Raman spectroscopic measurement of base stacking in solutions of XXXX , @entity860 , @entity855 , and oligoadenylates.

@entity2642 @entity859 @entity2036 @entity860 @entity855
Measurements of the colligative properties of @entity2642 and their derivatives have shown that bases form transient aggregates in solution [Ts'o (1967) J. Am. Chem. Soc. 89, 3612-3622]. Aggregation of @entity2036 cannot be measured by osmometry due to the presence of counterions. Sedimentation measurements are difficult to obtain and have been complicated by differences in pH [Ferguson et al. (1974) Biophys. Chem. 1, 325-337]. Raman studies of oligonucleotides have shown that the intensities due to base vibrational modes depend on the extent of base stacking, but this dependence has not been quantitated. We have measured this dependence by relating changes in the Raman spectra of @entity2036 and @entity2642 with previous measurements of colligative properties. Visible Raman spectra of @entity855 , @entity860 , and @entity859 , taken over a range of concentrations from 1 to 1000 mM, show that the peak intensity ratio (I1305 + I1380)/I1340 varies linearly with the log of the concentration for all three bases. This concentration-dependent change correlates with published molal osmotic coefficient data for functionally similar bases with a correlation coefficient of 0.99. In contrast, UV resonance Raman spectra of the same bases show changes that vary linearly with concentration.
