Poly(rA)•poly(rU) with Ni2+ ions at different temperatures:: Infrared absorption and vibrational circular dichroism spectroscopy

Phase transitions were studied of the sodium salt of poly(rA)(.)poly(rU) induced by elevated temperature without Ni2+ and with Ni2+ in 0.07 M concentration in D2O (similar to0.4[Ni]/[P]). The temperature was varied from 20degrees C to 90degrees C. The double-stranded conformation of poly(rA)(.)poly(rU) was observed at room temperature (20degrees C - 23degrees C) with and without Ni2+ ions. In the absence of Ni2+ ions, partial double- to triple-strand transition of poly(rA)(.)poly(rU) occurred at 58degrees C, whereas only single-stranded molecules existed at 70degrees C. While poly(rU) did not display significant helical structure, poly(rA) still maintained some helicity at this temperature. Ni2+ ions significantly stabilized the triple-helical structure. The temperature range of the stable triple-helix was between 45degrees C and 70degrees C with maximum stability around 53degrees C. Triple- to single-stranded transition of poly(rA)(.)poly(rU) occurred around 72degrees C with loss of base stacking in single-stranded molecules. Stacked or aggregated structures of poly(rA) formed around 86degrees C. Hysteresis took place in the presence of Ni2+ during the reverse transition from the triple-stranded to the double-stranded form upon cooling. Reverse Hoogsteen type of hydrogen-bonding of the third strand in the triplex was suggested to be the most probable model for the triple-helical structure. VCD spectroscopy demonstrated significant advantages over infrared absorption or the related electronic CID spectroscopy.