Novel,Monomeric Cyanine Dyes as Reporters for DNA Helicase Activity

The dimeric cyanine dyes, YOYO-1 and TOTO-1, are widely used as DNA probes because of their excellent fluorescent properties. They have a higher fluorescence quantum yield than ethidium homodimer, DAPI and Hoechst dyes and bind to double-stranded DNA with high affinity. However, these dyes are limited by heterogeneous staining at high dye loading, photocleavage of DNA under extended illumination, nicking of DNA, and inhibition of the activity of DNA binding enzymes. To overcome these limitations, seven novel cyanine dyes (Cyan-2, DC-21, DM, DM-1, DMB-2OH, SH-0367, SH1015-OH) were synthesized and tested for fluorescence emission, resistance to displacement by Mg²⁺, and the ability to function as reporters for DNA unwinding. Results show that Cyan-2, DM-1, SH-0367 and SH1015-OH formed highly fluorescent complexes with dsDNA. Of these, only Cyan-2 and DM-1 exhibited a large fluorescence enhancement in buffers, and were resistant to displacement by Mg²⁺. The potential of these two dyes to function as reporter molecules was evaluated using continuous fluorescence, DNA helicase assays. The rate of DNA unwinding was not significantly affected by either of these two dyes. Therefore, Cyan-2 and DM-1 form the basis for the synthesis of novel cyanine dyes with the potential to overcome the limitations of YOYO-1 and TOTO-1.     

Lanthanide Complex-Based Fluorescence Label for Time-Resolved Fluorescence Bioassay

Different from organic fluorescence dyes, fluorescent lanthanide complexes have the fluorescence properties of long fluorescence lifetime, large Stokes shift and sharp emission profile, which makes them favorable be used as the fluorescent labeling reagents for microsecond time-resolved fluorescence bioassay. Lanthanide complex-based fluorescence labels have been successfully used for highly sensitive time-resolved fluorescence immunoassay, DNA hybridization assay, cell activity assay, and bioimaging microscopy assay. Since the technique allows easy distinction of the specific fluorescence signal of the long-lived label from short-lived background noises associated with biological samples, scattering lights (Tyndall, Rayleigh and Raman scatterings) and the optical components (cuvettes, filters and lenses), the sensitivity of fluorescence bioassay has been remarkably improved. This paper summarized the recent developments of lanthanide complex-based fluorescence labels and their applications in time-resolved fluorescence bioassays mainly based on the authors’ researches and relative publications.     

光学分子成像技术观察纳流芯片对DNA分子的研究

λ-DNA与荧光染料YOYO-1结合,利用荧光显微技术对DNA分子在毛细现象作用下进入宽40 nm、深60 nm的纳米沟道内,并在其内部被拉伸以及沿沟道移动的情形进行了观察.讨论了DNA分子在沟道内的运动情况.结合光学分子成像技术与该尺寸范围的纳流芯片,将有助于研究生物分子的动力学和静力学性质.     

Spectro Analytical,Computational and In Vitro Biological Studies of Novel Substituted Quinolone Hydrazone and it’s Metal Complexes

Some novel transition metal [Cu (II), Ni (II) and Co (II)] complexes of nalidixic acid hydrazone have been prepared and characterized by employing spectro-analytical techniques viz: elemental analysis, ¹H-NMR, Mass, UV–Vis, IR, TGA-DTA, SEM-EDX, ESR and Spectrophotometry studies. The HyperChem 7.5 software was used for geometry optimization of title compound in its molecular and ionic forms. Quantum mechanical parameters, contour maps of highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) and corresponding binding energy values were computed using semi empirical single point PM3 method. The stoichiometric equilibrium studies of metal complexes carried out spectrophotometrically using Job’s continuous variation and mole ratio methods inferred formation of 1:2 (ML₂) metal complexes in respective systems. The title compound and its metal complexes screened for antibacterial and antifungal properties, exemplified improved activity in metal complexes. The studies of nuclease activity for the cleavage of CT- DNA and MTT assay for in vitro cytotoxic properties involving metal complexes exhibited high activity. In addition, the DNA binding properties of Cu (II), Ni (II) and Co (II) complexes investigated by electronic absorption and fluorescence measurements revealed their good binding ability and commended agreement of K_b values obtained from both the techniques. Molecular docking studies were also performed to find the binding affinity of synthesized compounds with DNA (PDB ID: 1N37) and “Thymidine phosphorylase from E.coli” (PDB ID: 4EAF) protein targets.     

SYBR Green I: Fluorescence Properties and Interaction with DNA

In this study, we have investigated the fluorescence properties of SYBR Green I (SG) dye and its interaction with double-stranded DNA (dsDNA). SG/dsDNA complexes were studied using various spectroscopic techniques, including fluorescence resonance energy transfer and time-resolved fluorescence techniques. It is shown that SG quenching in the free state has an intrinsic intramolecular origin; thus, the observed >1,000-fold SG fluorescence enhancement in complex with DNA can be explained by a dampening of its intra-molecular motions. Analysis of the obtained SG/DNA binding isotherms in solutions of different ionic strength and of SG/DNA association in the presence of a DNA minor groove binder, Hoechst 33258, revealed multiple modes of interaction of SG inner groups with DNA. In addition to interaction within the DNA minor groove, both intercalation between base pairs and stabilization of the electrostatic SG/DNA complex contributed to increased SG affinity to double-stranded DNA. We show that both fluorescence and the excited state lifetime of SG dramatically increase in viscous solvents, demonstrating an approximate 200-fold enhancement in 100?% glycerol, compared to water, which also makes SG a prospective fluorescent viscosity probe. A proposed structural model of the SG/DNA complex is compared and discussed with results recently reported for the closely related PicoGreen chromophore.     

Synthesis,Spectral Characterization,DNA/ Protein Binding,DNA Cleavage,Cytotoxicity, Antioxidative and Molecular Docking Studies of Cu(II)Complexes Containing Schiff Base-bpy/Phen Ligands

Ternary Cu(II) complexes [Cu(II)(L)(bpy)Cl] 1, [Cu(II)(L)(Phen)Cl] 2 [L = 2,3–dimethyl-1-phenyl-4(2 hydroxy-5-methyl benzylideneamino)-pyrazol-5-one, bpy = 2,2^′ bipyridine, phen =1,10 phenanthroline) were synthesized and characterized by elemental analyses, UV-Visible, FT-IR, ESR, Mass, thermogravimetric and SEM EDAX techniques. The complexes exhibit octahedral geometry. The interaction of the Cu(II) with cailf thymus DNA (CT-DNA) was explored by using absorption and fluorescence spectroscopic methods. The results revealed that the complexes have an affinity constant for DNA in the order of 10⁴ M^?1 and mode of interaction is intercalative mode. The DNA cleavage study showed that the complexes cleaved DNA without any external agent. The interaction of Cu(II) complexes with bovine serum albumin (BSA) was also studied using absorption and fluorescence techniques. The cytotoxic activity of the Cu(II) complexes was probed in HeLa (human breast adenocarcinoma cell line), B16F10 (Murine melanoma cell line) and HEPA1–6 celllines, complex 1 has good cytotoxic activity which is comparable with the doxarubicin drug, with IC₅₀ values ranging from 3 to 12.6 μM. A further molecular docking technique was employed to understand the binding of the complexes towards the molecular target DNA. Investigation of the antioxidative properties showed that the metal complexes have significant radical scavenging activity potency against DPPH radical.     

SPECTROSCOPIC METHODS FOR CHARACTERIZATION OF NONVIRAL GENE DELIVERY SYSTEMS FROM A PHARMACEUTICAL POINT OF VIEW

Introduction of nucleic acids into mammalian and plant cells has become, in recent years, a well established procedure in basic and applied research, and the methods involved therein are now useful for the development of gene-based medicines as a new class of pharmaceuticals.

The incorporation of the gene of interest into a plasmid construct by molecular biology techniques, the complexation and condensation of nucleic acids by means of cationic agents, is the first step for enabling DNA to get into the cells of interest in a biologically active state. Monitoring this condensation procedure for scientific and quality control purposes is mostly performed by optical spectroscopy methods.

A fluorimetric, high-throughput-assay has been developed for the characterization of non-viral gene delivery systems. Protamine sulfate and cationic DOTAP liposomes were used to condense the plasmid DNA. The DNA was labeled with nucleic acid stains, and the quenching of fluorescence by the addition of condensing agents was measured. PicoGreen? was compared to a number of common nucleic acid stains (ethidium bromide, ethidium- homodimer-2, acridine orange, BOBO-1, POPO-1, TOTO-1, YOYO-1, BOBO-3, POPO-3, TOTO-3, YOYO-3, BO-PRO-1, PO-PRO-1, TO-PRO-1, YO-PRO-1, BO-PRO-3, PO-PRO-3, TO-PRO-3, YO-PRO-3), and was found to be an advantageous nucleic acid stain for the fluorimetric characterization of condensation. Stability of nucleic acid-dye complex, reproducibility and the signal-to-noise ratio make PicoGreen? a dye of choice for condensation experiments.

Condensation was quantified by the fitting of condensation curves to the “Hill equation”. Relative fluorescence intensity, Hill slope and kinetics of DNA-condensation provide the calculated values for advanced characterization of DNA-condensation.

Fluorescence spectroscopy are compared to agarose gel electrophoresis as another approach for biophysical characterization of DNA-condensation. Advantages and disadvantages of the two methods are discussed.     

Propidium Iodide and PicoGreen as Dyes for the DNA Fluorescence Correlation Spectroscopy Measurements

Many experimental designs, in which nucleic acid conformational changes are of interest, require reliable fluorescence labeling. The appropriate fluorescence probe should have suitable optical properties and, more importantly, should not interfere with the investigated processes. In order to avoid chemical modifications the fluorescence label needs to be associated with nucleic acid via weak non-covalent interactions. There are a number of fluorescent probes that change their fluorescent properties (i.e. their quantum yield and/or spectral characteristics) upon association with nucleic acid. Such probes are frequently used to detect, visualize and follow processes involving nucleic acid and its conformational changes. In order to obtain reliable data regarding macromolecule or aggregate topology a detailed knowledge of probe–nucleic acid interactions on the molecular level is needed. In this paper we show that the association of propidium iodide with DNA alters its conformation and that it selectively labels plasmid fragments and/or its subpopulations in a concentration-dependent meaner. Another dye, PicoGreen, exhibits better properties. It labels nucleic acid uniformly and without any concentration-dependent artifacts.     

Synthesis,Characterization, DNA Binding Properties and Antioxidant Activity of Ln(III) Complexes with Schiff Base Ligand Derived from 3-Carbaldehyde Chromone and Aminophenazone

A novel Schiff base ligand, chromone-3-carbaldehyde-aminophenazone (L) and its Ln(III) (Ln = La, Yb) complexes were synthesized and characterized by physicochemical methods. The interaction between the ligand, Ln(III) complexes and calf thymus DNA in physiological buffer (pH = 7.10) was investigated by using UV–vis spectroscopy, fluorescence spectra, ethidium bromide experiments and viscosity measurements, indicating that the studied compounds can all bind to DNA via an intercalation binding mode and the complexes have stronger binding affinity than the free ligand alone. Furthermore, antioxidant activity of the ligand and its complexes was determined by superoxide and hydroxyl radical scavenging methods in vitro, suggesting that Ln(III) complexes inhibit stronger antioxidant activity than the ligand alone and some standard antioxidants, such as mannitol and vitamin C.     

Fluorescence Dynamics of DNA Condensed by the Molecular Crowding Agent Poly(Ethylene Glycol)

Condensation of extended DNA into compact structures is encountered in a variety of situations, both natural and artificial. While condensation of DNA has been routinely carried out by the use of multivalent cations, cationic lipids, detergents, and polyvalent cationic polymers, the use of molecular crowding agents in condensing DNA is rather striking. In this work, we have studied the dynamics of plasmid DNA condensed in the presence of a molecular crowding agent, polyethylene glycol (PEG). Steady-state and time-resolved fluorescence of the recently established condensation-indicating DNA binder, YOYO-1 [G. Krishnamoorthy, G. Duportail, and Y. Mely (2002), Biochemistry 41, 15277–15287] was used in inferring the dynamic aspects of DNA condensates. It is shown that DNA condensed by PEG is more flexible and less compact when compared to DNA condensed by binding agents such as polyethyleneimine. The relevance of such differences in dynamics toward functional aspects of condensed DNA is discussed.     

Homogeneous Detection of Specific DNA Sequences by Fluorescence Quenching and Energy Transfer

The use of fluorescence quenching and energy transfer in DNA hybridization assays is reviewed. Placement of DNA probe labels within interacting distances by hybridization of DNA probes to target DNA or to one another allows rapid homogeneous analysis of specific DNA sequences. Due to the inherently lower sensitivity relative to heterogeneous assays, the fluorescence assays have been coupled with DNA amplification methods such as PCR to provide highly sensitive, clinically relevant homogeneous assays which can be performed in closed systems.     

Rare Earth Complexes with 3-Carbaldehyde Chromone-(Benzoyl) Hydrazone: Synthesis,Characterization, DNA Binding Studies and Antioxidant Activity

A new ligand, 3-carbaldehyde chromone-(benzoyl) hydrazone (L), was prepared by condensation of 3-carbaldehyde chromone with benzoyl hydrazine. Its four rare earth complexes have been prepared and characterized on the basis of elemental analyses, molar conductivities, mass spectra, ¹H NMR spectra, UV-vis spectra, fluorescence studies and IR spectra. The Sm(III) complex exhibits red fluorescence under UV light and the fluorescent properties of Sm(III) complex in solid state and different solutions were investigated. In addition, the DNA binding properties of the ligand and its complexes have been investigated by electronic absorption spectroscopy, fluorescence spectra, ethidium bromide displacement experiments, iodide quenching experiments, salt effect and viscosity measurements. Experimental results suggest that all the compounds can bind to DNA via an intercalation binding mode. Furthermore, the antioxidant activities of the ligand and its complexes were determined by superoxide and hydroxyl radical scavenging methods in vitro. The rare earth complexes were found to possess potent antioxidant activities that are better than those of the ligand alone.     

Enhanced Emission Induced by FRET from a Long-Lifetime, Low Quantum Yield Donor to a Long-Wavelength, High Quantum Yield Acceptor

We report observation of high quantum yield, long-lifetime fluorescence from a red dye BO-PRO-3 excited by resonance energy transfer (RET). The acceptor fluorescence was highly enhanced upon binding to the donor-labeled DNA. A ruthenium complex (Ru) was chosen as a donor in this system because of its long fluorescence lifetime. Both donor and acceptor were non-covalently bound to DNA. Emission from the donor-acceptor system (DA) at wavelengths exceeding 600 nm still preserves the long-lifetime component of the Ru donor, retaining average fluorescence lifetimes in the range of 30–50 ns. Despite the low quantum yield of the Ru donor in the absence of acceptor, its overall quantum yield of the DA pair was increased by energy transfer to the higher quantum yield acceptor BO-PRO-3. The wavelength-integrated intensity of donor and acceptor bound to DNA was many-fold greater than the intensity of the donor and acceptor separately bound to DNA. The origin of this effect is due to an efficient energy transfer from the donor, competing with non-radiative depopulation of the donor excited state. The distinctive features of DA complexes can be used in the development of a new class of engineered luminophores that display both long lifetime and long-wavelength emission. Similar DA complexes can be applied as proximity indicators, exhibiting strong fluorescence of adjacently located donors and acceptors over the relatively weak fluorescence of separated donors and acceptors.     

Dipyrrylmetheneboron Difluorides as Labels in Two-Photon Excited Fluorometry. Part II–Nucleic Acid Hybridization Assays

Five two-photon excitable dipyrrylmetheneboron difluoride labels (dipyrrylmethene-BF₂ labels) with fluorescence emission maximum between 530 and 590 nm, and a frequently used rhodamine label, TAMRA, were conjugated to aminomodified oligonucleotides. The performance of the labeled oligonucleotides was studied in a separation-free nucleic acid hybridization assay using ArcDia^™ TPX bioaffinity assay technology. The results show that oligonucleotide conjugates of dipyrrylmethene-BF₂ labels provide higher two-photon excited fluorescence yield and better assay sensitivity than corresponding TAMRA conjugate. The effect of conjugation on photophysical properties of the labels and performance of the labeled oligonucleotides in separation-free hybridization assay is discussed.     

Hydrophilic Labeling Reagents of Dipyrrylmethene-BF2 Dyes for Two-Photon Excited Fluorometry: Syntheses and Photophysical Characterization

Recently introduced bioaffinity assay technology, ArcDia TPX, is based on two-photon excited fluorescence (TPE) and it enables separation-free ultra-sensitive immunoassays from microvolumes. Here we present syntheses of novel two-photon excitable fluorescent labeling reagents which have been specially designed to be used as label molecules in the ArcDia TPX assay technique. The labeling reagents are based on dipyrrylmetheneboron difluoride (dipyrrylmethene-BF2) chromophore, which have been substituted with aryl, heteroaryl or arylalkenyl chemical groups to extend the pi-electron conjugation. These substitutions results in a series of dipyrrylmethene-BF2 fluorophores with different photophysical properties. Dipyrrylmethene-BF2 fluorophores have been further substituted with a dipeptide linker unit and finally activated as succinimidyl esters to enable specific coupling with primary amino groups. The dipeptide linker serves as a spacer arm between the label and a target, and enhances the solubility of the label in aqueous solutions. Study of the chemical and photophysical performance of the new labeling reagents is described. The new labeling reagents exhibit high fluorescence quantum yields, and molar absorption coefficients. The results show that the new labels with the hydrophilic dipeptide linker unit provide large two-photon excitation cross-sections, high fluorescence quantum efficiency and good solubility in aqueous solutions. The results suggest that the novel dipyrrylmethene-BF2 labels are highly applicable to bioaffinity assays based on two-photon excitation of fluorescence.     

La~(3+)掺杂Eu~(3+)偏苯三酸邻菲咯啉三元配合物的合成和荧光性能

以偏苯三酸(TLA)为第一配体,邻菲咯啉(phen)为第二配体,合成了铕偏苯三酸邻菲咯啉及铕镧系列发光配合物Eu1-xLax(TLA)phen(x=0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8)。通过红外光谱、TG-DTG和扫描电子显微镜对配合物进行了表征;通过荧光光谱分析,探讨了掺杂荧光惰性离子对三元配合物的发光性能的影响。结果表明:该系列配合物均表现为强的Eu3+的特征荧光,La3+的掺入能增强配合物的的荧光强度,但发射峰的位置基本上没有变化,其中5D0→7F1和5D0→7F2的跃迁发射较强,所有掺杂配合物的荧光强度都大于未掺杂的配合物的荧光强度。     

Modeling single-scattering properties of small cirrus particles by use of a size-shape distribution of ice spheroids and cylinders

In this study, we model single-scattering properties of small cirrus crystals using mixtures of polydisperse, randomly oriented spheroids and cylinders with varying aspect ratios and with a refractive index representative of water ice at a wavelength of 1.88 μm. The Stokes scattering matrix elements averaged over wide shape distributions of spheroids and cylinders are compared with those computed for polydisperse surface-equivalent spheres. The shape-averaged phase function for a mixture of oblate and prolate spheroids is smooth, featureless, and nearly flat at side-scattering angles and closely resembles those typically measured for cirrus. Compared with the ensemble-averaged phase function for spheroids, that for a shape distribution of cylinders shows a relatively deeper minimum at side-scattering angles. This may indicate that light scattering from realistic cirrus crystals can be better represented by a shape mixture of ice spheroids. Interestingly, the single-scattering properties of shape-averaged oblate and prolate cylinders are very similar to those of compact cylinders with a diameter-to-length ratio of unity. The differences in the optical cross sections, single-scattering albedo, and asymmetry parameter between the spherical and the nonspherical particles studied appear to be relatively small. This may suggest that for a given optical thickness, the influence of particle shape on the radiative forcing caused by a cloud composed of small ice crystals can be negligible.     

激光焊接熔透特征信号同轴增效提取方法研究

熔透检测是实现高功率激光焊接质量在线控制的重要环节,但由于介观尺度下的低辐值熔透特征信号产生于激光匙孔底部被匙孔喷射物质和周围干扰信号完全掩盖,熔透状态难以被直接获取,常规检测多以间接测量为主。将光谱透视技术、红外显微成像技术、光电传感技术及空间定位提取技术相结合,提出一种激光焊接熔透特征信号同轴增效提取方法。以高功率激光在匙孔内壁激发的荧光辐射源作为直接检测信号,利用不同发光体的谱段特性在红外谱段有效分离并抑制激光焊接匙孔上方的等离子体、金属蒸汽焰、粒子团簇等强干扰信号,使红外荧光信号得到有效增强,实现光谱透视显像效果。同时采用自行研制的激光焊接同轴显微光路系统,利用红外显微成像原理提取到匙孔内壁受激辐射荧光的红外显微实像。并以此为基础对高功率激光焊接熔透状态与匙孔内部影像特征进行关联研究,发现与熔透状态直接相关的低辐射值特征现象及特征区域的存在。通过视觉辅助定位调节和熔透特征位置试验矫正等寻位方式,依次提高定位精度,直至将传感器光电感应芯片高精度定位至荧光辐射实像中的熔透特征区域。由此通过光谱透视-显微成像-介观寻位萃取的逐层光学分离方式,实现了对匙孔熔透特征数据的精准提取和最大化增强。试验结果表明,基于多种光谱及光学处理技术复合应用的大功率固体激光焊熔透特征同轴增效提取方法对激光熔透特征信号增强效果显著,可作为一种新型的高功率激光焊接熔透在线检测手段。     

Spectrophotometric Study on the Binding of Two Water Soluble Schiff Base Complexes of Mn (III) with ct-DNA

In this work, binding of two water soluble Schiff base complexes: Bis sodium (5-sulfosalicylaldehyde) o- phenylendiiminato) Manganese (III) acetate (Salophen complex) and Bis sodium (5-sulfosalicylaldehyde) 1, 2 ethylendiiminato) Manganese (III) acetate (Salen complex) with calf thymus (ct) DNA were investigated by using different spectroscopic and electrometric techniques including UV-vis, Circular dichroism (CD) and fluorescence spectroscopy, viscommetry and cyclic voltammetry (CV). Both complexes have shown a hyperchromic and a small bathochromic shift in the visible region spectra. A competitive binding study showed that the enhanced emission intensity of ethidium bromide (EB) in the presence of DNA was quenched by the addition of the two Schiff base complexes indicating that they displace EB from its binding site in DNA. Moreover structural changes in the CD spectra and an increase in the CV spectra with addition of DNA were observed. The results show that both complexes bind to DNA. The binding constants have been calculated using fluorescence data for two complexes also K_b was calculated with fluorescence Scatchard plot for Salophen. Ultimately, the experimental results show that the dominant interactions are electrostatic while binding mode is surface binding then followed by hydrophobic interactions in grooves in high concentration of complexes.     

Fluorescence Study of DNA–Dye Complexes Using One-Photon and Two-Photon Picosecond Excitation

Preliminary results of investigation of one-photon- and two-photon-induced fluorescence of acridine orange (AO), epirubicin (ER), hypericin (HYP), and ethidium bromide (EB) in complexes with DNA are presented. A spectrofluorometer based on a picosecond Nd:YAG laser was used for investigations of two-photon (1064-nm, 1-mJ, 40-ps) and one-photon (532- and 355-nm) dye excitation. The spectra of two-photon-induced fluorescence of dyes and their complexes with DNA as well as the kinetics of dyes' fluorescence intensification during their interactions with DNA in dependence on the biomacromolecule concentration were obtained. The intensities of AO, HYP, and EB fluorescence were increased 2.4, 3.2, and 8 times, respectively, after binding with DNA at two-photon excitation, while at one-photon excitation the corresponding values were 2.5, 3.7, and 10 times. The difference in fluorescence enhancement during DNA–dye complex formation at linear and nonlinear excitation may possibly be associated with the fact that the cross sections of one-photon and two-photon absorption, in general, change unequally during the binding of dyes to organic molecules and bathocromic shift of the electronic transitions. It was shown that the peak of AO fluorescence shifted to a longer wavelength on 10 nm after two-photon excitation at 1064 nm in comparison with one-photon excitation at 532 nm.