Conformational dependence of the Raman scattering intensities from polynucleotides. III. Order‐disorder changes in helical structures

Abstract Raman spectra are presented on ordered and presumably helical structures of DNA and RNA as well as the poly A·poly U helical complex, polydAT, and the helical aggregates of 5′‐GMP and 3′‐GMP. The changes in the frequency and the intensity of the Raman bands as these structures undergo order‐disorder transitions have been measured. In general the changes we have found can be placed into three categories: ( 1 ) A reduction in the intensities of certain ring vibrations of the polynucleotide bases is observed when stacking or ordering occurs (Raman hypochromism). Since the ring vibrational frequencies are different for each type of base, we have been able to obtain some estimate of average amount of order of each type of base in partially ordered helical systems. ( 2 ) A very large increase in the intensity of a sharp, strongly polarized band at about 815 cm −1 is observed when polyriboA and polyriboU are formed into a helical complex. Although this band is not present in the separated chains at high temperature, a broad diffuse band at about 800 cm −1 is present. The 815 cm −1 band undoubtedly arises from the vibrations of the phosphate‐sugar portions of the molecule and provides a sensitive handle to the back‐bone conformation of the polymer. This band also appears upon ordering of RNA, formation of the helical aggregate of 5′‐riboGMP, and to some extent in the selfstacking of the polyribonucleotides polyA, polyU in the presence of Mg ++ , PolyC, and polyG. No such intense, polarized band is found, however, in ordered DNA, polydAT, or the 3′‐riboGMP aggregate, although there is a conformationally independent band at about 795 cm −1 in DNA and polydAT. ( 3 ) Numerous frequency changes occur during Conformational changes. In particular the 1600–1700 cm −1 region in D 2 O shows significant conformationally dependent changes in the CO stretching region analogous to the changes in this region which have been observed in these substances in the infrared. Thus, Raman scattering appears to provide a technique for simultaneously observing the effects of base stacking, backbone conformation and carbonyl hydrogen bonding in nucleic acids in moderately dilute (10–25 mg/ml) aqueous solutions.