Raman spectroscopy of nucleic acid triple helices

Abstract

Raman spectroscopy has been used very successfully to study double-helical structures of nucleic acids and in particular to characterize the geometries of the sugar–phosphate backbone and the base-sugar orientation using Raman lines sensitive to the sugar pucker and the glycosidic torsion angle χ (anti or syn). We present here Raman spectra of a series of intermolecular and intramolecular triple helices obtained in solution. A large conformational diversity is found for the sugar–phosphate backbone, which can adopt ‘A family’ or ‘B family’ geometries. Depending on the base sequence and the type of sugar (deoxyribose or ribose) present in the strands, characteristic lines around 815 cm−1 [and 836 cm−1 for U·(A·U) triplets] and 840 cm−1 are observed reflecting sugar–phosphate backbone chains with C3′-endo or C2′-endo sugar puckers, respectively. The base-sugar orientation is found to be anti in all triplexes studied. Combination of the Raman data with results obtained by Fourier transform IR spectroscopy and molecular modeling allows third strand base pairing schemes and third strand orientations to be proposed. Copyright © 1999 John Wiley & Sons, Ltd.