Consequences of Substituting 2NH₂A for a in Synthetic DNA’S

Abstract

Chemical and spectroscopic consequences of replacing A with 2NH₂A have been examined in a variety of synthetic DNA’s. This substitution, which permits formation of a third hydrogen bond in AT pairs, increases the stability of these pairs. The T_m elevation, however, is much smaller in the deoxy (∆T_m 12–15°) than in the ribo series (∆T_m 27–33°). Sequence effects appear to be small. CD spectra of all helices having the 2NH₂A substitution have a relatively strong extremum at 286 to 298 nm. This band is positive for B-form helices (deoxy-deoxy pairs in low salt) and negative for A-form helices (ribo-ribo and deoxy-ribo pairs). These results are consistent with the unusual CD spectrum of S-2L DNA (Kirnos et al.). This natural DNA has all A’s replaced by 2NH₂A and positive CD bands at 290 nm and 265 nm. We assign the band at ~290 nm in these helices to the B_2u transition of 2NH₂A, displaced to longer wavelength by exciton splitting, and suggest that it is relatively unperturbed by transitions of other bases. Alternating (d2NH₂A-dT)_n undergoes a cooperative transition to an altered conformation in the presence of 4M NaC1 or 2 x 10⁻⁴M hexammine cobalt. CD, IR, and ³¹P NMR experiments reveal similarities to the behavior of (dG-dC)_n as well as some differences. The results are consistent with a Z conformation for the high salt form but do not establish it. The alternating polymers (d2NH₂A-dC)_n•(dG-dT)_n and (d2NH₂A-dC)_n•(dI-dT)_n were also observed with CD. The former did not undergo a discrete transition in high salt. The latter did undergo a transition, but the structural nature of the change is not clear.