The present study (see ref 1) delineates the scope and limitations of porphyrin chromophores for structural studies by the exciton coupled circular dichroic (CD) method. A distance dependency of the porphyrin coupling was investigated in the range between 10 and 50 Å. Over short interchromophoric distances, significant changes in the conformational distribution introduced by the bulky porphyrin chromophores were observed. Over longer distances, the porphyrins showed ca. 10-fold sensitivity increase over commonly used chromophores, and an effective direction for the interacting porphyrin transition moments was assigned by comparison. Porphyrins at the termini of dimeric steroids and brevetoxin B exhibited exciton coupling over interchromophoric distances up to 50 Å. These results represent the porphyrins as promising reporter chromophores for extending the exciton coupled CD method to structural studies of biopolymers.

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.