Nature of conformational changes in poly[d(A-T)-d(A-T)] in the premelting region.

Abstract

The conformation of the synthetic DNA, poly[d(A-T).cntdot.d(A-T)], was investigated both in the solid state and in dilute aqueous solutions at different temperatures below its melting point. The change of the circular dichroism (CD) spectra of poly[d(A-T).cntdot.d(A-T)] solutions with decreasing temperatures from just below the melting point to 0.degree. involves a specific decrease of the intensity of the 262 nm CD band. This conformational change was assigned to a gradual and partial transition from the B to C form, on the basis of the following results: By the use of IR dichroism measurements on oriented films the humidity and salt conditions under which B and C forms of poly[d(A-T).cntdot.d(A-T)](Li+) are stable were defined. Ammonium salts induce the C form of poly[d(A-T).cntdot.d(A-T)] even at high relative humidity. CD studies of the films of the Li salt of poly[d(A-T).cntdot.d(A-T)] under the same conditions gave CD spectra corresponding to the B and C forms of this polynucleotide. The CD spectrum of the ammonium salt of poly[d(A-T).cntdot.d(A-T)] in solution approaches that of the C form in films. The conformational change of poly[d(A-T).cntdot.d(A-T)] as a function of temperature can be entirely explained on the basis of changes in the double-stranded base-paired structure. The data rule out H-bond breaking and unstacking or "breathing" as an explanation of the premelting changes. Curves of the continuous variation of CD (.DELTA..epsilon. at 262 nm) as a function of temperature (from 0.degree. to the melting zone) show similar slopes in the presence of different agents stabilizing the double-stranded structure, such as Mg2+, or at different salt concentration (KCl), indicating that the nature of the process is independent of ionic strength. Some specific effects were observed in the influence of certain neutral salts; ammonium induces the C form whereas Mg2+ favors the B form. CD data give direct evidence that a DNA like poly[d(A-T).cntdot.d(A-T)] need not change conformation upon transition from a dilute aqueous solution to a highly hydrated (film/gel) solid state. The change of conformation begins only at a defined partial dehydration.