Oligothymidylates covalently linked to an acridine derivative and with modified phosphodiester backbone: circular dichroism studies of their interactions with complementary sequences.

Oligothymidylates involving alternating alkyl phosphotriester-phosphodiester or methylphosphonate-phosphodiester backbones and covalently linked to an acridine derivative have been studied using circular dichroism. Two isomers with the same diastereoisomeric configuration for all the phosphotriesters (ethyl triester and neopentyl triester) or the methylphosphonate linkages were studied. These six compounds were compared to the parent oligonucleotide with unmodified phosphodiester bonds. Intramolecular interactions between the acridine and the bases of the oligonucleotides were revealed by the induced circular dichroism of the acridine dye. Binding to poly(rA) and poly(dA) induced large changes in the circular dichroism signal. All oligothymidylates formed double-stranded complexes with poly(rA). Substitution of phosphotriesters and methylphosphonates to phosphates allowed both double- and triple-stranded structures to be formed with with poly(dA). The double-stranded structures formed with poly(rA) and poly(dA) were characterized by different environments of the acridine dye. The circular dichroism spectra of the complexes with poly(dA) and the thermal stabilities of the complexes formed with both poly(rA) and poly(dA) were drastically dependent of the diastereoisomeric configuration of the phosphate modification. For the complexes formed with the pseudoequatorial stereoisomer the modification of the phosphate groups increased the stability of the complexes as compared with the oligothymidylate containing only phosphodiester linkages whereas it decreased it for pseudoaxial modifications.     

Spectroscopic properties of complexes of acridine orange with glycosaminoglycans. I. Soluble complexes.

The interaction of acridine orange with dermatan and chondrotin sulfates results in the formation of complexes containing bound dye molecules ordered into dissymmetric arrays. Complexes containing an excess of available disaccharide residues compared to dye are completely soluble, and exhibit biphasic circular dichroism bands. Analysis of the dependence of the extrinsic circular dichrosim on dye aggregation indicates the presence of extended dye stacks bound to the glycosaminoglycan. Complexes formed in solutions containing an excess of dye are only partially soluble, and exhibit circular dichroism spectra having band shifts and intensity changes relative to the soluble complexes. The latter complexes show a sharp drop in induced circular dichroism with temperature, due to a cooperative change in the structure of the complex. The structural order of the dye–glycosaminoglycan complex may differ from the intrinsic structure of the glycosaminoglycan itself in dilute solution.     

Spectral control of metal admixtures in tetracycline]

Analysis of circular dichroism spectra made it possible to offer a method for estimation of tetracycline solutions contamination with metal ions. By its sensitivity the method is much superior to the spectrophotometric one used at present for determination of the antibiotic purity. In the latter method formation of complexes with metals is traced by batochromic displacement of the absorption spectra. The new method is rapid, relatively selective and requires comparatively small quantities of the substance for the analysis, which provides its use under both laboratory and manufacture conditions. The method is based on identification of the circular dichroism spectra of tetracycline complexes with metals in the long wavelength region. The presence of the circular dichroism concervative bands with strictly defined extremums in the spectra of tetracycline low acid solutions contaminated by multiply charged metal ions allowed vs. the circular dichroism spectra of pure tetracycline sample to conclude that the solution contained admixtures and to suggest their nature. It was shown that the charge, ion radius and tetracycline:metal relation were the factors defining the mark and location of the dichroism band extremums. At lambda(extr)-410-415 nm the tetracycline complexes with light metal ions such as Mg2+, Al3+ and Ca2+ were detected by the circular dichroism negative band in the spectra, while the complexes with heavy metal ions such as Sc3+, Sr3+, Cu3+, Cd3+, Ba2+, Y3+ and the cerium subgroup lanthanides were detected by the circular dichroism positive band. The tetracycline complexes with the lanthanides of the second half of the yttrium subgroup (Ho(3+)-Lu3+) were characterized by the presence of the circular dichroism minimum at lambda(min)-425 nm. When the tetracycline concentration was above 1.5 x 10(-3) M, multiligand complexes with circular dichroism negative extremum at lambda(min)-400 nm formed.     

Spectroscopic properties of complexes of acridine orange with glycosaminoglycans II. Aggregated complexes-evidence for long-range order.

Aggregated complexes of acridine orange with dermatan and chondroitin sulfates have been studied in aqueous solution by absorption and circular dichroism spectroscopy. Aggregation was found to be favored at high-dye and glycosaminoglycan concentrations, and in solutions where anionic sites of the glycosaminoglycan are effectively complexed with dye. The aggregates can be removed from solution by centrifugation at 27,000 × g for 1 hr or by filtration through a membrane containing pores of 0.1 μm diameter. The aggregated complexes exhibit large-magnitude-ellipticity circular dichroism bands. In addition, the circular dichroism spectrum observed for a solution containing aggregated acridine orange/chondroitin 4-sulfate complexes is nearly a mirror image of that obtained for aggregated acridine orange/dermatan sulfate complexes. Cooperative alterations (sharp transitions) in the circular dichroism ellipticities of the aggregates occur at elevated temperatures, and result in spectroscopically distinct aggregates upon cooling. The circular dichroism properties and temperature effects are attributed to a supramolecular ordering of acridine orange/glycosaminoglycan complexes within the aggregates, which can be reorganized to a more stable form at high temperatures. Mixed aggregates, containing two different glycosaminoglycans, can be formed. The circular dichroism properties of the mixed aggregates also indicate the existence of long-range order in the arrangement of the complexes. Mixed aggregates containing dermatan sulfate and either chondroitin 4-sulfate or chondroitin 6-sulfate resemble pure dermatan sulfate aggregates in circular dichroism characteristics.     

Vacuum-ultraviolet circular dichroism study of saccharides by synchrotron radiation spectrophotometry

Vacuum-ultraviolet circular dichroism (VUVCD) spectra of five monosaccharides (D-glucose, D-mannose, D-galactose, D-xylose, and D-lyxose) and five disaccharides (maltose, isomaltose, cellobiose, gentiobiose, and lactose) were measured to 160 nm using a synchrotron-radiation VUVCD spectrophotometer in aqueous solution under high vacuum at 25 degrees C. Most of the saccharides show a positive peak with some shoulders at around 170 nm, except for D-galactose and lactose, which show two distinct negative peaks at around 165 and 177 nm. These spectra are influenced by such structural factors as alpha and beta anomers at C-1, axial and equatorial hydroxyl groups at C-2 and C-4, trans (T) and gauche (G) conformations of the hydroxymethyl group at C-5, and the type of glycosidic linkage. Deconvolution of the VUVCD spectra of D-glucose, D-mannose, and D-galactose into six independent Gaussian components for alpha-GG, alpha-GT, alpha-TG, beta-GG, beta-GT, and beta-TG conformations suggests that the alpha anomer has red-shifted spectra relative to the beta anomer, and that GG and GT conformations have positive and negative circular dichroism signs, respectively, while the sign for TG conformation is anomer dependent. These speculations from the deconvolution analyses are also supported by the VUVCD spectra of disaccharides. These results give new insight into the equilibrium conformations of saccharides, demonstrating the usefulness of synchrotron-radiation VUVCD spectroscopy.     

Condensation of DNA by the C-terminal domain of histone H1. A circular dichroism study

The condensation of DNA by the C-terminal domain of histone H1 has been studied by circular dichroism in physiological salt concentration (0.14 M NaF). As the intact H1 molecule, its C-terminal domain induces the so-called psi state of DNA that is characterized by a nonconservative circular dichroism spectrum which is currently attributed to ordered aggregation of the DNA molecules. On a molar basis, intact H1 and its C-terminal domain give spectra of similar intensity. Neither the globular domain of H1 nor an N-terminal fragment, that includes both the globular and N-terminal domains, has any effect on the conservative circular dichroism of DNA. From these results it is concluded that the condensation of DNA mediated by histone H1 is mainly due to its C-terminal domain. The effect of the salt concentration and the size of DNA molecules on the circular dichroism of the complexes are also examined.     

The 5-55 single-disulphide intermediate in folding of bovine pancreatic trypsin inhibitor.

An analogue of the BPT1 folding intermediate that contains only the disulphide bond between Cys-5 and Cys-55 has been prepared by mutation of the other four Cys residues to Ser. On the basis of its circular dichroism and 1H-nuclear magnetic resonance spectra and its electrophoretic mobility, this intermediate is shown to be at least partially folded at low temperatures. This probably accounts for several of the unique properties of this intermediate observed during folding.     

Accessibility of the minor groove of DNA in chromatin to the binding of antibiotics netropsin and distamycin A

The interaction of the antibiotics distamycin A, distamycin analogue and netropsin with chromatin of calf thymus has been studied by circular dichroism measurements and by gel filtration. The minor groove of DNA in chromatin is accessible by 83–89% to the binding of these antibiotics as compared with that of free DNA. The present results combined with our data on the methylation of chromatin with dimethylsulphate [3] strongly suggest that the minor groove of DNA in chromatin is not occupied by chromatin proteins.Abbreviations DM distamycin A - DM₂ analogue of distamycin - Nt netropsin - CD spectra circular dichroism spectra     

Reconstitution of the B873 light-harvesting complex of Rhodospirillum rubrum from the separately isolated alpha- and beta-polypeptides and bacteriochlorophyll a

The light-harvesting complex of Rhodospirillum rubrum was reversibly dissociated into its component parts: bacteriochlorophyll and two 6-kilodalton polypeptides. The dissociation of the complex by n-octyl beta-D-glucopyranoside was accompanied by a shift of the absorbance maximum from 873 to 820 nm (a stable intermediate form) and finally to 777 nm. In the latter state, bacteriochlorophyll was shown to be free from the protein. Complexes absorbing at 820 and 873 nm could be re-formed from the fully dissociated state with over 80% yield by dilution of the detergent. Absorbance and circular dichroism properties of the re-formed B820 complex were essentially identical with those of B820 formed from chromatophores. Phospholipids and higher concentrations of complex were required to obtain the in vivo circular dichroism spectrum for reassociated B873. Reconstitution of the light-harvesting complexes from separately isolated alpha- and beta-polypeptides and bacteriochlorophyll was also demonstrated. Absorbance and circular dichroism spectra of these complexes were identical with those of complexes formed by the reassociation of the dissociated complex. Bacteriochlorophyll and the beta-polypeptide alone formed a complex that had an absorbance at 820 nm, but an 873-nm complex could not be formed without addition of the alpha-polypeptide. The alpha-polypeptide alone with bacteriochlorophyll did not form any red-shifted complex. In preliminary structure-function studies, some analogues of bacteriochlorophyll were also tested for reconstitution.     

Formation and structure of Cu (II) — poly (L-arginine) complexes in aqueous solution

Cu (II) — poly (L-arginine) (PLA) complexes have been studied using potentiometric titrations, optical absorption and circular dichroism spectra. Three different complexes have been observed. The first one (complex I) is formed up to pH 8 and results from the coordination of two guanidinium groups to the metal ion. The second and third complexes (complexes II_A and II_B) are formed between pH 8 and 11, in different proportions which are dependent on PLA: Cu molar ratio. In these two complexes two guanidinium groups and two peptide nitrogens participate as ligands around the copper ion.     

A theoretical study on the exciton circular dichroism of propeller‐like metal complexes of bipyridine and tripodal tris(2‐pyridylmethyl)amine derivatives

Time‐dependent density functional theory (TD‐DFT) has been employed to simulate the circular dichroism (CD) spectra of bipyridyl ruthenium(II) complexes as well as zinc(II) and copper(II) complexes containing tris(2‐pyridylmethyl)amine (TPA) derivatives. A qualitative model is used to account for the mechanism by which the bis‐ and tris‐bipyridine complexes (or analogous systems) exhibit exciton CD. The model is further used to predict the sign of the exciton CD bands. The predictions are in agreement with experiment and DFT calculations. A comprehensive analysis is presented of the subtle differences in the CD spectra of this series of related complexes. Chirality, 2011. © 2010 Wiley‐Liss, Inc.     

Interaction of DNA with actinocin amides containing cationoid centers in the amide groups

Complexes of DNA with actinocin derivatives containing ω-dialkylaminoalkyl groups in the1 and/or 9 positions of the chromophore were studied by spectrophotometric titration, circular dichroism, and viscometry. Induced circular dichroism (ICD) spectra of the DNA-ligand complexes were compared for the cases of the complexes of known structure established by other methods. It was shown that the presence of an isoelliptic point in the long-wavelength absorption band of the ICD spectra of the ligand under monomeric binding conditions could indicate intercalation of the actinocin chromophore into DNA. The separation of the cationoid center and the chromosphore upon elongation of the methylene chain increases the aggregability of the ligand pn the surface of the DNA double helix, which prevents the intercalation of the chromophore.     

Formation and structure of Cu(II)-poly(L-lysine) complexes in aqueous solution.

Cu(II)-poly(L-lysine) complexes have been studied using potentiometric titrations, optical absorption and circular dichroism spectra. As in the Cu(II)-poly(L-arginine) system studied previously potentiometric and spectral data consistently show that two types of complexes are formed. The first formed below pH 7.6 contains two amine nitrogens and two oxygen from water molecules at the corners of a square in which the metal occupies the center. The second is obtained at pH above 7.6 when the oxygen atoms are replaced by two adjacent peptide nitrogens.     

Circular dichroism of DNA frayed wires.

Ultraviolet circular dichroism spectra are reported for the oligonucleotide d(A15G15) in aqueous solutions containing 5 mM MgCl2 at several temperatures and in the presence of partially complementary oligonucleotides. Oligonucleotides with several consecutive terminal guanine residues self-associate to form aggregates, called frayed wires, that consist of integer numbers of strands. A "stem" is formed through interactions between the guanine residues of the associated oligonucleotides, whereas the adenine "arms" remain single stranded. Upon subtracting the circular dichroism spectrum of d(A15) from that of d(A15G15), one obtains a spectrum that closely resembles previously published spectra of poly(G). Subtracting spectra measured at temperatures between 10 degrees C and 60 degrees C reveals the resultant spectra to be independent of temperature, consistent with the extreme thermal stability observed for the aggregated structures. Upon the addition of d(T15) to the solution, complexes with the adenine portion of the d(A15G15) frayed wires are formed. Subtraction of d(A15):d(T15) spectra measured at several temperatures from those of the d(A15G15):d(T15) does not significantly alter the spectrum of the guanines. The helix-coil transition temperature of d(A15):d(T15) duplex is identical to that of the unbinding of d(T15) from d(A15G15):d(T15) complexes. Experiments using oligonucleotides in which the adenines were replaced with sequences of bases yielded similar results. By varying the length of the nonguanine tract, it is shown that the solubility of the complexes increases with the length of the nonguanine region of the oligonucleotide.     

Complexes of cobalt (II) and manganese (II) with adenosine 5'-diphosphate and adenosine 5'-triphosphate. A circular dichroism study.

For studies of interactions between Co2+ and adenosine 5'-diphosphate or adenosine 5'-triphosphate (ADPH4+ and ATPH5+ in strongly acidic medium) visible circular dichroism (d-d transitions of Co2+) and ultraviolet circular dichroism (adenine transitions) have proven to be very sensitive to structural changes. Drastic variation of spectra as a function of pH and concentration enabled us to show the existence of various species, to state their stoichiometry and eventually, their self-association. With ATPH22-, C.D. results are in agreement with recent N.M.R. results. With ligands bearing three negative charges, complexes (1 metal:2 nucleotides)n are formed in which bases of the two nucleotides of the molecule are self-associated. With ADP3-, the visible C.D. spectrum of this complex is intense and hides the spectra of the complexes formed with other protonated species of ADP; this self-associated complex is detected up to a lower limit of 5 X 10(-4) M concentration. With ATPH3-, a complex exhibiting the same characteristics as the one with ADP3- is formed but in about twenty times less amount which explains why it was not detected by potentiometry. With 0.1 M ATP4-, dimeric (or polymeric) complexes, of 1:2 and 1:1 stoichiometry are observed. With 0.01 M ATP4-, 1:1 monomeric and 2:1 dimeric (or polymeric) complexes are detected. The interactions between Mn2+ ions and ADP or ATP have been studied by C.D. on the UV range. The same species as with Co2+ ions have been found but the 1:2 complex formation with ADP3- was shown to occur to a lesser extent and was not observed below a 10(-2) M ADP concentration.     

Comparisons between hog intestinal peroxidase and bovine lactoperoxidase-compound I formation and inhibition by benzhydroxamic acid.

The bihelical polydeoxyribonucleotides DNA and poly (deoxyadenylate-deoxythymidylate form at least two distinct complexes with the dye Hoechst 33258. The nonfluorescent complex formed at low polymer/dye ratios is replaced at high polymer/dye ratios by an intensely fluorescent complex. The transition is accompanied by pronounced changes in circular dichroism and absorption spectra and may be interpreted in terms of a noncooperative replacement of dye molecules bound in proximity by isolated molecules of bound dye. In the case of the bihelical polyribonucleotides the transition exhibits positive cooperativity and major differences from the deoxyribose polymers exist in the circular dichroism spectra, suggesting a different geometry for the complex species.     

Analysis of low temperature magnetic circular dichroism of high spin ferrihemoproteids in the near UV region

Magnetic circular dichroism spectra of fluoride complexes of metmyoglobin, methemoglobin, and horseradish peroxidase in the region of 300-450 nm at temperatures from 300 to 2.1 K were measured and analyzed. The temperature dependence of magnetic circular dichroism in the Soret region was found to be different from that of other paramagnetic forms and from the theoretically predicted dependence. The difference is explained by the superposition of the pi-->pi*-transition of porphyrin with one (peroxidase) or two charge transfer transitions and by substantially different temperature dependences of magnetic circular dichroism for the transitions of the two types. By minimization of differences between the expected and observed temperature dependences of magnetic circular dichroism, the parameters of its temperature dependence for charge transfer transitions and the parameter D of the zero-field splitting of the electronic ground state of the heme were found. The values of D for the fluoride complexes of metmyoglobin (5.8 cm-1) and methemoglobin (6.1 cm-1) agree well with those obtained by other methods. The D value for the fluoride complex of horseradish peroxidase (8.8 cm-1) was determined for the first time.     

Fluorescence-detected circular dichroism studies of serum albumins

Multidimensional fluorescence-detected circular dichroism (FDCD) is used to investigate the binding of bilirubin to four mammalian serum albumins. It is shown that the complexes formed with the albumins have distinctly different FDCD spectra. The effect of the pH-dependent transition from basic to acidic conditions on the complexes is examined. The binding of warfarin to albumin is also presented to demonstrate the general analytical utility of the multidimensional FDCD measurement for biochemical analysis.     

The interaction between small molecules and nucleic acids studied by circular dichroism

The circular dichroism (CD) spectra of complexes between aromatic hydrocarbons and quinolines with DNA and complexes between proflavine and nucleic acids have been measured.     

Complex formation of di-oligodeoxyadenylyl-5',5'-pyrophosphatess with polyuridylic acid]

The complex formation of P1,P2-bis-trideoxyadenylyl-, P1-trideoxyadenylyl, P2-hexadeoxyadenylyl and P1,P2-bis-deoxyadenylyl-5',5-pyrophosphates with polyuridylic acid has been studied. It is shown that these compounds form triple-stranded complexes with poly-U, which have much the same absorption and circular dichroism spectra as those of (oligo-dA).2(poly-U). These results are considered as a support of an earlier suggestion about the irregular relative orientations of the oligodeoxyadenylates in the triple-stranded complexes with poly-U.