Circular Dichroism Spectra Of Poly Research Articles

Self-structure formation in polyadenylic acid by small molecules: new insights from the binding of planar dyes thionine and toluidine blue O

Thionine and toluidine blue targeting poly(A).

Binding of the phenothiazinium dye methylene blue with single stranded polyriboadenylic acid

The binding of the phenothiazinium dye methylene blue to single stranded poly(riboadenylic acid) was investigated by spectroscopic and calorimetric techniques. The binding was cooperative and the affinity was of the order of 10 6 M −1 at 100 mM [Na +] as determined from absorbance, fluorescence and calorimetric studies. Ferrocyanide quenching studies showed intercalative binding of methylene blue to poly(riboadenylic acid). The binding perturbed the circular dichroism spectrum of poly(riboadenylic acid) with concomitant formation of prominent exciton split type of extrinsic CD bands in the 550–700 nm region. The interaction involved a single binding mode with a 1:2 binding stoichiometry. The binding affinity increased with [Na +] ion concentration in the range 10–200 mM [Na +]. Dye binding induced self-assembled duplex formation in poly(riboadenylic acid). The biological utility of the dye methylene blue in probing nucleic acid structure is revealed from these studies.

Simulation of amide I′ band profiles of trans polyproline based on an excitonic coupling model

We measured the amide I′ band profile of the IR, isotropic Raman, anisotropic Raman, and Vibrational Circular Dichroism spectrum of poly- l-proline in D 2O. The band shapes were modeled by using an algorithm that exploits the delocalized character of the excited vibrational states [R. Schweitzer-Stenner, J. Phys. Chem. B. 108 (2004) 16965]. The band shapes could be quantitatively reproduced by invoking the polyproline II or 3 1-helix conformation for all peptide residues. This corroborates the notion that the combined use of the above spectroscopies is an ideal tool to discriminate different conformations associated with the so-called random coil state of peptides.

Polyglutamine aggregation behavior in vitro supports a recruitment mechanism of cytotoxicity

In expanded CAG repeat diseases such as Huntington’s disease, proteins containing polyglutamine (poly(Gln)) sequences with repeat lengths of about 37 residues or more are associated with development of both disease symptoms and neuronal intranuclear inclusions (NIIs). Disease physiology in animal and cellular models does not always correlate with NII formation, however, and the mechanism by which aggregate formation might lead to cytotoxicity is unknown. To help evaluate various possible mechanisms, we determined the biophysical properties of a series of simple poly(Gln) peptides. The circular dichroism spectra of poly(Gln) peptides with repeat lengths of five, 15, 28 and 44 residues are all nearly identical and are consistent with a high degree of random coil structure, suggesting that the length-dependence of disease is not related to a conformational change in the monomeric states of expanded poly(Gln) sequences. In contrast, there is a dramatic increase in both the kinetics and the thermodynamic favorability of the spontaneous formation of ordered, amyloid-like aggregates for poly(Gln) peptides with repeat lengths of greater than 37 residues. At the same time, poly(Gln) peptides with repeat lengths in the 15–20 residue range, despite their poor abilities to support spontaneous, self-nucleated aggregation, are capable of efficiently adding to an already-formed aggregate. We also find that morphologically small, finely divided aggregates are much more efficient at recruiting poly(Gln) peptides than are large aggregates, suggesting a possible explanation for why disease pathology does not always correlate with the observable NII burden. Together, these data are consistent with a model for disease pathology in which critical cellular proteins possessing poly(Gln) sequences of modest length become inactivated when they are recruited into aggregates of an expanded poly(Gln) protein.

Infrared absorption and vibrational circular dichroism spectra of poly(vinyl ether) containing diastereomeric menthols as pendants

The absorption and vibrational circular dichroism (VCD) spectra in the 1700 to 830 cm −1 region are reported and qualitatively interpreted for poly(vinyl ether) with (+)-menthol (I), (+)-isomenthol (II) and (+)-neomenthol (III) as pendants.

Conformation of Poly(L-lysine) and Poly(L-ornithine) in α, ω-Type Surfactant Solutions

Circular dichroism spectra of poly(L-ornithine) and poly(L-lysine) were measured in disodium α, ω-alkanedisulfate [Na2C nH2 n(SO4)2( n = 8,10, 12,16) (RDS)] solutions in the presence and absence of NaCl at various tempera tures. The 1,16-RDS induced an α-helix in poly(L-ornithine) and a β-sheet in poly(L-lysine) at 30°C, while 1,10- and 1,8-RDS induced no conformational change in either polypeptide even at a surfactant concentration where turbid ity appears. Although 1,12-RDS induced no conformational change in poly(L- ornithine), it does induce α-helix, β-sheet or stepwise transition from coil to β-sheet and then to α-helix with increasing 1,12-RDS concentration, depending on the temperature and concentration of added NaCl. The plots of α-helix con tent against temperature at various concentrations of 1,12-RDS are quali tatively consistent with the dependence of α-helix content on the size growth of surfactant cluster bound to polypeptide.

Absorption and circular dichroism spectra of CuCl2 complexed with poly(S‐carboxymethyl‐L‐cysteine) and poly(S‐carboxyethyl‐L‐cysteine)

AbstractThe interaction of CuCl2 with poly(S‐carboxymethyl‐L‐cysteine) (poly[Cys(CH2COOH)]) and poly(S‐carboxyethyl‐L‐cysteine) (poly[Cys(C2H4COOH)]) were studied by absorption spectra and circular dichroism (CD). On mixing CuCl2 with polypeptide solutions, absorption bands appeared at 320–325 nm in both polypeptides, and at 255–260 nm in the case of poly[Cys(CH2COOH)]. A stable bound species was formed in the case of poly[Cys(CH2COOH)], since the apparent molar absorption coefficient of the bound species did not depend on the mixing ratio. From the absorption data, it was inferred that Cu2+ ions were complexed with the side chains, most probably with sulfur atoms and carboxyl groups. Induced optical activities were observed for the two polypeptides. The CD spectra of poly[Cys(CH2COOH)] + CuCl2 gave simpler aspects than those of poly[Cys(C2H4COOH)] + CuCl2.

Zinc Z-DNA

Circular dichroism spectra of poly(dG-dC) in the presence of some zinc complexes exhibit the characteristic inversion associated with the formation of a left handed helix. The transition of B to Z DNA is cooperative and slow. The concentration of zinc complex at the mid point of the transition is strongly dependent upon the nature of the ligand bound to zinc. The most efficient species is one with a tetradentate amine for which the mid point is observed at a zinc:nucleotide ratio of 1:24. 31P spectra of one of these complexes confirm the presence of a left handed helix.

Effect of aliphatic alcohols on the conformation of poly ( l-ornithine hydrobromide) as studied by square-pulse and reversing-pulse electric birefringence

The electric birefringence and circular dichroism spectra of poly( l-ornithine hydrobromide) have been measured in ethanol/water, 2-propanol/water and tertiary butyl alcohol/water mixtures of various compositions. This charged polypeptide underwent a transition from the coil conformation to the helical conformation at high alcohol content in every case tested. Anomalous birefringence signals, indicative of a field-induced helix-to-coil transition. were observed at high electric fields only in the case of ethanol/water mixtures. The reversing-pulse electric birefringence of this polypeptide has been studied in ethanol/water mixtures and in neutral aqueous solution. Upon rapid reversal of the pulse field, no transient could be observed. This confirms that the electric-field orientation of poly( l-ornithine hydrobromide) results predominantly from the contribution of the counterion-induced dipole moment, regardless of its molecular conformations. It is very probable that the backbone permanent dipole moment of the helical conformation is largely suppressed by the counterion-induced dipole moment in the ionized form.

A basic isozyme of yeast glyceraldehyde-3-phosphate dehydrogenase with nucleic acid helix-destabilizing activity

A nucleic acid helix-destabilizing protein has been purified from Saccharomyces cerevisiae using affinity chromatographic techniques. Crude protein extracts at low ionic strength (approx. 0.05 M) were applied sequentially to tandem columns of native DNA-cellulose, aminophenyl-phosphoryl-UMP-agarose, poly(I · C)-agarose, poly(U)-cellulose and denatured DNA-cellulose. The 2 M NaCl eluant of the poly(U)-cellulose column was dialyzed to low ionic strength and recycled through native DNA-cellulose, poly(I · C)-agarose and poly(U)-cellulose. Purified helix-destabilizing protein eluted from the poly(U)-cellulose between 0.1 and 0.5 M NaCl. On the basis of enzymatic activity, immunological cross-reactivity, mobility on SDS gels, amino acid analysis and preliminary peptide mapping experiments, this material was identified as an isozymic fraction of glyceraldehyde-3-phosphate dehydrogenase. The major crystallizable isozyme of this enzyme from yeast is, however, considerably more acidic than the helix-destabilizing protein, and displays significantly lower helix-destabilizing activity. Stoichiometric levels of the isolated protein at low (approx. 0.01) ionic strength depress the T m of poly(A-U) and poly[d(A-T)] by as much as 28 and 22°C, respectively. Longer double helices, poly(A · U) and Clostridium perfringens DNA, are also denatured by the helix-destabilizing protein, but at relatively slow rates. The binding of this protein to [ 3H]-poly(U) on nitrocellulose filters is [Na +]-dependent, with a 50% reduction at 0.09 M NaCl. Based on its effect on the circular dichroism spectrum of poly(A), the protein was shown to distort the conformation of the polynucleotide chain. An analogous protein from mammalian cells, P8, was also shown to depress poly(A-U) T m .

The B goes to Z transition of poly(dG-dC) . poly(dG-dC) modified by some platinum derivatives.

Poly(dG-dC) . poly(dG-dC) was modified by chlorodiethylenetriamino platinum (II) chloride, cis-dichlorodiammine platinum (II) and trans-dichlorodiammine platinum (II), respectively. The conformation of these modified poly(dG-dC) . poly(dG-dC) was studied by circular dichroism. In 4 M Na+, the circular dichroism spectra of poly(dG-dC)dien-Pt (0 less than or equal to rb less than or equal to 0.2) are similar (rb is the amount of bound platinum per base). It is concluded that the conformation of these polymers belongs to the Z-family. Dien-Pt complexes stabilize the Z-form. The midpoint of the Z goes to B transition of poly(dG-dC)dien-Pt(0.12) is at 0.2 M NaCl. Moreover another B goes to Z transition is observed at lower salt concentration (midpoint at 6 mM NaCl). In 1 mM phosphate buffer, the stability of Z-poly(dG-dC)dien-Pt(0.12) is greatly affected by the presence of small amounts of EDTA. Poly(dG-dC) . poly(dG-dC) modified by cis-Pt and trans-Pt complexes do not adopt the Z-form even in high salt concentration.

THE STEPWISE CONFORMATIONAL CHANGE OF POLY(l-LYSINE) IN AQUEOUS SOLUTION OF SODIUM 1-OCTANESULFONATE

Abstract The circular dichroism spectrum of poly(l-lysine)(PLL) in aqueous 1-octanesulfonate solution was measured as a function of surfactant concentration at varying temperatures and the conformational phase diagram was constructed. At temperatures above 10°C, the increase in surfactant concentration causes PLL to change stepwise from coil to β-form and from β-form to helical conformation, Upon lowering temperature, the surfactant concentration range, where PLL assumes β-form, becomes narrower and eventually disappears at around 10°C.

Conformational studies on Cu(II) polycomplexes of pyridoxal Schiff bases of polypeptides

AbstractStructures of Cu(II) complexes of pyridoxal Schiff bases with poly(L‐lysine), poly(L‐ornithine), and poly(L‐α,γ‐diaminobutyric acid) were investigated by absorption spectra, CD, and conformational analysis.Although the polypeptides retain their typical right‐handed α‐helical conformation, opposite Cotton effects were found for the poly(L‐lysine) and poly(L‐ornithine) polycomplexes in the whole range of wavelengths from 600 to 250 nm. As in the analogous derivatives of salicyladehyde, this effect seems to be due to a stereospecific binding of the square planar Cu(II)‐bis‐pyridoxylideneimine group to the α‐helical matrix. Circular dichroism spectrum of poly(L‐α,γ‐diaminobutyric acid) polycomplex is similar to that found for poly(L‐lysine) derivative, but indicates large tetrahedral distortion of the square‐planar coordination of copper ion.

Circular dichroism study of polyriboxanthylic acid.

We report in the present paper the circular dichroism spectra of poly(X) at different pH and temperature values. The spectra are characteristic of three stable forms of poly(x) in the pH range of protonation of xanthosine. An electrostatic barrier is proposed to account for the hysteresis and metastability observed in a certain pH range. Some results on oligo(X) at basic pH are also presented. Poly(X) at basic pH is investigated also by hydrodynamic techniques.

Circular dichroism spectra of poly[d(AC):d(GT)], poly[r(AC):r(GU)], and hybrids poly[d(AC):r(GU)] and poly[r(AC):d(GT)] in the presence of ethanol.

AbstractUltraviolet circular dichroism spectra have been obtained in aqueous solutions in the presence and absence of ethanol for a synthetic DNA, poly[d(AC):d(GT)], a synthetic RNA, poly[r(AC):r(GU)], and two DNA:RNA hybrids, poly[d(AC):r(GU)] and poly[r(AC):d(GT)]. In the absence of ethanol, we find that the RNA and DNA spectra are dissimilar, while the spectra of the hybrids show differing degrees of similarity to that of the RNA. In the presence of 60–80% ethanol by weight, the spectra of the DNA and both hybrids become much closer to the spectrum of the RNA, which remains relatively unchanged. We interpret the results as indicating that DNA can undergo a change to an A‐type conformation in the presence of ethanol and that the DNA:RNA hybrids are not wholly restricted to an RNA‐like conformation in the absence of ethanol.

Protonated polynucleotide structures

The circular dichroism spectra of poly(dG). poly(dC) have been studied as a function of pH in 0.15 M NaCl solution. Acid titration to pH 2.5 showed two transitions, one around pH 5, the second below pH 3. These transitions are disproportionation reactions and are not due to the dissociation of the complexes. Alkaline back titration to neutrality showed only one step above pH 7, without appearance of the intermediate form. The hysteresis loop observed gave rise to a metastable (probably protonated) form at pH 7 which reverted to the neutral form upon heating or alkali treatment. In order to obtain again the metastable hysteretic form, a whole titration cycle to pH 2.5 had to be performed.

A specific photoreaction in polydeoxyadenylic acid.

Ultraviolet photosensitivity of the single-stranded forms of poly(A) and poly(dA) is compared. In contrast to poly(A), poly(dA) is rather sensitive to ultraviolet irradiation. Relatively low doses of ultraviolet light lead to characteristic changes of the ultraviolet and circular dichroism spectra of poly(dA), suggesting formation of a specific photoproduct in poly(dA) that cannot be formed in poly(A). The quantum yields in poly(dA) (varphi = 2.5 x 10(-3)) are about a factor of 10 higher than in poly(A), indicating a high structure specificity. The base-pairing capacity of irradiated probes of poly(dA) to poly(dT) is inhibited. These results demonstrate a relatively high probability of DNA photolesions, that cannot be repaired by simple repair enzyme systems.

The effects of thioketo substitution upon uracil-adenine interactions in polyribonucleotides. Synthesis and properties of poly (2-thiouridylic acid) and poly(2,4-dithiouridylic acid).

The physical and biological properties of two new poly(U) analogs, poly(2‐thiouridylic acid) or poly(s2U) and poly(2,4‐dithiouridylic acid) or poly(s2s4U) have been investigated. Ultraviolet absorption and circular dichroism spectra of poly(s2U) and poly(s2s4U) as well as those of the corresponding monomers were measured. Absorption‐temperature and absorption‐pH profiles of both poly(s2U) and poly(s2s4U) displayed sharp cooperative transitions. The phase transition diagrams of poly(s2U) and poly(s2s4U) show the high stability of their secondary structures. Neither poly(s2U) nor poly(s2s4U) formed helical complexes with poly(A). It was concluded from the corresponding phase transition diagrams that the reason for this behaviour is the larger thermodynamical stability of the poly(s2U) or poly(s2s4U) helices over the hypothetical complexes poly(s2U) · poly(A) or poly(s2s4U) – poly(A). Sedimentation velocity analysis of poly(s2U) and poly(s2s4U) revealed sedimentation coefficients S20,w of 28 S and 12 S, respectively. A more detailed analysis of poly(s2U) lead to the conclusion that poly(s2U) exists as an intra‐molecular associate of two anti‐parallel poly(s2U) strands in the form of a large hairpin. Consistent with their physical properties, poly(s2U) and poly(s2s4U) are not able to replace poly(U) as messengers in the cell‐free synthesis of poly(phenylalanine). Poly(s2U) is only poorly, poly(s2s4U) not at all phosphorolyzed by polynucleotide phosphorylase.

Optical activity and the conformation of polynucleotide models of nucleic acids

The interaction between polymers of adenylic and uridylic acids has been investigated using homopolyadenylate and homopolyuridylate, and copolymers containing various ratios of AMP and UMP randomly distributed. The measurements of circular dichroism in the region of 230 to 320 mμ indicate that the formation of the two-stranded poly (A + U)† helical complex causes pronounced changes of the spectra as compared to that of the components. This is reflected in the decrease of the intensity of the circular dichroic positive and negative bands, and broadening of the positive band with concomitant decrease of the rotational strength value. The dichroic spectra of the AU copolymer (1 : 1) is very similar to that of the poly (A + U) complex. The similarity between the circular dichroism spectra of poly (A + U), AU copolymer (and also RNA) probably reflects comparable two-stranded helical conformations. The three-stranded poly (A + U + U) complex exhibits a circular dichroism spectrum different from that of the components. Such results following the formation of multistranded helices composed by the interaction of different monomeric units are in contrast to those obtained on helical molecules formed by the interaction of identical homopolymers, like poly A. On the basis of measurements of circular dichroism, an analysis has been made of the optical rotatory dispersion curves in the visible region. For the helical homopolynucleotides, i.e. the two forms of poly A and poly U, the contributions of the transitions occurring in the region of 230 to 300 mμ determine the optical rotatory dispersion curves. In the case of nucleic acids and their models, i.e. two-stranded helical molecules formed by the interaction of different monomeric units, ultraviolet electronic transitions occurring further in the ultraviolet contribute strongly to the rotatory dispersion curves in the visible, and might be related to the helical conformation.