5'')-pyrimidine steps (Calladine, C. R., 1982). These observations require an .apprxeq. 3.4 A separation between the minor groove edges of adenosines on adjacent base pairs for the dA-dA step but predict a smaller separation for the dT-dA step and a larger separation for the dA-dT step in a d(A-T-T-A).cntdot.d(T-A-A-T) fragment. These predictions were confirmed from steady-state nuclear Overhauser effect measurements between assigned minor groove adenosine H-2 protons on adjacent base pairs in the proton NMR spectrum of the d(C1-G2-A3-T4-T5-A6-T6-A5-A4-T3-C2-G1) self-complementary dodecanucleotide duplex (henceforth called the Pribnow 12-mer) in solution. The measured cross-relaxation rates (product of steady-state nuclear Overhauser effect and selective spin-lattice relaxation rates) translate to interproton separations between adjacent adenosine H-2 protons of 4.22 .ANG. in the (dA3-dT4).cntdot.(dA4-dT3) step, of 3.56 .ANG. in the (dT4-dT5).cntdot.(dA5-dA4) step, and of 3.17 .ANG. in the (dT5-dA6).cntdot.(dT6-dA5) step for the Pribnow 12-mer duplex with an isotropic rotational correlation time of 9 ns at 5.degree. C. These proton NMR results show that the sequence-dependent base-pair stacking resulting from base-pair propeller twisting of defined handedness for right-handed DNA in the solid state is maintained in aqueous solution.