Raman spectroscopy of nucleic acid triple helices

Raman spectroscopy has been used very successfully to study double-helical structures of nucleic acids and in particular to characterize the geometrie s of the sugar-phosphate backbone and the base-sugar orientation using Rama n lines sensitive to the sugar pucker and the glycosidic torsion angle chi (anti or syn). We present here Raman spectra of a series of intermolecular and intramolecular triple helices obtained in solution. A large conformatio nal diversity is found for the sugar-phosphate backbone, which can adopt 'A family' or 'B family' geometries, Depending on the base sequence and the t ype 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 res ults obtained by Fourier transform IR spectroscopy and molecular modeling a llows third strand base pairing schemes and third strand orientations to be proposed. Copyright (C) 1999 John Wiley & Sons, Ltd.