Energy migration in DNA evaluated by the sensitized fluorescence of an intercalation dye

An equation is obtained to calculated the efficiency of energy migration along a biopolymer with transfer of excitation to a fluorescence dye using excitation and absorption spectra. With the aid of bromoethydium intercalating into DNA-phage it is shown that in a solution at room temperature energy is transferred to it only from one or two neighboring nucleotides. The low efficiency of energy migration in relation to DNA under these conditions is explained by the low probability of each event of “cold” and “hot” migration. Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, 142292, Moscow Region, Russia. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 65, No. 5, pp. 794–798, September–October, 1998.     

Funnels in energy landscapes

Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a “folding funnel” that is concisely defined in terms of energy minima and saddle points, while at the same time conforming to a notion of a “folding funnel” as it is discussed in the protein folding literature.     

The effect of electron irradiation on the optical properties of the natural armenian zeolite-clinoptilolite

Infrared (IR) absorption and luminescence in chemically and radiation-modified natural Armenian Zeolite (clinoptilolite) samples have been studied. The luminescence was studied in 390–450 nm and 620–710 nm wavelength bands, and the IR measurements were carried out in the 400–5400 cm⁻¹ range. It is shown that the luminescence intensity depends on the content of pure clinoptilolite in the samples and, probably on the distribution of “passive” luminescence centers over Si and Al sites that became “active” under radiation or chemical treatment. The samples of electron irradiated clinoptilolite have higher luminescence intensity than the chemically and thermally treated ones. A decrease in the intensity of IR absorption bands at 3550 cm⁻¹ and 3650 cm⁻¹ was found after irradiation.     

Fast photoprocesses in a symmetric indotricarbocyanine dye (HITC) in solutions

Spectral-kinetic and photochemical properties of HITC dye with iodide and perchlorate counterions have been studied in environments where the dye molecules exist in different ionic forms. In ethanol, the dye molecules exist as free ions; in dichlorobenzene, as contact ion pairs. Superfast transformation of non-stationary spectra in an HITC dye bleaching band is found. The observed effects are interpreted within the framework of concepts on “burning out” a notch in the contour of a non-uniformly widened vibronic band of S ₀ → S ₁-absorption. Qualitative differences in recorded absorption spectra from the dye excited electronic states for weakly and highly polar solvents are found. It is shown that the observed differences are caused by superfast charge transfer in the contact ion pairs that results in the formation of free radicals.     

Complexation of heterocyclic ligands with DNA in aqueous solution

We have used spectrophotometry to study self-association and complexation with DNA by organic heterocyclic compounds in the acridine and phenothiazine series: proflavin, thionine, and methylene blue. Based on the experimental concentration dependences of the molar absorption coefficient of the molecules in an aqueous buffer solution (0.01 M NaCl, 0.01 M Na₂EDTA, 0.01 M Tris, pH 7.4, T = 298 K), we have determined the equilibrium dimerization constants for the dyes and the DNA complexation parameters using the Scatchard and McGhee-von Hippel models. The observed increase in the cooperativity parameters as the dimerization constants of the ligands increase allowed us to hypothesize that the same interactions occur between dye molecules adsorbed on DNA as in their self-association. The equilibrium DNA-binding constants for the ligands, obtained using the McGhee-von Hippel cooperative model, are (20.9 ± 2.7)·10³ M⁻¹ for proflavin and (33.8 ± 4.1)·10³ M⁻¹ for thionine. Using the Scatchard model, taking into account intercalation and “external” binding of ligands with DNA, we determined the DNA complexation constants for methylene blue: (26.4 ± 4.6)·10³ and (96 ± 17)·10³ M⁻¹ respectively. Based on analysis of the data obtained, we hypothesized that the predominant type of binding with DNA is intercalation binding in the case of proflavin and thionine, and “external” binding with the DNA surface in the case of methylene blue. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 75, No. 2, pp. 242–249, March–April, 2008.     

Studies of Interaction Between Cyanine Dye T-284 and Fibrillar Alpha-Synuclein

A key feature of Parkinson’s disease is the formation and accumulation of amyloid fibrils of the natively unfolded protein α-synuclein (ASN) inside neurons. Recently we have proposed novel sensitive monomethinecyanine dye T-284 as fluorescent probe for quantitative detection of ASN amyloid fibrils. In this study the T-284 dye complex with ASN fibril was characterized by means of fluorescence anisotropy, atomic force microscopy and time-resolved fluorescence techniques to give further insights into the mode of dye interaction with amyloid fibrils. The fluorescence anisotropy of T-284 was shown to noticeably increase upon addition of aggregated proteins indicating on stable dye/amyloid fibril complex formation. AFM imaging of fibrillar wild-type ASN revealed differences in heights between ASN fibrils alone and in presence of the T-284 dye (6.37 ± 1.0 nm and 8.0 ± 1.1 nm respectively), that is believed to be caused by embedding of T-284 dye molecules in the “binding channel” running along the fibril. Fluorescence decay analysis of the T-284 in complexes with fibrillar ASN variants revealed the fluorescence lifetime values for T-284/fibril complexes to be an order of magnitude higher as compared to the free dye. Also, the fluorescence decay of free T-284 was bi-exponential, while dye bound to protein yields tri-exponential decay. We suppose that in complexes with fibrillar ASN variants T-284 dye might exist in different “populations” due to interaction with fibrils in different conformers and ways. The exact binding mode of T-284 with ASN fibrils needs further studies. Studied parameters of dye/amyloid fibril complexes are important for the characterization and screening of newly-developed amyloid-sensitive dyes.     

Specificity of Cyanine Dye L-21 Aggregation in Solutions with Nucleic Acids

Optical spectroscopy experiments were used to study the features of cyanine dye 3,3′-dimethyl-9-(2-thienyl)-thiacarbocyanine iodide (L-21) aggregation in binary solutions DMF:Tris–HCl buffer (pH = 8) containing nucleic acids (DNA or RNA). The appearance of absorption and luminescence bands associated with J-aggregates and dimers that are formed within the minor groove of DNA has been observed. The model of L-21 J-aggregate structure is proposed. It has been found that dimers are the building blocks of L-21 J-aggregates. Disorientation in dimers caused by the minor groove curvature is reason of observation of Davydov splitting in absorption spectrum of L-21 J-aggregates. In the solution containing DNA the absorption and luminescence bands of L-21 J-aggregates exhibit the specific properties that allows the dye L-21 to be used as a fluorescent probe for DNA detection.     

Quantum chemical modelling of “green” luminescence in ABO perovskites

The origin of the intrinsic excitonic (“green”) luminescence in ABO₃ perovskites remains a hot topic over the last quarter of a century. We suggest as a theoretical interpretation for the “green” luminescence in these crystals, the recombination of electron and hole polarons forming a charge transfer vibronic exciton. In order to check quantitatively the proposed model, we performed quantum chemical calculations using the Intermediate Neglect of Differential Overlap (INDO) method combined with the periodic defect model. The luminescence energies calculated for four perovskite crystals are found to be in good agreement with experimental data. Received 19 December 2001 and Received in final form 14 March 2002 Published online 25 June 2002     

Control of optical properties of polymethine dye <Emphasis Type="Italic">J</Emphasis>-aggregates using different additives

The effect of various additives (NaCl, DNA, and CPB surfactant) on the structure and optical properties of luminescent molecular nanoclusters, J-aggregates of L-21 polymethine dye, has been investigated using stationary and time-resolved optical spectroscopy. It has been shown that all investigated additives enhance the dye aggregation and change its aggregate structure as manifested in a change of tilt angle between molecules in the molecular chain. Salt causes the biggest change of tilt angle whereas surfactant causes the smallest. It has been found that a decrease of tilt angle leads to an increase of J-aggregate luminescence intensity. The addition of CPB surfactant is shown to modify the exciton dynamics in J-aggregates whereas the other additives affect only their structure. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 76, No. 2, pp. 250–255, March–April, 2009.     

Investigation of the Doughnut Effect in Cy3-Labeled Protein Microarrays using Scanning Near-Field Optical Microscope

We demonstrate the fluorescence mapping of protein microarrays by the technique of scanning near-field optical microscopy (SNOM) and confocal microscopy. Micron sized spots (300 μm) of human Immunoglobulin G (hIgG) protein with and without a Cy3 dye labeling have been fabricated on glass substrates by an immobilization method which makes use of calixcrown derivatives termed Prolinker. We have also tried to probe into the well-known “doughnut effect” observed in fluorescence images of proteins using the SNOM technique. The topographic and fluorescence SNOM images revealed that the number of proteins at the boundary of the spot were more than at the center in the case of the microarray spot which showed brighter luminescence at the edge than at the center in the confocal image.     

Tunable wavelength laser medical system for treating oncological diseases

A new laser medical system (LMS) “LITT-FDT” for treating oncological diseases is presented. The laser system is based on a dye laser pumped by a copper vapor laser. The system features gradual wavelength tuning which allows operation almost with any photosensitizer (PS) when treating oncological diseases by the photodynamic therapy (PDT) method. The results of clinical trials of skin cancer treatment by the PDT method using the “LITT-FDT” laser system are considered.     

Slow nucleic acid unzipping kinetics from sequence-defined barriers

Recent experiments on unzipping of RNA helix-loop structures by force have shown that ≈40-base molecules can undergo kinetic transitions between two well-defined “open” and “closed” states, on a timescale ≈1 sec [Liphardt et al., Science 297, 733-737 (2001)]. Using a simple dynamical model, we show that these phenomena result from the slow kinetics of crossing large free energy barriers which separate the open and closed conformations. The dependence of barriers on sequence along the helix, and on the size of the loop(s) is analyzed. Some DNA and RNA sequences that could show dynamics on different time scales, or three(or more)-state unzipping, are proposed. Our dynamical model is also applied to the unzipping of long (kilo-basepair) DNA molecules at constant force. Received 29 July 2002 / Received in final form 5 February 2003 Published online: 16 April 2003 RID="a" ID="a"e-mail: cocco@ldfc.u-strasbg.fr RID="b" ID="b"e-mail: jmarko@uic.edu RID="c" ID="c"e-mail: monasson@lpt.ens.fr     

Anti-stokes luminescence of Zn<Subscript>0.6</Subscript>Cd<Subscript>0.4</Subscript>S solid solutions with adsorbed organic dye molecules and few-atom silver clusters

For microcrystals of Zn_0.6Cd_0.4S with adsorbed molecules of a number of organic dyes, we have observed sensitized anti-Stokes luminescence excited by radiation with wavelengths in the range 610–750 nm and flux density 10¹⁴–10¹⁵ photons/cm²·sec. The positions of the bands in the excitation spectra for such luminescence match those of the absorption spectra for the adsorbed dye molecules, which is evidence in favor of a cooperative mechanism for its appearance. We have shown that enhancement of the anti-Stokes luminescence is possible when silver atoms and few-atom clusters appear on the Zn_0.6Cd_0.4S surface in addition to the dye molecules. We hypothesize that its excitation in the latter case occurs as a result of two-photon optical transitions. These transitions occur sequentially, with transfer of an electron or the electronic excitation energy from the dye molecules to silver atoms and few-atom clusters adsorbed on the surface of Zn_0.6Cd_0.4S, creating deep localized states in the bandgap with photoionization energies 1.80–2.00 eV. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 74, No. 5, pp. 617–621, September–October, 2007.     

Electronic spectrum of a two-dimensional Fibonacci lattice

The electronic spectrum and wave functions of a new quasicrystal structure—a two-dimensional Fibonacci lattice—are investigated in the tight-binding approximation using the method of the level statistics. This is a self-similar structure consisting of three elementary structural units. The “central” and “nodal” decoration of this structure are examined. It is shown that the electronic energy spectrum of a two-dimensional Fibonacci lattice contains a singular part, but in contrast to a one-dimensional Fibonacci lattice the spectrum does not contain a hierarchical gap structure. The measure of allowed states (Lebesgue measure) of the spectrum is different from zero, and for “central” decoration it is close to 1. The character of the localization of the wave functions is investigated, and it is found that the wave functions are “critical.” Zh. éksp. Teor. Fiz. 116, 1834–1842 (November 1999)     

Interaction of ethidium bromide and caffeine with DNA in aqueous solution

Two component (ethidium bromide–caffeine, ethidium bromide–DNA) and three component (ethidium bromide–caffeine–DNA) systems in aqueous saline (0.01 M NaCl) phosphate buffer solutions (pH 6.86, T = 298 K) are studied spectrophotometrically. The equilibrium constants for dimerization of caffeine, K _D  = 1.22 ± 2 M⁻¹, and for heteroassociation of ethidium bromide with caffeine, K = 71 ± 8 M⁻¹, in ethidium bromide–caffeine systems are determined. When the concentration of caffeine is increased, the dynamic equilibrium of the solution shifts toward formation of heterocomplexes which are, presumably, stabilized by dispersive and hydrophobic interactions of chromophores. The equilibrium parameters for ethidium bromide complex formation with DNA are calculated: the coupling constant for the dye with the biopolymer, K ₁ = (232 ± 16)⋅103 M⁻¹, and the number of base pairs of the biopolymer participating in bonding with the ligand, n ₁ = 3.6 ± 0.2, are calculated. Given these values, it is suggested that under these experimental conditions there are two types of bonding between ethidium bromide and the nucleic acid — intercalation and “external” bonds. A McGhee–von Hippel model for a three component system and the numerical values of the parameters for molecular complex formation in two component systems are used to calculate the bonding constant for caffeine with DNA, K ₂ = 127 ± 30 M⁻¹, and the number of base pairs of DNA which bond with caffeine, n ₂ = 1.7 ± 0.2. The concentrations of ethidium bromide and caffeine in the composition of two and three component complexes are calculated as functions of the nucleic acid content in the solution. An analysis of the concentration dependences shows that heteroassociation of ligands has a significant effect on the reduction in the concentration of ethidium bromide–DNA complexes in a three component system for low DNA concentrations, while at high DNA concentrations the bonding of caffeine with the biopolymer has this effect. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 76, No. 1, pp. 143–151, January–February 2009.     

Fluorescence quenching in bichromophoric systems with nonconjugated chromophores: 5-substituted derivatives of l,3,5-triaryl-2-pyrazoline

The spectral and fluorescent properties of l,3,5-triphenyl-2-pyrazoline derivatives with acceptor substituents in benzene ring in the 5 position of the pyrazoline cycle were investigated. The corresponding pyrazoline derivative, in which phenyl radical in the 5 position is replaced by a fragment with an extended conjugated system-2.5-diphenyloxazolyl-was studied as well. The noticeable decrease in fluorescence quantum yield in comparison with the nonsubstituted molecule is characteristic of the compounds studied, which belong to the broader class of bichromophoric molecules with nonconjugated chromophores. The existence of excited states of “ mixed ” or “cross” (charge transfer) type, formed with participation of occupied molecular orbitals of one chromophoric fragment and vacant molecular orbitals of another, is typical of such a bichromophoric system. On the basis of our experimental and theoretical data, the assumption was made that the fluorescence quenching in the investigated bichromophoric molecules could be connected with the thermal population of the excited states of “mixed” type.     

Measurement of the Majorana effect in a molecule using a switched magnetic field and quantum beat detection

By means of quantum beat spectroscopy we investigated the dynamics of magnetic moments associated with hyperfine levels in the molecule under “spin-flip conditions”. Oriented molecules in a cold beam were prepared by excitation with a circularly polarized laser pulse () in a weak magnetic field (). Subsequently, they were exposed to a rapid field inversion which left the magnetic moment in its initial orientation. The initially created coherences among the excited hf levels were conserved after field reversal and thus were explored to characterize the changes in the level structure due to this “Majorana spin-flip” process. Received: 4 February 1999     

Similarity of Co-Species in Co and CoMo-sulfide catalysts supported on carbon and alumina. A Mössbauer emission spectroscopic study

It is shown that, irrespective of the application of carbon or alumina as a support, the local structure of the “Co-sulfide” phase formed during sulfidation of Co-and CoMo-catalysts is the same. A relation is found between the quadrupole splitting (Q.S. value) of the “Co-sulfide” phase and its dispersion. The higher the dispersion, the larger the Q.S. value. The so-called “Co-Mo-S” doublet is observed in all cases and it turns out to be related to a highly dispersed “Co-sulfide” phase instead of a Co, Mo and S containing phase.     

A unified framework for the algebra of unsharp quantum mechanics

On the basis of the concrete operations definable on the set of effect operators on a Hilbert space, an abstract algebraic structure of sum Brouwer-Zadeh (SBZ)-algebra is introduced. This structure consists of a partial sum operation and two mappings which turn out to be Kleene and Brouwer unusual orthocomplementations. The Foulis-Bennett effect algebra substructure induced by any SBZ-algebra, allows one to introduce the notions of unsharp “state” and “observable” in such a way that any “state-observable” composition is a standad probability measure (classical state). The Cattaneo-Nisticò BZ substructure induced by any SBZ-algebra permits one to distinguish, in an equational and simple way, the sharp elements from the really unsharp ones. The family of all sharp elements turns out to be a Foulis-Randall orthoalgebra. Any unsharp element can be “roughly” approximated by a pair of sharp elements representing the best sharp approximation from the bottom and from the top respectively, according to an abstract generalization introduced by Cattaneo of Pawlack “rough set” theory (a generalization of set theory, complementary to fuzzy set theory, which describes approximate knowledge with applications in computer sciences). In both the concrete examples of fuzzy sets and effect operators the “algebra” of rough elements shows a weak SBZ structure (weak effect algebra plus BZ standard poset) whose investigation is set as an interesting open problem.     

Investigation of fatigue relaxation of luminescence in porous silicon by time-resolved spectroscopy

This paper describes the first investigations of how the intensities of various time-resolved components of the luminescence from porous silicon relax with time. A paradoxical correlation is observed between the macro-and microtemporal relaxation of luminescence from porous silicon under pulsed photoexcitation: namely, a relative increase in the rate of macrorelaxation for the slower components of the luminescence. Spectral investigations show that the difference in the rates of fatigue relaxation “tiredness” is maximum at the long-wavelength edge of the luminescence band. We propose a model that allows us to explain the observed effects starting from the assumption that photoexcitations drift toward radiative recombination centers. Fiz. Tverd. Tela (St. Petersburg) 39, 1165–1169 (July 1997)