Structural Transitions and pH-Dependent Equilibria between Unusual Double and Triple Helical Conformations of Nucleic Acid Polymers, Studied by UV Resonance Raman Spectroscopy

Abstract

In order to study pH-driven associations and equilibria between nucleic acid helices containing the homopolymers poly(A) and poly(U), the pH-value of solutions of poly(A) or poly(A)*poly(U) or the triple helix poly(U)*poly(A)*poly(U) was varied in steps of 0.5 pH units between pH = 7.0 and pH = 2.5. Resonance Raman spectra were taken with 260-nm and 220-nm excitation, both in H2O and in D2O solvent. For the solutions containing poly(A) only, marked spectral changes between pH = 6.0 and pH = 5.5 can be attributed to the formation of the parallel stranded double helix poly(A)+*poly(A)+. The cooperativity of this duplex formation is better represented in the 260-nm than in the 220-nm excitation spectra. The double helix poly(A)*poly(U) remains stable down to pH = 5.0. At pH = 4.5 and 4.0, the experimental spectra can be understood by means of a superposition of the spectra of the triple helix poly(U)*poly(A)*poly(U) and the protonated double helix poly(A)+*poly(A)+. The triple helix itself is stable at these pH values, as can be concluded from the spectra of solutions of this polymer. Below pH = 4.0, the spectra can be calculated by the sum of poly(A)+*poly(A)+ and the single-stranded poly(U) polymer. All the helical transitions observed are better represented in the spectra excited with 260 nm, whereas the protonation state is better resolved in the 220-nm spectra. The data reported here provide a basis for further studies of unusual nucleic acid structures as triple and quadruple helices and they show that UV-resonance Raman spectroscopy is a sensitive tool for studying the kinetics and dynamics of the formation of these structures.