2NH2A X T helices in the ribo- and deoxypolynucleotide series. Structural and energetic consequences of 2NH2A substitution.

Polynucleotide helices formed by the interaction of (d2NH2A)n, (r2NH2A)n, (dT)n, and (rT)n have been prepared and their physical and spectroscopic properties examined. Thermal transitions, dependence of Tm on salt concentration, stoichiometry, phase diagrams, and calculated enthalpies are reported. UV, CD, and IR spectra are reported. All of the deoxy-deoxy helices containing 2NH2A have positive CD first extrema near 290 nm and appear to have B-form structure. All the ribo-ribo or hybrid helices have negative first extrema in this region and appear to have A-form structure. Elevation of Tm by the 2-NH2 group of 2NH2A is much smaller in the deoxy than in the ribo series. We have applied an equation based on the electrostatic theory of Manning [Manning, G.S. (1972) Bopolymers 11, 937-949; Manning, G.S. (1978) Q. Rev. Biophys. 11, 179-246; Record M.T., Anderson, C.F., & Lohman, T.M. (1978) Q. Rev. Biophys. 11, 103-178] to calculate ethalpies of the helix-coil transitions of the complexes reported here. These calculated enthalpies are larger for 2NH2A X T than for A X T helices, but the difference is much smaller in the deoxy than in the ribo series. We attribute these effects on Tm and delta H in the deoxy series to loss of stabilization of the spine of hydration in B-form structures caused by interference of the 2-NH2 group in the minor groove of the helix [Dickerson, R.E., Drew, H.R., Conner, B.N., Wing, R.M., Fratini, A.V., & Kopka, M.L. (1982) Science (Washington, D.C.) 216, 475-485]. Complete phase diagrams for all 2NH2A,T systems and some A,T systems are reported. The diagrams differ widely and can be placed in four groups according to the number of transitions each system possesses.