Evaluation of RNA conformation from circular dichroism and optical rotatory dispersion data

An analysis of optical rotatory dispersion and circular dichroism of RNA is described which leads to an estimate of the degree of base pairing. By the use of new standards for the double-helical parts of the molecule, based on data for two-stranded viral RNA species, a good fit between calculated and observed curves can be achieved. Where data are available the results of analyses of optical rotatory dispersion and circular dichroism in general show satisfactory consistency.     

A system for automatic temperature-programmed recording of circular dichroism and optical rotatory dispersion

The effect of temperature on the circular dichroism (CD) and the optical rotatory dispersion (ORD) of macromolecules, and particularly nucleic acids, provides useful information regarding macromolecular conformation (1–3). Instruments which can perform this function, however, are not commercially available. The dependence of CD upon temperature is usually measured by manual variation of the temperature of a jacketed-cell assembly positioned within the spectropolarimeter. We wish to report a modification of the Beckman T_m Analyzer ¹, which is designed to record temperature-optical density profiles, permitting the use of this instrument in conjunetion with a Durrum-Jasco recording spectropolarimeter ². This assembly provides for automatic recording of CD or ORD versus temperature at wavelengths between 190 and 700 mμ. We recently employed this system in studies of the temperature dependence of CD in DNA-ethidium bromide complexes (4,5).     

Optical properties of hyaluronic acid. Ultraviolet circular dichroism and optical rotatory dispersion

The molar optical rotation at 220 nm and ellipticity values at 210 nm of both sodium hyaluronate and hyaluronic acid are greatly enhanced in comparison to the values for the monomeric units and oligosaccharides indicating a degree of preferred order. With increasing hydrogen ion concentration, there is no appreciable change in the 210 nm circular dichroic band, but the second circular dichroic band below pH 4 changes abruptly to the positive side and reaches a maximum value at pH 2·5. This positive circular dichroic band of hyaluronic acid is temperature and concentration dependent. The major change in sign and position of the second circular dichroic band of hyaluronic acid below pH 4 is attributed to the conformational change of a single polysaccharide chain or to a chain-chain interaction. The results indicate that increase in concentration or decrease in temperature and in the ionization of carboxyl group promotes the formation of ordered cross-link regions. The conformational changes found in solution have been interpreted as an order-disorder transition in the crosslink regions based on the interconversion of random coil and double helix.     

Study by circular dichroism and optical rotatory dispersion of polypeptides with aromatic side-chain chromophores

Poly(ortho-, meta-, and para-γ-nitrobenzyl-L -glutamates) were studied by circular dichroism (CD) and optical rotatory dispersion (ORD) in two helicogenic solvents, hexafluoroisopropanol (HFIP) and dichloroethane (EDC), and two non-helicogenic solvents, dichloracetic acid (DCA) and trifluoroacetic acid (TFA). The corresponding glutamates were also studied in DCA and TFA. The symmetric nitrobenzylic chromophore is optically active when the polymers are in solution in DCA and TFA. The corresponding glutamates are also optically active under the same conditions. Thus, it was not possible to explain the origin of the optical activity of the side-chain chromophore when the polymer is in solution in a helicogenic solvent. Nevertheless, from a side-chain dichroic band, a helix–coil transition curve was determined and the stability of each poly(γ-nitrobenzyl-L -glutamate) given; this stability depends on the position of the nitro substituent on the aromatic ring.     

Circular dichroism,optical rotatory dispersion,and absorption studies on the conformation of bovine rhodopsin in situ and solubilized with detergent

Circular dichroism, optical rotatory dispersion and absorption of rhodopsin, the visual pigment of bovine rod outer segment membranes, were studied in situ and in membranes solubilized with various detergents. The -helical content of the membrane protein is approximately 30%. The membrane protein possesses little -structure. Solubilization of the membrane by the detergents, Emulphogene BC-720 and cetyltrimethylammonium salts, results in loss of protein helical structure and perturbation of aromatic residues. These effects are not observed on digitonin solubilization.In regard to the structural stability of the membrane during bleaching, the following conclusions were reached: (1) Delocalized conformational changes of rhodopsin in situ involving secondary and/or tertiary structure are very unlikely. (2) Localized conformational changes of rhodopsin in situ involving secondary structure must be limited to the involvement of no more than three amino acid residues and localized conformational changes involving tertiary structure must be limited to very short segments of the protein chain containing, at the most, only a few aromatic residues. (3) Large changes in the interaction of lipid and protein moieties of the membrane are unlikely. (4) The detergents, Emulphogene, cetyltrimethylammonium salts, and digitonin, significantly decrease the conformational stability of rhodopsin as compared to the in situ conditions. The effect is smaller with digitonin.Evidence is presented against a proposed mechanism by which optical activity of the prosthetic group, retinal, is induced by resonance coupling of the transition dipoles of retinal and the lowest energy transitions of the aromatic groups of the apoprotein, opsin. A mechanism in which atropisomers of retinal are preferentially bound by opsin is consistent with the present results. The optical activity of the prosthetic group is markedly changed upon solubilization of the membrane by detergent. This change in optical activity is probably coupled to changes in conformation of the protein moiety induced by solubilization.This work is based in part upon a Ph.D. dissertation submitted by C.N.R. to The Ohio State University (1974). A preliminary report of this work was presented at the sixteenth annual meeting of the Biophysical Society, Toronto, Canada, February, 1972, Abstracts SaPM-H8 and SaPM-H9     

Optical rotatory dispersion and circular dichroism of carbanilyl polysaccharides

Measurements of optical rotatory dispersion (ORD) and circular dichroism (CD) have been made in the range of 600-210 mμ for the β-glycan carbanilates as for instance, 2,3,6-tricarbanilylcellulose (I), 2,3,6-tricarbanilylmannan (II), 2,3-dicarbanilylcellulose (III), and octacarbanilylcellobiose (IV) and also for the α-glycan carbanilates, such as 2,3,6-tricarbanilylamylose (V), tricarbanilylpullulan (VI), 2,3-dicarbanilylamylose (VII), and octacarbanilylmaltose (VIII). Furthermore, the 2,3,4,6-tetracarbanilyl-α-methyl-glucopyranoside (IX) and the 1,2,3,4,6-pentacarbanilylglucose (X) have been measured in dioxane at 20°C. For the β-glycans a small negative CD in the region of 238–240 mμ and nearly symmetrical ORD curve with a crossover point at 238–240 mμ are found; this indicates a simple negative Cotton effect. In the case of α-glycosides, a strong negative CD with a maximum at 240–242 mμ and a strong positive CD with a maximum at 223–225 mμ were found; the ORD curves are asymmetrical and cross the abscissa in two places, at 241–243 and 220–222 mμ. With 2,3,4,6-tetracarbanilyl-α-methylglucoside (IX) no CD and ORD in the ultraviolet region and with 1,2,3,4,6-pentacarbanilyl-glucopyranoside (X) the ORD, but not the CD, could be measured. The ORD curve is nearly symmetrical, like those of the β-glycans but is of opposite sign. It seems impossible to discuss the striking difference of the CD and ORD spectra between the α-and the β-glycans in terms of contributions of single independant chromophores influenced by their individual different steric arrangements and their spatial relation to the glycosidic bond in C₁. The exciton theory of Moffitt, which is suitable for explaining the ORD and CD spectra of helical polymers, has been applied to α- and β-glycans. A structure with helical parts is proposed for the α-glycans while a nearly planar arrangement is assumed for the β-glycans.     

Optical rotatory dispersion and circular dichroism of benzoyl polysaccharides

Measurements of optical rotatory dispersion (ORD) and circular dichroism (CD) were made in the range of 400–205 nm for polysaccharide tribenzoates such as 2,3,6-tri-O-benzoyl amylose (I), 2,3,4-tri-O-benzoyl dextran (II), tri-O-benzoyl pullulan (III), 2,3,6-tri-O-benzoyl cellulose (IV), 2,3,6-tri-O-benzoyl mannan (V), and polyglycan dibenzoates such as 2,3,-di-O-benzoyl amylose (VI), cellulose (VII), and mannan (VIII). All compounds exhibit Cotton effects in the region of their UV absorption bands (206–285 nm). Comparison of the corresponding di- and tribenzoyl polysaccharides shows a qualitative agreement in number, position and sign of the CD bands but differences in ellipticity magnitude. The disubstituted derivatives exhibit smaller amplitudes than the trisubstituted ones. The contribution of the C(6) chromophore (linked by a CH₂-group to the asymmetric C(5) atom) was determined to be of the same sign as the combined contribution of the C(2) and C(3) substituents. The CD bonds of the individual polysaccharide derivatives, which differ in number, sign, and position, were discussed in terms of the steric position of the single chromophores and the steric arrangement and interaction caused by the configuration of the polysaccharides. The optical behavior of these polysaccharide derivatives was found to be not strongly influenced by a definite chain conformation in solution.