Premelting and the hydrogen‐exchange open state in synthetic RNA duplexes

Here we attempt to relate equilibrium temperature‐dependent spectral changes in two synthetic RNA homopolymer duplexes—poly(rA) · poly(rU) and poly(rI) · poly(rC)—to the conformational opening detected in stopped‐flow hydrogen–deuterium exchange experiments on these molecules. We are concerned with changes in several spectral properties that occur well below onset of the thermally induced helix‐coil “melting” transition in these systems. These are known as “premelting” transitions, and can be detected in uv CD spectra as well as in vibrational bands of the bases in the ir. Both CD and ir spectra exhibit isoelliptic or isosbestic points consistent with a well‐defined two‐state premelting process. Application of a least‐squares analysis to two‐state models for premelting using data from different bands in the CD and ir shows that the enthalpies are substantially greater than that of the hydrogen‐exchange opening. Thus the hydrogen‐exchange open state represents only one premelting reaction among several that lead to equilibrium changes in helix geometry or base vibrational modes. The latter include processes that occur on a rapid time scale, including potential base‐pair openings not productive for the exchange reaction. It appears that the former, and not the hydrogen‐exchange opening, dominates the premelting alterations monitored by ir and CD spectroscopy.