Intercalation of cationic dyes in the DNA double helix: introductory theory

The effect of salt on the intercalation of acridine dyes and DNA is rather well explained by the Gouy-Chapman double-layer theory as applied to a cylinder model of the DNA–dye complex. The free energy of transfer of a dye ion from the bulk solution to the complex is divided into several parts, one of which, ΔF₀, accounts for the short-range, nonelectrostatic interactions. The assumption that ΔF₀ should not depend on the amount of dye in the complex leads to an internal dielectric constant of the cylinder of about D_i = 7. The scatter in ΔF₀ values, as calculated from individual experimental points, is of order 0.5 kT per dye ion. This scatter is large enough to mask possible effects of heterogeneity in DNA sequences. The calculations are made for a long cylinder with radius 10 Å, with the DNA phosphate charges smeared uniformly at the surface, a uniform spacing of dye charges at the cylinder axis, and a length of b = 3.37 Å per base pair. Each intercalated dye ion also adds a length b to the total length of the cylinder. The salt-dependent part of the electric free energy of intercalation, ΔF₁, is tabulated for complexes with r = 0–0.24 dye ions per DNA phosphate in 0.002–0.2M monovalent salt and dye solutions.     

Energy transfer in polynucleotide homopolymers and copolymers

Using the fluorophore Tb³⁺ as a reporter, the effect of thallium (Tl⁺¹) on the transfer of energy in polyribonucleotides and polydeoxynucleotides at room temperature has been studied. In p(G), p(G, I), and pd(G)₆ thallium greatly increases the transfer of uv energy absorbed by the bases to Tb³⁺. In DNA, p(G, U), p(G, A), p(A, U), p(X), p(A), p(U), p(I), pd(G, A)₆, and pd(G, T)₅ thallium has little or no effect. Thallium increases intersystem crossing to the triplet states only in p(G), p(G, I), and pd(G)₆, and the triplets overlap the excited singlet state in Tb³⁺. In those G- and X-containing polymers showing little thallium effect, the evidence suggests that intersystem crossing is comparatively high to begin with. These polymers, including DNA, appear to transfer absorbed energy to triplet states efficiently at room temperature.     

Dielectric relaxation of DNA solutions. IV. Effects of salts and dyes

The effects of salts (NaCl, LiCl, Me₄NCl, AgNO₃, MgCl₂, CuCl₂ and MnCl₂) and dyes (acridine orange and methylene blue) on the low-frequency dielectric relaxation (0.1 Hz–30 kHz) of dilute aqueous solutions of DNA were investigated with varying salt or dye concentrations. Both the dielectric relaxation time τ_D and the rotational relaxation time τ estimated from the reduced viscosity decrease in quite parallel ways with increasing M/P (M/P being the normality ratio of cation to phosphate residue), reflecting the contraction of DNA molecule due to electrostatic shielding and cation binding. The agreement between τ_D and τ through the whole range of M/P supports our previous conclusion that the low-frequency relaxation of DNA arises from rotation of the molecule. The dielectric increment Δε also decreases with increasing M/P on account of both the contraction of DNA and the decrease in effective degree of dissociation of DNA. Δε as a function of M/P is interpreted in terms of a quasi-permanent dipole due to counterion fluctuation. These effects of cations are the strongest for divalent cations and rather weak for Na⁺, Li⁺, and Me₄N⁺. Effects of dye on τ_D and Δε are also well explained by the rotation of DNA molecule with a quasi-permanent dipole due to counterion fluctuation on the basis of intercalation of dye at D/P < 0.2 (D/P being the molarity ratio of dye to phosphate residue) and external binding at 0.2 < D/P < 1.0.     

Mechanisms of Inhibition of Pyrimidine Dimer Formation in Deoxyribonucleic Acid by Acridine Dyes

The ultraviolet (UV)-induced formation of cyclobutyl pyrimidine dimers in Escherichia coli deoxyribonucleic acid (DNA) in vitro has been investigated in terms of the mechanism of inhibition by acridine dyes, the effect on dimer yield of specific singlet and triplet quenchers, and the mechanism of dimer formation. Our results indicate that (a) energy transfer is important in dimer reduction by acridines, (b) this transfer occurs from the singlet (S₁) of DNA, and (c) at room temperature triplet quenchers do not reduce dimer yield in DNA.     

Enhanced fluorescence of tetrasulfonated zinc phthalocyanine by graphene quantum dots and its application in molecular sensing/imaging

When excited at 435 nm, tetra‐sulfonate zinc phthalocyanine (ZnPcS₄) emitted dual fluorescence at 495 and 702 nm. The abnormal fluorescence at 495 nm was experimentally studied and analyzed in detail for the first time. The abnormal fluorescence at 495 nm was deduced to originate from triplet–triplet (T–T) energy transfer of excited phthalocyanine (³*ZnPcS₄). Furthermore, graphene quantum dots (GQDs) enhanced the 495 nm fluorescence quantum yield (Q) of ZnPcS₄. The fluorescence properties of ZnPcS₄–GQDs conjugate were retained in a cellular environment. Based on the fluorescence of ZnPcS₄–GQDs conjugate, we designed and prepared an Apt29/thrombin/Apt15 sandwich thrombin sensor with high specificity and affinity. This cost‐saving, simple operational sensing strategy can be extended to use in sensing/imaging of other biomolecules.     

Interaction between enzyme-generated triplet carbonyls and molecules intercalated into DNA

The phosphorescence from enzyme-generated and -protected triplet acetone is very efficiently quenched by dyes intercalated into DNA. The process is unlikely to be due to energy transfer and is tentatively ascribed to electron transfer occurring within the DNA helix complex with the acting enzyme. This quenching markedly protects DNA from breaks induced by triplet acetone. In the case of some barely emissive enzyme-generated triplet carbonyl species, it is possible to detect a weak emission resulting from the interaction with dye X DNA; this emission may be associated with back electron transfer.     

Thermodynamics of mucopolysaccharide–dye binding. II. Binding constant and cooperativity parameters of acridine orange–dermatan sulfate system

In the acridine orange–dermatan sulfate system, free and bound dye can be distinguished from each other spectroscopically. This permits the use of fluorometric methods to study the binding of acridine orange to the acid mucopolysaccharide dermatan sulfate. Experiments were conducted at 24°C in 10^?3 M citrate/phosphate buffer at pH = 7.0. The binding of the dye is highly cooperative, as evidenced by considerable interaction between adjacent bound dye molecules. Analysis of the data indicates that dermatan sulfate binds 2.3 ± 0.3 mol of acridine orange per dermatan sulfate uronic acid residue with a cooperative binding constant, K_q ranging from 4.9 to 6.0 × 10⁵ M^?1 which corresponds to a free energy of 7.74 ? ΔG° ? 7.86. The cooperativity parameter q apparently increases with increasing polymer-to-dye ratio.     

Evidence for an O2-barrier in the light-harvesting chlorophyll-a/b-protein complex LHC II

An O₂-barrier in the intact light-harvesting complex LHC II protects chlorophylls (Chl) and xanthophylls (Car) from photooxidation. Direct evidence for the limited access of O₂ to pigment sites comes from the decay kinetics of the first excited triplet state of Car (³Car-). The LHC-bound ³Car- in air-saturated solution decays mono-exponentially with a lifetime of 6.7-7.1 µs as compared to the approx. 1.2 µs of the -carotene triplet in hexane and the 8.8-9 µs observed for both systems under anaerobiosis. Further properties of the photostable complex are the limited access of protons to pigment sites and the efficient energy transfer from ¹Car- to Chl-a and from ³Chl- to Car. Fatty acids with increasing chain length increasingly lower both, the efficiency of the O₂ barrier and the photo- and acid stability of the LHC-bound pigments while singlet and triplet energy transfer between the pigments is maintained. Therefore, the close proximity of Chl and Car is not sufficient to protect the pigments from photooxidation; in addition, an O₂-barrier limiting the access of O₂ to pigment sites is required for efficient photoprotection. Structural properties of the photostable LHC II possibly underlying its O₂-barrier function are discussed.     

Triplet excited state spectra and dynamics of carotenoids from the thermophilic purple photosynthetic bacterium <Emphasis Type="Italic">Thermochromatium tepidum</Emphasis>

Light-harvesting complex 2 from the anoxygenic phototrophic purple bacterium Thermochromatium tepidum was purified and studied by steady-state absorption, fluorescence and flash photolysis spectroscopy. Steady-state absorption and fluorescence measurements show that carotenoids play a negligible role as supportive energy donors and transfer excitation to bacteriochlorophyll-a with low energy transfer efficiency of ~30%. HPLC analysis determined that the dominant carotenoids in the complex are rhodopin and spirilloxanthin. Carotenoid excited triplet state formation upon direct (carotenoid) or indirect (bacteriochlorophyll-a Q_x band) excitation shows that carotenoid triplets are mostly localized on spirilloxanthin. In addition, no triplet excitation transfer between carotenoids was observed. Such specific carotenoid composition and spectroscopic results strongly suggest that this organism optimized carotenoid composition in the light-harvesting complex 2 in order to maximize photoprotective capabilities of carotenoids but subsequently drastically suppressed their supporting role in light-harvesting process.     

Triplet state spectra and dynamics of peridinin analogs having different extents of π-electron conjugation

The Peridinin-Chlorophyll a-Protein (PCP) complex has both an exceptionally efficient light-harvesting ability and a highly effective protective capacity against photodynamic reactions involving singlet oxygen. These functions can be attributed to presence of a substantial amount of the highly-substituted and complex carotenoid, peridinin, in the protein and the facts that the low-lying singlet states of peridinin are higher in energy than those of chlorophyll (Chl) a, but the lowest-lying triplet state of peridinin is below that of Chl a. Thus, singlet energy can be transferred from peridinin to Chl a, but the Chl a triplet state is quenched before it can sensitize the formation of singlet oxygen. The present investigation takes advantage of Chl a as an effective triplet state donor to peridinin and explores the triplet state spectra and dynamics of a systematic series of peridinin analogs having different numbers of conjugated carbon–carbon double bonds. The carotenoids investigated are peridinin, which has a C₃₇ carbon skeleton and eight conjugated carbon–carbon double bonds, and three synthetic analogs: C₃₃-peridinin, having two less double bonds than peridinin, C₃₅-peridinin which has one less double bond than peridinin, and C₃₉-peridinin which has one more double bond than peridinin. In this study, the behavior of the triplet state spectra and kinetics exhibited by these molecules has been investigated in polar and nonpolar solvents and reveals a substantial effect of both π-electron conjugated chain length and solvent environment on the spectral lineshapes. However, only a small dependence of these factors is observed on the kinetics of triplet energy transfer from Chl a and on carotenoid triplet state deactivation to the ground state.     

Spectroscopic investigation of alloyed quantum dot‐based FRET to cresyl violet dye

Quantum dots (QDs), bright luminescent semiconductor nanoparticles, have found numerous applications ranging from optoelectronics to bioimaging. Here, we present a systematic investigation of fluorescence resonance energy transfer (FRET) from hydrophilic ternary alloyed quantum dots (CdSeS/ZnS) to cresyl violet dye with a view to explore the effect of composition of QD donors on FRET efficiency. Fluorescence emission of QD is controlled by varying the composition of QD without altering the particle size. The results show that quantum yield of the QDs increases with increase in the emission wavelength. The FRET parameters such as spectral overlap J(λ), Förster distance R₀, intermolecular distance (r) , rate of energy transfer k_T (r), and transfer efficiency (E) are determined by employing both steady‐state and time‐resolved fluorescence spectroscopy. Additionally, dynamic quenching is noticed to occur in the present FRET system. Stern–Volmer (K_D) and bimolecular quenching constants (k_q) are determined from the Stern–Volmer plot. It is observed that the transfer efficiency follows a linear dependence on the spectral overlap and the quantum yield of the donor as predicted by the Förster theory upon changing the composition of the QD. Copyright © 2015 John Wiley & Sons, Ltd.     

Ethidium bromide–DNA complex: Wavelength dependence of pyrimidine dimer inhibition and sensitized fluorescence as probes of excited states

Ethidium bromide inhibits the formation of ultraviolet-induced pyrimidine dimers in DNA. The efficiency of dimer inhibition increases with increasing energy of the exciting photons. The efficiency of energy transfer from the DNA singlet to the dye singlet, as monitored by sensitized fluorescence, is independent of wavelength. The efficiency of singlet–singlet transfer agrees with that for dimer inhibition at photon energies corresponding to excitation of the lowest singlet state of DNA. Our results support a model in which dimers are formed both directly from the singlet state and also from the triplet state, with triplets arising from higher vibrational levels of the singlet.     

Evidence for heterogeneity in DNA-associated solvent mobility from acridine phosphorescence spectra

The mobility of solvent associated with native DNA in comparison with that of the bulk solvent is monitored from the temperature-dependent red shift in the phosphorescence spectra of acridines bound to DNA and free in glycol–buffer mixtures. Over the temperature range for which the red shift occurs the phosphorescence decay changes with emission wavelength, indicating the time-dependent nature of the process. Moreover, at these temperatures, emission anisotropy measurements establish that motions of the dye itself are not involved. Correspondence between perturbations to the solvent that influence the temperature at which the red shift occurs for free acridine with those for the DNA-bound dye confirm that “bound solvent” is responsible for the spectral changes. For the DNA-bound acridines the extent of the red shift is smaller and the midpoint T_1/2 of the transition is warmer. The reduction in the red shift reveals that the bound dye is less exposed to solvent and varies as 9-aminoacridine < acridine orange ～ proflavin, i.e., 9-amino-acridine is less exposed to solvent. On the other hand, the warmer T_1/2 indicates that DNA-associated solvent is considerably less mobile than bulk solvent. T_1/2 varies for proflavin bound to DNA, poly[d(AT)], poly[d(GC)], and poly(dG): poly(dC), and for proflavin, acridine orange, and 9-aminoacrine bound to DNA. These observations suggest that there is a heterogeneity in the mobility of DNA-associated solvent.     

Microstructural and Electronic Origins of Open‐Circuit Voltage Tuning in Organic Solar Cells Based on Ternary Blends

Organic ternary heterojunction photovoltaic blends are sometimes observed to undergo a gradual evolution in open‐circuit voltage (V_oc) with increasing amounts of a second donor or an acceptor. The V_oc is strongly correlated with the energy of the charge transfer state in the blend, but this value depends on both local and mesoscopic orders. In this work, the behavior of V_oc in the presence of a wide range of interfacial electronic states is investigated. The key charge transfer state interfaces responsible for V_oc in several model systems with varying morphology are identified. Systems consisting of one donor with two fullerene molecules and of one acceptor with a donor polymer of varying regio‐regularity are used. The effects from the changing energetic disorder in the material and from the variation due to a law of simple mixtures are quantified. It has been found that populating the higher‐energy charge transfer states is not responsible for the observed change in V_oc upon the addition of a third component. Aggregating polymers and miscible fullerenes are compared, and it has been concluded that in both cases charge delocalization, aggregation, and local polarization effects shift the lowest‐energy charge transfer state distribution.     

Carotenoid triplet state formation in Rhodobacter sphaeroides R-26 reaction centers exchanged with modified bacteriochlorophyll pigments and reconstituted with spheroidene

Triplet state electron paramagnetic resonance (EPR) experiments have been carried out at X-band on Rb. sphaeroides R-26 reaction centers that have been reconstituted with the carotenoid, spheroidene, and exchanged with 13²-OH-Zn-bacteriochlorophyll a and [3-vinyl]-13²-OH-bacteriochlorophyll a at the monomeric, accessory bacteriochlorophyll sites B_A,B or with pheophytin a at the bacteriopheophytin sites H_A,B. The primary donor and carotenoid triplet state EPR signals in the temperature range 95–150 K are compared and contrasted with those from native Rb. sphaeroides wild type and Rb. sphaeroides R-26 reaction centers reconstituted with spheroidene. The temperature dependencies of the EPR signals are strikingly different for the various samples. The data prove that triplet energy transfer from the primary donor to the carotenoid is mediated by the monomeric, BChl_B molecule. Furthermore, the data show that triplet energy transfer from the primary donor to the carotenoid is an activated process, the efficiency of which correlates with the estimated triplet state energies of the modified pigments.Abbreviations BChl bacteriochlorophyll - BPhe bacteriopheophytin - Chl chlorophyll - EPR electron paramagnetic resonance - LDAO lauryl-dimethylamine-N-oxide - Phe pheophytin     

Interaction between tryptophan‐Sm(III) complex and DNA with the use of a acridine orange dye fluorophor probe

The interaction of the Trp–Sm(III) complex with herring sperm DNA (hs‐DNA) was investigated with the use of acridine orange (AO) dye as a spectral probe for UV‐vis spectrophotometry and fluorescence spectroscopy. The results showed that the both the Trp–Sm(III) complex and the AO molecule could intercalate into the double helix of the DNA. The Sm(III)–(Trp)₃ complex was stabilized by intercalation into the DNA with binding constants: K^?_25°C = 7.14 × 10⁵ L·mol^?1 and K^?_37°C = 5.28 × 10⁴ L·mol^?1, and it could displace the AO dye from the AO–DNA complex in a competitive reaction. Computation of the thermodynamic functions demonstrates that Δ_rH_m^? is the primary driving power of the interaction between the Sm(III)(Trp)₃ complex and the DNA. The results from Scatchard and viscometry methods suggested that the interaction mode between the Sm(III)(Trp)₃ complex and the hs‐DNA is groove binding and weak intercalation binding. Copyright © 2015 John Wiley & Sons, Ltd.     

Characterization of the binding of paylean and DNA by fluorescence,UV spectroscopy and molecular docking techniques

The interaction of paylean (PL) with calf thymus DNA (ctDNA) was investigated using fluorescence spectroscopy, UV absorption, melting studies, ionic strength, viscosity experiments and molecular docking under simulated physiological conditions. Values for the binding constant K_a between PL and DNA were 5.11 × 10³, 2.74 × 10³ and 1.74 × 10³ L mol^–1 at 19, 29 and 39°C respectively. DNA quenched the intrinsic fluorescence of PL via a static quenching procedure as shown from Stern–Volmer plots. The relative viscosity and the melting temperature of DNA were basically unchanged in the presence of PL. The fluorescence intensity of PL–DNA decreased with increasing ionic strength. The value of K_a for PL with double‐stranded DNA (dsDNA) was larger than that for PL with single‐stranded DNA (ssDNA). All the results revealed that the binding mode was groove binding, and molecular docking further indicated that PL was preferentially bonded to A–T‐rich regions of DNA. The values for ΔH, ΔS and ΔG suggested that van der Waals forces or hydrogen bonding might be the main acting forces between PL and DNA. The binding distance was determined to be 3.37 nm based on the theory of Förster energy transference, which indicated that a non‐radiation energy transfer process occurred. Copyright © 2015 John Wiley & Sons, Ltd.     

Towards an explanation of carboxylation/oxygenation bifunctionality in Rubisco. Transition structure for the carboxylation reaction of 2,3,4-pentanetriol

We construct a theoretical model of the transition structure for the carboxylation reaction of ribulose-1,5-biphosphate catalyzed by Rubisco. This is a first-order saddle point on the energy hypersurface for the nucleophilic attack of carbon dioxide on CH₃-(CHOH)₃-CH₃ at the C2 center.Ab initio analytical gradients methods at a 4-31G basis set level are used.The carbon framework and oxygens of the stationary structure superpose with the corresponding atoms of 2-carboxyarabinitol-1,5-biphosphate, which is a transition state analog that has recently been highly refined with X-ray methods. The hydroxyl group in C3 iscis to the C2 oxygen. The C3 center is somewhat pyramidized, the dienol O2-C2-C3-O3 is not planar.The geometry of the transition state allows for simple explanations of both the enolization of Rubisco's substrate ribulose-1,5-biphosphate, O₃PO-CH2-CO-(CHOH)₂-CH₂-OPO₃ and oxygenation reaction. The former is due to the pyramidal deformation at C3 and out of plane of O2-C2-C3-O3 framework: the enoliation is intramolecular and is probably enhanced by proton tunnelling. The latter is related with the fact that a rotation around an ethylene-like bond brings the triplet state down in energy. The reactive skeleton has a stationary geometry in the triplet state not very different from the one obtained in the global transition structure. There, the triplet is only 9 kcal/mol above the singlet. The spin densities at C2 and C3 centers clearly indicate the place where oxygenation will take place.     

Thermodynamics of mucopolysaccharide–dye binding. III. Thermodynamic and cooperativity parameters of acridine orange–heparin system

Binding isotherms for acridine orange (AO)–heparin systems can be evaluated solely on the basis of quantitative fluorescence spectroscopic measurements. The evaluation of thermodynamic parameters indicates that the interactions of AO with heparins from several animal sources are similar to each other in magnitude. Binding is highly exothermic (ΔH = ?6 kcal mol^?1) and is stabilized by dye–polymer and dye–dye (coopertive) interactions, as well as by entropic factors (ΔS = +7 e.u.). The predominant stabilizing factor appears to be the electrostatic attraction between the AO cation and the heparin polyanion, although the other factors are important as well. At 24°C the value of the cooperative binding constants for the various heparins range from 8.8 to 11.3 × 10⁵M^?1, corresponding to a free energy of ?8 kcal mol^?1. The degree of cooperativity, which is a direct measure of dye–dye interaction, varies with polymer:dye ratio; the theoretical basis for this variation remains to be elucidated. Electrophoretic data indicate that each heparin sample consists of a mixture of species, each with its own charge density. This precludes definitive interpretation of observed small differences in the values of the thermodynamic parameters among the various samples until each sample can be resolved into its components.     

Primary photochemistry in photosystem-I

In this review, the main research developments that have led to the current simplified picture of photosystem I are presented. This is followed by a discussion of some conflicting reports and unresolved questions in the literature. The following points are made: (1) the evidence is contradictory on whether P700, the primary donor, is a monomer or dimer of chlorophyll although at this time the balacnce of the evidence points towards a monomeric structure for P700 when in the triplet state; (2) there is little evidence that the iron sulfur centers F_A and F_B act in series as tertiary acceptors and it is as likely that they act in parallel under physiological conditions; (3) a role for F_X, probably another iron sulfur centrer, as an obligatory electron carrier in forward electron transfer has not been proven. Some evidence indicates that its reduction could represent a pathway different to that involving F_A and F_B; (4) the decay of the acceptor A₂ ^– as defined by optical spectroscopy corresponds with 700⁺ % MathType!MTEF!2!1!+-% feaafeart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamOramaaBa% aaleaadaqdaaqaaiaadIfaaaaabeaaaaa!37D1!\[F_{\overline X } \] recombination under some circumstances but under other conditions it probably corresponds with P700⁺ A₁ ^– recombination; (5) P700⁺ A₁ ^– recombination as originally observed by optical spectroscopy is probably due to the decay of the P700 triplet state; (6) the acceptor A₁ ^– as defined by EPR may be a special semiquinone molecule; (7) A₀ is probably a chlorophyll a molecule which acts as the primary acceptor. Recombination of P700⁺ A₀ ^– gives rise to the P700 triplet state.A working model for electron transfer in photosystem I is presented, its general features are discussed and comparisons with other photosystems are made.