UV resonance Raman study of PolyA and PolyU complexes: Mg2+-induced formation of PolyU·PolyA·PolyU triplexes

• Measured and analyzed UV resonance Raman spectra with 244-nm cw excitation of PolyA and PolyU mixtures.
• Identified markers of RNA duplex and triplex.
• Effect of Mg2+ ions on triplex formation in equimolar mixture of PolyA and PolyU investigated at millimolar nucleotide concentration; the critical [Mg2+]/[phosphate] concentration ratio is 12/1.

The 244-nm excited resonance Raman (RR) spectra of polynucleotides, namely polyA, polyU, and their mixtures forming polyA·polyU double helices and polyU·polyA·polyU triple helices, were measured with good spectral resolution, precise spectral calibration, and reliable intensity normalization. Difference spectra were constructed to visualize changes caused by the formation of the complexes and analyzed with respect to known interactions influencing the adenosine and uridine moieties in such complexes. This analysis enabled us to verify or to reject interpretations of certain Raman bands proposed in the literature. RR-monitored Mg2+ titration of an equimolar polyA and polyU mixture was performed to investigate the effect of induced triplex formation at a mM nucleoside concentration. The critical [Mg2+]/[phosphate] concentration ratio of approximately 12/1 was determined.