Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities.

Circular dichroism (CD) spectroscopy is widely used to characterize the structures of DNA G-quadruplexes. CD bands at 200-300 nm have been empirically related to G-quadruplexes having parallel or antiparallel sugar-phosphate backbones. We propose that a more fundamental interpretation of the origin of the CD bands is in the stacking interactions of neighboring G-quartets, which can have the same or opposing polarities of hydrogen bond acceptors and donors. From an empirical summation of CD spectra of the d(G)5 G-quadruplex and of the thrombin binding aptamer that have neighboring G-quartets with the same and opposite polarities, respectively, the spectra of aptamers selected by the Ff gene 5 protein (g5p) appear to arise from a combination of the two types of polarities of neighboring G-quartets. The aptamer CD spectra resemble the spectrum of d(G3T4G3), in which two adjacent quartets have the same and two have opposite polarities. Quantum-chemical spectral calculations were performed using a matrix method, based on guanine chromophores oriented as in d(G3T4G3). The calculations show that the two types of G-quartet stacks have CD spectra with features resembling experimental spectra of the corresponding types of G-quadruplexes.

Determination of the absolute configuration of rubroflavin by comparison of measured and calculated CD spectra of its thermolysis product 3-methanesulfinyl-5-methylmercaptophenol.

The absolute configuration of rubroflavin has been determined indirectly by comparison of the measured and the calculated CD spectrum of its thermal decomposition product 3-methanesulfinyl-5-methylmercaptophenol. Performing geometry optimizations at the HF/6-31+G* level we found fifteen local minima for the (R)-isomer of 3-methanesulfinyl-5-methylmercaptophenol. The CD spectrum of the compound was then obtained as a superposition of the Boltzmann-weighted spectra for each structure calculated with the non-empirical CIS method. The corresponding Boltzmann factors have been calculated employing the relative energies of these minima determined at the ZPE + MP2/6-31+G*//HF/6-31+G* level of ab initio theory. Comparing the signs of the observed and calculated longest wave length Cotton effect we assign an absolute configuration to the thermolysis product. Since additional calculations revealed that the tricoordinate sulfur atom in rubroflavin and in its decomposition product is configurationally stable under the conditions of thermolysis we conclude that the absolute configuation at the corresponding sulfur atom of rubroflavin is the same.