Structural information from electric dichroism measurements of DNA and alternating GC nucleic acids in solution: The question of base tilt

Abstract

Abstract Values of the apparent intrinsic dichroism of the 260‐nm transition of duplex poly(dG‐dC) and poly(dG‐m 5 dC) in both B‐ and Z‐conformations are determined from electric dichroism (ED) measurements by extrapolation of the data at high field strengths. These values are compared to each other and to values of the intrinsic dichroism calculated for the Z‐ and B‐forms generated respectively from the crystal structure coordinates [(1981) A. H. J. Wang, G. J. Quigley, F. J. Kolpak, G. Van der Marel, T. H. Van Boom & A. Rich, Science 211 , 171–176.] of the d(CpGpCpGpCpGp) hexamer and from the coordinates [(1982) A. V. Fratini, M. L. Kopka, H. R. Drew & R. E. Dickerson, J. Biol. Chem. 257 , 14686–14707.]. of the terminal CpGpCpGp base pairs of the crystal of straight B‐form dodecamer d(CpGpCpGpApApTpTpCpGpCpGp). Direct association of the dichroism with the orientation of the optical transition moments with respect to the helix axis of poly(dG‐dC) implies that the average tilt of the bases is much different than the values calculated from the structural coordinates. The experimental values for both the B‐ and Z‐forms are, however, almost identical to those observed with fragments of “random” sequence B‐form DNA of the same molecular length . It is argued that this descrepancy and other anomalies reported in the literature are due to the theoretically predicted unusual high field behavior associated with diffuse ion atmosphere polarization. Unlike either permanent dipoles or induced moments based on bond polarizabilities, the orienting dipole energy from the polarization of the counterions surrounding DNA approaches a finite limiting value, dependent on DNA length, at very high field strengths. This can result in extrapolated dichroisms that do not reflect structure at perfect orientation, but rather structure at some limiting orientation. Consequently, we believe, the conclusion drawn from ED measurements on short fragments of DNA that the bases are highly tilted from the perpendicular to the helix axis by propeller twisting or otherwise is suspect.