Double and Triple Helices of Nucleic Acid Polymers, Studied by UV‐Resonance Raman Spectroscopy

Abstract

AbstractUY‐resonance Raman (RR) spectra with laser excitation at 260 nm and 220 nm were taken of the triple helix poly (U) · poly(A) · poly(U), the double helix poly(A) · poly(U) and a random copolymer poly(AU). The experiments were carried out both in H2O and in D2O as solvent. It is shown that by appropriate choice of excitation wavelength, structure‐spectra correlations can be established that allow these different conformations to be clearly distinguished. Whereas the formation of the double helix poly(A) · poly(U) results in both frequency and intensity changes, only minor frequency shifts are discernible when we compare the spectra of the double helix and the triple helix poly(U) · poly(A) · poly(U). As far as the uracil modes are concerned, no significant differences between the spectra of the triple and the double helices can be discerned. Therefore the RR‐spectra indicate a very similar base conformation of the two poly(U) strands in poly(U) · poly(A) · poly(U) and that in poly(U) · poly(A). However, there are considerable changes in the relative intensities of strong adenine modes with 260 nm excitation. For example, the intensity ratio of bands around 1480 cm−1 and 1338 cm−1 increases from 0.8 in poly(A), and 0.95 in poly(A) · poly(U) to 1.4 in poly(U) · poly(A) · poly(U). The spectra suggest that both the poly(U) strands in the triple helix are of quite similar structure, whereas the conformation of the poly(A) strands changes when triple helix is formed. With 220 nm excitation, no prominent marker bands or intensity patterns are found that would allow a distinction between double and triple helical conformations. The experiments demonstrate that UV‐Raman spectroscopy, with its possibility to choose an appropriate excitation wavelength adds a valuable degree of freedom in identifying different nucleic acid structures on the basis of intensity criteria.