Circular intensity differential scattering and chromatin-DNA structure

Circular intensity differential scattering (CIDS) has been proven a powerful method in determining the higher-order structure of large biopolymers, such as chromatin. Theoretical predictions of the expected differential light scattering of circularly polarized light have previously been made for chromatin, either within the Born approximation, treating nucleosomes as noninteracting, oblate ellipsoids, or within a multiple dipole approximation, treating nucleosomes as interacting spheres. In order to conduct a meaningful interpretation of the CIDS signal in terms of given geometric parameters of the chiral structure, we have in this paper combined the two approaches considering the mutual interactions of ellipsoidal nucleosomes. In the process we have also found a confirmation for rthe validity of the Born approximation itself.     

Circular dichroism and circular polarization of luminescence of reduced nicotinamide adenine dinucleotide in solution and bound to dehydrogenases.

The CD (circular dichroism) and CPL (circular polarization of luminescence) spectra of NADPH in aqueous solution were studied and found to be markedly different. The spectra were not affected by cleavage of the coenzyme molecule with phosphodiesterase. The differences are thus not due to the existence of extended and folded conformations of NADPH and it is concluded that they originate in excited state conformational changes of the nicotinamide--ribose fragment. Opposite signs of both the CD and CPL spectra were observed for NADH bound to horse liver alcohol dehydrogenase and to beef heart lactate dehydrogenase indicating structural differences between the nicotinamide binding sites. The binding of substrate analogues to enzyme--coenzyme complexes did not affect the CD spectra and hence no significant conformational changes are induced upon formation of the ternary complexes. No changes in the CPL spectrum of NADH bound to lactate dehydrogenase were observed upon adding oxalate to form the ternary complex. Marked differences were found between the CPL spectra of binary and ternary complexes with liver alcohol dehydrogenase, while the CD spectra of these complexes were identical. It is concluded that a conformational change of the excited NADH molecule occurs in the binary but not in the ternary complex involving LADH, thus indicating an increased rigidity of the latter complex.     

Circular dichroism of aminoacridines bound to DNA

The binding curves of 1-, 2-, 3-, and 9-aminoacridine and proflavine on native DNA and the circular dichroism (CD) spectra of the bound cations have been determined under the same conditions. The variation of the CD spectra with the amount (r) of aminoacridine bound per DNA phosphorus was of two main kinds: (1) the rotational strength of those aminoacridines which possess a 3-amino group depended markedly on r and decreased to relatively small values (or zero) at zero r; or, (2) the rotational strength changed relatively little with r and tended to a finite value at zero r. The relevance of these observations is discussed with respect to interelation models of the complexes and with respect to possible explanations of the basis of this induction of optical activity.     

Circular intensity differential scattering and chromatin-DNA structure. A combined theoretical approach

Circular intensity differential scattering (CIDS) has been proven a powerful method in determining the higher-order structure of large biopolymers, such as chromatin. Theoretical predictions of the expected differential light scattering of circularly polarized light have previously been made for chromatin, either within the Born approximation, treating nucleosomes as noninteracting, oblate ellipsoids, or within a multiple dipole approximation, treating nucleosomes as interacting spheres. In order to conduct a meaningful interpretation of the CIDS signal in terms of given geometric parameters of the chiral structure, we have in this paper combined the two approaches considering the mutual interactions of ellipsoidal nucleosomes. In the process we have also found a confirmation for the validity of the Born approximation itself.     

Circular dichroism of acridine orange bound to DNA

The circular dichroism (CD) spectra of DNA–acridine orange (DNA–AO) complex in the visible region were measured at DNA phosphate-to-dye ratios (P/D) from 1 to 550. The CD spectrum of DNA–AO complex in the P/D ratio between 1 and approximately 40 consists of four components, i.e., positive CD bands centered at 510 and 480 mμ, and negative CD bands at 497 and 468 mμ. The CD bands at 510 and 468 mμ are optimum at P/D = 4, and the change of ε₁ ? ε_r with P/D suggests that both of them are induced from the interaction between dye molecules bound to adjacent DNA binding sites, each of which is composed of four nucleotides. This is supported by the fact that the values of ε₁ ? ε_r for both decrease with increasing temperature or increasing methylene blue concentration added to the complex. The negative Cotton effect at, 497 mμ is most favored at larger P/D ratio (～8), and the suggested assignment is to the interaction between two dye molecules bound with an empty site between them. A positive Cotton effect at 480 mμ is observed at P/D ratio of less than 4 and is optimum at 1. Above P/D ratio of 40, the CD spectrum of the complex can not be resolved into its components and even at sufficiently high P/D ratio (550) the complex shows a small Cotton effect.     

Expressions for the interpretation of circular intensity differential scattering of chiral aggregates

The derivation of compact expressions of the circular intensity differential scattering (CIDS) of chiral molecules is presented in the first Born approximation of the fields. The expressions derived are valid for a suspension of scattering chiral particles free to adopt any orientation in solution. The connection is established between the preferential scattering cross section for right- vs left-circularly polarized light for a given scattering angle and the geometrical parameters of the molecule. As observed experimentally, the equations predict that the circular differential scattering patterns must show as a function of the scattering angle a series of lobes of alternating sign. In between these lobes, zeros in the differential scattering cross section occur. For the case of two dipole moments arranged in chiral fashion, an expression is derived that shows how the relative arrangement of the dipoles and their separation relative to the wavelength of light control the number and the position of the zeros. A compact expression predicting the CIDS of a sample for very small angles of scattering is derived for a system of helices whose dimensions are small compared with the wavelength of light. Finally, the presence of CIDS in a sample is related to the appearance of anomalous signals in the CD spectrum of chiral systems. Expressions and computations of the magnitudes and sign of the anomalies are presented. The expressions obtained confirm the main features of the experimental CIDS patterns of chiral molecules previously published.     

Circular dichroism analyses of membrane proteins: an examination of differential light scattering and absorption flattening effects in large membrane vesicles and membrane sheets

The circular dichroism spectra of membrane suspensions are distorted by differential light scattering and absorption flattening effects, which arise as a consequence of the large size of the membrane particles relative to the wavelength of light and the high concentration of proteins in the membranes. In this paper, the consequences of these phenomena on the protein spectra of large membrane particles are discussed, and methods for eliminating them are examined. The distortions due to differential light scattering are relatively small in membrane systems, and can be compensated for by use of a large detector acceptance angle geometry. Several methods for correcting for differential flattening, which introduces a substantial distortion, have been evaluated, and a new method, the flattening quotient approach, which produces by far the best results, is described. Since the secondary structures calculated from circular dichroism spectra are highly dependent on accurate spectral shape and magnitude, this method for correcting the spectra may find general application in circular dichroism studies of membrane proteins.     

Dendritic crystal growth, differential circular scattering, and the origin of biomolecular homochirality

Phthalic acid rapidly crystallizing in thin aqueous films is deposited radially and rhythmically as dendritic banded spherulites that have heterochiral meso-textures in hemi-circles. The chiral fields differentially scatter left and right circularly polarized light. A scenario for chiral amplification and the origin of biomolecular homochirality is thus proposed that combines the influences of crystals and light.     

Absorption and circular dichroism spectra of methylene blue bound to alginate

The addition of methylene blue to certain samples of Na alginate produces a complex succession of spectrally distinguishable aggregated (metachromatic) dye species. Three of these species are active in CD; they are interpreted as aggregates of dye, but probably dimers, bound in orientations characteristic of the constituent copolymer blocks of alginate to which they are tentatively assigned. The aggregates compete with divalent metal ions and hydrogen ion for the binding sites of the polymer. Other samples of alginate give a modified succession of aggregated spectral species, which are almost devoid of CD activity. Mild treatment with acid, insufficient for hydrolysis, converts forms of alginate with CD activity into modified forms without it, the absorption spectra of which resemble those of samples originally devoid of activity. It is implied, subject to confirmation, that the chiral properties of the binding sites of the native polysaccharide are diminished or lost by acid treatment during commercial preparation.     

Circular dichroism spectroscopy of a cationic porphyrin bound to DNA

Recently, the porphyrin photosensitizer meso-tetra(4-N-methyl-pyridyl)-porphine was identified as a DNA-reactive agent demonstrating both electrostatic and intercalative binding. A series of porphyrin derivatives were synthesized and studied to see if similar compounds manifested identical behavior. One derivative, meso-tetra(p-N-trimethylanilinium) porphine did not exhibit intercalation behavior but did show avid binding and novel circular dichroic features when bound to B-form DNA. At an ionic strength of 1.02, the binding constant was found to be on the order of 10⁴ and higher at lower ionic strength. The large binding constants and induced optical activity suggest that at large porphyrin/DNA ratios the final porphyrin · DNA complex may take the form of a suprahelical helix.     

Fluorescence and differential light absorption recordings with calcium probes and potential-sensitive dyes in skinned cardiac cells

This report describes an optical system for microspectrophotometry in a single cardiac cell from which the sarcolemma has been removed by microdissection (skinned cardiac cell). This system is attached to the high power inverted microscope used for the microdissection and includes (a) a single variable wavelength microspectrophotometer used to define the spectrum of a given dye or Ca2+ probe; and (b) a dual wavelength, differential microspectrophotometer used to record differentially between the optimum wavelength and a wavelength separated by 25--30 nm. Results are presented using the following optical methods: (a) fluorescence measurements with chlorotetracycline to monitor the amount of Ca2+ bound to the inner face of the sarcoplasmic reticulum (SR) membrane; (b) differential absorption measurements with arsenazo III to measure changes of myoplasmic [Ca2+]free resulting from Ca2+ release from the SR; (c)fluorescence and (or) differential absorption measurements with the potential-sensitive dyes merocyanine 540, NK 2367, and di-S-C3(5) to monitor changes of charge distribution on the SR membrane during Ca2+ accumulation in the SR, as well as before and during Ca2+-induced release of Ca2+ from the SR. A small and rapid signal is observed which precedes the Ca2+-induced release of Ca2+ from the SR. It is detected as an increase of CA2+ binding inside the SR with chlorotetracycline and as a "hyperpolarization" with potential-sensitive dyes, while no transient change of myoplasmic [Ca2+]free is detected with arsenazo III. This small and rapid signal preceding the Ca2+ release may be a first hint to an understanding of the mechanism whereby a small increase of [Ca2+]free outside the SR triggers Ca2+ release from the SR.     

The differential scattering of circularly polarized light by chloroplasts and evaluation of their true circular dichroism

Chloroplasts isolated from pea leaves display an intense circular dichroism in the range 600 to 720nm. Circularly polarized light is also differentially scattered by chloroplasts, and this effect can be confused with circular dichroism. By using an instrumental modification it was possible to distinguish, and record separately, the ellipticities of the transmitted light (circular dichroism) and of the scattered light in the same c.d. instrument. By means of a light-scattering apparatus, the intensity of unpolarized light scattered by chloroplasts was measured as a function of wavelength and of angle. This measurement allowed the aforementioned ellipticities to be corrected for mutual interference. At a concentration of 4mug of chlorophyll/ml (the optimum practical concentration of chloroplasts at which there was no significant interaction of scattering and absorption effects) spectra of true circular dichroism (circular differential absorption) and circular differential scattering were obtained. The former showed maxima, positive at 688nm and negative at 676nm, with an intensity Deltatheta=8.3m degrees .litre.(mg of chlorophyll)(-1).cm(-1). The latter had a maximum at 683nm with an intensity of +47m degrees with respect to the solvent baseline; this value is independent of the concentration of chloroplasts in dilute suspensions. It is suggested that the intense circular dichroism of chloroplasts reflects specific chlorophyll-chlorophyll interactions in the light-harvesting pigment. The advantages of this method for determining the c.d. of scattering suspensions over those of other investigators are discussed.     

Helically organized macroaggregates of pigment-protein complexes in chloroplasts: evidence from circular intensity differential scattering

Angle dependence of circular intensity differential scattering (CIDS) and of nonpolarized scattering was determined in isolated spinach chloroplasts at 514.5 nm. CIDS between 0 degrees and 170 degrees was independent of the nonpolarized scattering and showed intense lobes of alternating signs, exhibiting the negative and positive maxima around 15 degrees and 70 degrees, respectively. These results provide experimental evidence for the existence of large helically organized macroaggregates of pigment-protein complexes in thylakoid membranes. Modeling of the CIDS data by a simple helical array of uniaxial polarizable groups suggests that the chiral structure is left-handed with pitch and radius of the order of 385 nm.     

Tightly bound DNA-protein complexes representing stable attachment sites of large DNA loops to components of the matrix

This study describes tightly bound DNA-protein complexes in DNA of matrices isolated from Friend erythroleukemia cells. When after radio-iodination of the associated proteins, such DNA is electrophoresed on agarose and the gel is subsequently subjected to autoradiography, the protein components of three or four complexes are visualized. Their two-dimensional electrophoretic analysis revealed that each possesses a simple but specific polypeptide composition, including a set of five non-histone proteins, characteristic for the matrix, and the core histones H3 and H4. Since the polypeptides dissociate from DNA by treatment with SDS, it is suggested that the linkage is not covalent. Reassociation and hybridization analysis of the DNA of the complexes indicated that it is enriched in highly repetitive, satellite sequences. The latter were found to be, to a great extent, similar to sequences localized at the base of large, dehistonized DNA loops obtained by high-salt extraction of isolated nuclei. Further experiments emphasized the complete conservation of this type of attachment throughout erythroid differentiation of Friend cells. It is proposed that the complexes represent attachment sites of basic, 30-100-kbp loop units of DNA.     

Induced circular dichroism of acridine orange bound to double-stranded RNA and transfer RNA

The induced circular dichroism (CD) in the visible region of acridine orange bound to the double-stranded RNA from cytoplasmic polyhedrosis virus and to yeast tRNA has been measured as a function of RNA phosphate-to-dye ratio (P/D), under the conditions of 0.01 M Na⁺ at pH 7.0. The shape of the CD spectrum of acridine orange bound to the double-stranded RNA was quite different from the spectrum of the dye bound to DNA. The CD spectral features of acridine orange bound to the double-stranded regions in tRNA closely resembled those of the double-stranded RNA-dye complex, suggesting that the dyes bind similarly to the two RNA's. It was further found that the CD spectrum of the tRNA-dye complex at sufficiently high P/D ratios, which is assignable to monomeric, intercalated dye to the base-paired parts in tRNA, is also distinct from the corresponding spectrum of the DNA-dye complex.     

Differential polarization imaging. V. Numerical aperture effects and the contribution of preferential scattering and absorption to the circular dichroism images.

Chiral objects which scatter and absorb preferentially left versus right circularly polarized light give rise to bright-field circular dichroism (CD) images containing contributions from both these two phenomena. These contributions are separated and characterized mathematically, and the effect of the dimensions of the chiral object on their relative magnitude is discussed. CD images of the long-range chiral organization of the thylakoid membranes in chloroplasts are obtained at two different wavelengths to illustrate the diverse wavelength dependence of the preferential absorption and scattering contributions to the images. The bright field CD images not only depend on the magnitude and sign of the preferential scattering and preferential absorption contributions, but also on the numerical aperture of the lens used. This dependence is obtained formally and a method to extract the angle dependent preferential scattering contributions to the images is presented. The validity of this method is confirmed experimentally.     

An analysis of circular intensity differential scattering measurements: studies on the sperm cell of Eledone cirrhosa

This study represents the first systematic attempt to characterize the possible sources of artifacts that can interfere with the measurement of circular intensity differential scattering (CIDS) as a function of the scattering angle. A theoretical analysis of the effect of imperfect incident circular polarizations in the measurement of baselines from nonchiral scatterers and in the signals from chiral samples is derived. From this analysis the requirements of the tolerance on the quality of the incident circular polarizations to unequivocally measure the CIDS effect are established. The protocol for alignment of the CIDS instrument and the characterization of the incident polarizations utilized in these studies are described in detail. CIDS measurements on suspensions of helical sperm cells are presented. The experimental results are modeled computationally with the use of the current CIDS theory. Good agreement between the data and the computations is obtained. The results clearly indicate the ability of CIDS to provide information on the long-range chiral organization of samples in solution.