Spectroscopic Properties of Fluorescein and Rhodamine Dyes Attached to DNA

We report the spectroscopic properties of fluorescein, x-rhodamine, tetramethyl-rhodamine, attached to single strand, duplex DNA, and to the digestion products by DNAse I. The properties reported include: molar absorptivity, quantum yield, absorbance and fluorescence spectra, fluorescence lifetime, intrinsic lifetime (τ⁰), static quenching (S) and the Förster critical distances (R₀) between fluorescein and x-rhodamine or tetramethyl-rhodamine (acceptors). These spectroscopic properties depend strongly on the local dye environment. Fluorescein was studied: (1) attached to biotin (BF), (2) BF bound to avidin; and attached to two positions in DNA. X-rhodamine and tetramethyl-rhodamine were studied as free dyes and attached at the 5′-end of DNA. We propose a general method to determine the molar absorptivity and τ⁰ of a dye attached to DNA based on the reaction of a biotinylated and dye-labeled oligomer with standardized avidin. The molar absorptivity of a second dye attached to a DNA duplex can be obtained by comparing spectra of doubly and singly labeled sequences. S, arising from dye–DNA interactions can then be determined. R₀ for free and attached dyes showed differences from 1.1 to 4.2 Å. We present evidence for the direct interaction of dyes attached to the termini of various single-stranded DNA sequences.     

Tetrahydrofuran Activates Fluorescence Resonant Energy Transfer from a Cationic Conjugated Polyelectrolyte to Fluorescein‐Labeled DNA in Aqueous Media

A cationic water‐soluble conjugated polyelectrolyte, poly[9,9‐bis(6′′‐(N,N,N‐trimethylammonium)hexyl)fluorene‐co‐alt‐2,5‐bis(6′‐(N,N,N‐trimethylammonium)hexyloxyphenylene) tetrabromide], was synthesized. Fluorescence resonant energy transfer (FRET) experiments between the polymer and fluorescein‐labeled single‐stranded DNA (ssDNA‐Fl) were conducted in aqueous buffer and THF/buffer mixtures. Weak fluorescence emission in aqueous buffer was observed upon excitation of the polymer, whereas addition of THF turned on the fluorescence. Fluorescence self‐quenching of ssDNA‐Fl in the ssDNA‐Fl/polymer complexes as well as electron transfer from the polymer to fluorescein may account for the low fluorescence emission in buffer. The improved sensitization of fluorescence by the polymer observed in THF/buffer could be attributed to the weaker binding between the polymer and ssDNA‐Fl and a decrease in dielectric constant of the solvent mixture, which disfavors electron transfer. THF‐assisted signal sensitization was also observed for the polymer and fluorescein‐labeled double‐stranded DNA (dsDNA‐Fl). These results indicate that the use of cosolvent provides a strategy to improve the detection sensitivity for biosensors based on the optical amplification provided by conjugated polymers.     

A cationic tetrahedral chromophore for amplified DNA detection

The tetrahedral cationic chromophore, tetrakis [4-(9,9-bis(6′-(N,N,N-trimethylammonium)hexyl)-2-fluorenyl)phenyl]methane (1) shows better fluorescence resonance energy transfer (FRET) to the fluorescein (Fl) attached to the 5′-terminus of double-stranded DNA (dsDNA-Fl) as compared to the linear oligomers 2 and 3 and also provides efficient DNA hybridization detection.     

Syntheses of Novel Triphenylene-Aminoanthraquinone Dimers and Studies on Their Mesomorphic and Fluorescence Properties

Two novel triphenylene-aminoanthraquinone dimers 4a and 4b were synthesized by reacting triphenylene carboxyl derivatives 3a or 3b with 2-aminoanthracene-9,10-dione in yields of 80% and 78%, respectively. Their structures were confirmed by ¹H NMR, electrospray ionization (ESI-MS), and elemental analysis. Their mesomorphic properties were studied by diffraction scanning calorimetry (DSC), polarizing optical microscopy (POM), and x-ray diffraction (XRD). The mesomorphic results suggested that they possess excellent mesophase properties. The investigation of fluorescence properties indicated that the strong cooperating fluorescence actions exist between two structural units. The fluorescence of dimers 4a and4b are seriously quenched due to the electron transfer from donor (triphenylene unit) to acceptor (aminoanthraquinone unit).     

Phthalocyanines formed from several precursors: synthesis,characterization, and comparative fluorescence and quinone quenching

Abstract

We have synthesized a new phthalonitrile with different substituents in 4- and 5-positions (1). Cyclotetramerization of 1 yielded phthalocyanines with cobalt(II) (2), zinc(II) (3), gallium(III)chloride (4), and indium(III)chloride (5) containing diethylamino-phenoxy and hexylsulfanyl substituents on each benzene unit. Elemental analyses, Fourier transform infrared spectra, ¹H-nuclear magnetic resonance spectra, mass spectra, and ultraviolet-visible spectra were used for characterization of the phthalocyanines. The aggregation behavior of the zinc phthalocyanine derivative was studied in different concentrations. Also four chloro and four diethyllaminophenoxy substituted zinc phthalocyanine (6) and octa-diethylaminophenoxy substituted zinc phthalocyanine (7) were synthesized. These phthalocyanines (3, 6, and 7) were compared for electronic absorption spectra, fluorescence quantum yields, fluorescent lifetimes, and fluorescence quenching in the presence of benzoquinone. The fluorescence quantum yield gives the efficiency of the fluorescence process. The fluorescence lifetime is an important parameter for practical applications of fluorescence such as fluorescence resonance energy transfer and fluorescence-lifetime imaging microscopy.     

DNA interactions,photocleavage, and cytotoxicity of fluorescein–porphyrinatozinc complexes with different lengths of links

Three fluorescein–porphyrinatozinc complexes Zn(Fl-PPTPP) (1) (Fl-PPTPp?=?5-(4-fluoresceinpropyloxy)phenyl-10,15,20-triphenylporphyrin), Zn(Fl-HPTPP) (2) (Fl-HPTPp?=?5-(4-fluoresceinhexyloxy)phenyl-10,15,20-triphenylporphyrin) and Zn(Fl-DPTPP) (3) (Fl-DPTPp?=?5-(4-fluoresceindecoxy)phenyl-10,15,20-triphenylporphyrin) have been synthesized and characterized by elemental analysis, IR, UV/Vis, Electrospray mass spectra, and ¹H NMR. The DNA-binding behaviors of these complexes with calf-thymus DNA (CT-DNA) were investigated by UV–vis absorption titration, fluorescence spectra, viscosity measurements, thermal denaturation, and circular dichroism. The results suggest that 1, 2, and 3 interact with CT-DNA by intercalation, and the conformation of fluorescein–porphyrin hybrids is an important factor affecting the DNA-binding affinities. The DNA-binding affinities (K _b values) follow the order 1?>?2?>?3. In addition, their photocleavage reactions with pBR322 supercoiled plasmid DNA were investigated by gel electrophoresis. All complexes exhibit significant DNA cleavage activity. These complexes have cytotoxic activities against myeloma cell (Ag8.653) and gliomas cell (U251) lines. Complex 1 was the most potent antitumor agent among the three complexes.     

Quantitative distance information on protein-DNA complexes determined in polyacrylamide gels by fluorescence resonance energy transfer

In polyacrylamide gels, we have quantitatively determined Forster transfer (fluorescense resonance energy transfer, FRET) between two fluorescent dyes attached to DNA in protein-DNA complexes. The donor-dye fluorescein labeled to DNA retains its free mobility in the polyacrylamide gel, however, its fluorescence properties change. The different quantum yield of fluorescein in the gel is found to be independent of the gel concentration and can thus be quantitatively taken into account by a reduced Forster distance R0 of 46 A compared to 50 A in solution. We have determined global structural properties of two proteins binding to double-labeled DNA using a novel gel-based fluorescence resonance energy transfer assay. In polyacrylamide gels we have analyzed the binding of integration host factor (IHF) and the high mobility group protein NHP6a to their substrate DNA. The measured Forster transfer efficiency allows us to deduce information on the overall shape and the DNA bending angle in the complex.     

A Micellar Complex of a Conjugated Polyelectrolyte for Efficient FRET to Dye‐Labeled DNA

A polymer–surfactant micellar complex has been studied as a fluorescence resonance energy transfer (FRET) donor to fluorescein‐labeled DNA (ssDNA‐Fl). In water, the molar absorptivity and fluorescence quantum efficiency of cationic poly(fluorene‐co‐phenylene) (c‐PFP) are substantially increased in the presence of non‐ionic surfactants. A TEM microscopic study shows the formation of a nanowire micellar complex of c‐PFP and the surfactants. About a 400% enhancement of the FRET signal is measured in c‐PFP/ssDNA‐Fl with Brij 30, relative to that without surfactants. The signal amplification is successfully modulated using different types of non‐ionic surfactants which perturb the complexation, fine‐structure of the complex (i.e., donor‐acceptor separation), and the resulting energy transfer process.

     

Copper-cysteamine nanoparticles encapsulating fluorocoumarin silicon(IV) phthalocyanines: synthesis,characterization, and photophysical properties

Abstract

Three nanohybrid materials (FCSiPc@PEG-Cu-Cy) using poly (ethylene glycol) copper-cysteamine (PEG-Cu-Cy) nanoparticles as a carrier to load three fluorocoumarin silicon(IV) phthalocyanines (FCSiPcs) were prepared. The morphologies of these nanohybrids were characterized by transmission electron microscopy (TEM). The interactions between PEG-Cu-Cy nanoparticles and three FCSiPcs were studied by UV/Vis and fluorescence spectroscopic methods. The photophysical and photochemical properties of these FCSiPcs were influenced by PEG-Cu-Cy nanoparticles and exhibited substituents dependent of phthalocyanines in nanohybrids. The fluorescence resonance energy transfer (FRET) occurred from FCSiPcs (donors) to PEG-Cu-Cy nanoparticles (acceptors). These nanohybrids may be potential photosensitizers for photodynamic therapy.     

Interaction of Fluorescein with Felodipine: A Spectrofluorometric and Thermodynamic Study

The interaction between fluorescein and felodipine (FLD) was investigated by the spectrofluorometric method. The fluorescence of FLD was quenched by fluorescein and quenching is in accordance with the Stern-Volmer relation. The binding constants of fluorescein with FLD were obtained at different temperatures. The binding constant and number of binding sites at different temperatures were calculated yielding the corresponding thermodynamic parameters ΔS, ΔH and ΔG. The distance r between the donor (FLD) and acceptor (fluorescein) molecules was obtained according to the fluorescence resonance energy transfer. The optimum conditions for the fluorometric determination of fluorescein were studied and the quenching method was successfully applied to estimate the fluorescein concentration of the pharmaceutical sample directly.     

Fluorescence Logic‐Signal‐Based Multiplex Detection of Nucleases with the Assembly of a Cationic Conjugated Polymer and Branched DNA

An energy‐transfer cascade is generated from a cationic conjugated polymer (PFP) and negatively charged, Y‐shaped DNA labeled with three dyes at its termini (fluorescein (Fl), Tex Red, and Cy5). Multistep fluorescence resonance energy transfer regulates the fluorescence intensities of PFP and the dyes. Different types of logic gates can be operated by observing the emission wavelengths of different dyes with multiplex nucleases as inputs.

     

Regioselective E(trans)-Z(cis) photoisomerization in naphthyldiene derivatives

Naphthyldiene derivatives,1-4, carrying electron-donating groups at one end and electron-withdrawing groups at the other, were synthesized to study the photoisomerization process. All the compounds showed efficient photoisomerization upon direct excitation leading to the formation of 4-Z isomer with high selectivity. Triplet sensitization studies indicated inefficientE-Z isomerization process. Room temperature fluorescence of1 and2 displayed fine structure in hexane solvent and the same was replaced by broad or structureless fluorescence in acetonitrile and methanol solvents. A mechanism involving a polarized or charge transfer singlet excited state is proposed for the observed photoisomerization in these naphthyldiene derivatives.     

Reduction of tellurite and deesterification of fluorescein diacetate are not well correlated with the viability of mycobacteria

Both Mycobacterium leprae and M. lepraemurium (MLM) were capable of reducing tellurium as tellurite ion (Te⁴⁺) to elemental tellurium (Te), seen by electron microscopy as fine crystals within the bacterial cells. There appeared to be close correspondence between the capacity to reduce tellurite, bright green fluorescence after staining with fluorescein diacetate (FDA) and the ability of M. smegmatis to multiply in culture. Likewise, there appeared to be correspondence between tellurite reduction and fluorescence after FDA staining for MLM subjected to prolonged storage in the cold or to heating at 70°C. However, correspondence with tellurite-reduction or fluorescence after FDA staining was not observed when death of MLM occured     

Fluorescence properties of fluorescein, tetramethylrhodamine and Texas Red linked to a DNA aptamer

We report the picosecond time-scale fluorescence dynamics of a dye-labeled DNA oligonucleotide or "aptamer" designed to bind specifically to Immunoglobulin E. Comparison of the photophysics of Texas Red (TR), fluorescein and 5'-carboxytetramethylrhodamine (TAMRA)-labeled aptamers reveals surprising differences with significant implications for measurements of oligonucleotide structure and dynamics. The fluorescence decay of the TR-aptamer is a simple single exponential with a weak temperature dependence. The fluorescence decay of the fluorescein-aptamer (fl-aptamer) is pH dependent and displays a complex temperature dependence with significant changes on melting of the aptamer tertiary structure. Despite its similarities to TR, TAMRA is strongly quenched when conjugated to the aptamer and displays complex fluorescence kinetics best described by a distributed rate model. Using the maximum entropy method, we have discovered two highly temperature-dependent fluorescence lifetimes for the TAMRA-aptamer. One of these lifetimes is similar to that of free TAMRA and displays the same temperature dependence. The other lifetime is quenched and displays a temperature dependence characteristic of a charge transfer reaction. These data set TR apart as an attractive alternative to TAMRA and fluorescein for studies such as fluorescence polarization and fluorescence resonance energy transfer, where environmental sensitivity of the probe is not desired.     

Light-harvesting organogel based on tris(phenylisoxazolyl)benzene

A novel light-harvesting organogel based on tris(phenylisoxazolyl)benzene, 1, was developed. A pyrene derivative, 2, possessing four phenylisoxazole substituents, was synthesised as an energy acceptor. The electronically excited-state energy of 1 was transferred to a small portion of 2 in the gel state, whereas the photo-induced energy transfer was not observed in solution. The coassembled structures of 1 and 2, formed in the decalin gel, exhibited light-harvesting behaviour. The study on the fluorescence quantum yield revealed that one molecule of 2 accepts the excited-state energy from approximately eight molecules of 1. Time-resolved fluorescence decay experiments revealed that the fluorescence resonance energy transfer is dominant in the energy transfer process in the gel state.     

Computational studies on G-quadruplex DNA-stabilizing property of novel Wittig-based Schiff-Base ligands and their copper(II) complexes

A series of mono imine (C=N) group that contained Wittig-based Schiff-Base ligands was optimized using the DFT-based computational method and Gaussian 09 program package. These optimized molecules were docked with Quadruplex DNA (PDB ID: 1KF1) and duplex DNA (PDB ID: 1BNA) using AutoDock Vina program along with the reference molecules. Schiff-Base ligands derived from fused aromatic rings contained amines and precursor aldehyde (PA-5 both Z and E isomers) showed lower binding energy for G-quadruplex DNA among all and N-5 category both Z and E isomer Schiff-Base ligands have shown high selectivity for G-quadruplex DNA over duplex DNA which is a very important phenomenon to develop the G-quadruplex DNA stabilizers. For a few Schiff-Base molecules like Ligand-6 (1-{[2-Hydroxy-5-(2-pyren-1-yl-vinyl)-benzylidene]-amino}-naphthalen-2-ol) of N-5 category both Z and E isomers with groove binding and end stacking modes, molecular dynamic calculations were carried out. The study revealed that Ligand-6 of N-5 category E isomer with groove binding mode has higher stabilizing effect on G-quadruplex DNA in spite of having the higher binding energy value. Among Schiff-Base copper(II) complexes, Complex-3 (E-(1-{[2-Hydroxy-5-(2-pyren-1-yl-vinyl)-benzylidene]-amino}-naphthalen-2-ol)Cu) is having high binding affinity for G-quadruplex DNA as compared to others.

     

An Extractive Spectrophotometric Method for the Determination of Nitrite Using Fluorescein Amine Isomer I

ABSTRACT

A sensitive spectrophotometric method for the determination of nitrite using fluorescein amine isomer I is described. The method is based on the formation of azido derivative of fluorescein amine isomer I, which is selectively extracted into 20% iso amyl alcohol in toluene and is stripped to aqueous phase using NaOH. Formation of the azido derivative depends on nitrite concentration and the system obeys Beer's law in the range 0-0.4 ppm of nitrite at 495 nm. The molar absorptivity of the colour system is 6.67 × 10⁴ L mol^-1 cm^-1 with a relative standard deviation of 3% for 10 determinations at 1 μg of nitrite. The proposed method is successfully applied for the determination of nitrite and nitrate in soil, water and radiator coolant sample, NO₂ gas in a laboratory fume cupboard is determined after fixing it as nitrite in sodium arsenite absorber solution.     

Combinatorial Energy Transfer between an End‐Capped Conjugated Polyelectrolyte and Chromophore‐Labeled PNA for Strand‐Specific DNA Detection

We report a macromolecular end‐capping approach to improve the detection sensitivity of cationic conjugated polymer (CCP) based DNA detection. A phenylethynyl anthracene (PEA) end‐capped cationic polyfluorene (PF) derivative ( P1 ) is synthesized via Suzuki coupling. Due to efficient fluorescence resonance energy transfer (FRET) from the polymer backbone to the end‐capper PEA units, the polymer ( P1 ) fluorescence is dominated by the emission from PEA even in dilute aqueous solution. P1 emission has a better spectral overlap with fluorescein (Fl) absorption compared to that for uncapped PF ( P2 ). In addition, the intra and intermolecular energy transfer for P1 is more efficient in the presence of DNA due to complexation‐induced polymer aggregation. These impart a combinatorial FRET between P1 and an Fl‐labeled probe which is more efficient than that between P2 and the same probe. P1 thus offers a better DNA detection sensitivity relative to P2 and opens up new opportunities to improve the performance of CCP based biosensors involving FRET.

     

One Mismatch Detection of DNA Hybridization Using Fluorescence Polarization

Abstract

The potential of fluorescent polarization analysis as a method for detection of mismatch DNA hybridization was investigated. The dependency of DNA hybridization rate on salt concentration was surveyed. In greater than 0.1 M NaCl, the hybridization of probe and target DNA proceeds rapidly and the reaction is complete within 3 min. Furthermore, the hybridization of probe DNA and one mismatch target DNAs was investigated. It was successfully shown that even one mismatch could be detected using fluorescence polarization analysis if the mismatch position was on the base that pairs with the probe DNA at the 5′ terminus where fluorescein isothiocyanate (FITC) is attached.     

Photoinduced intramolecular electron transfer between fluorescein and carbazole

Several dyads consisting of a fluoreseein covalently linked with a carhazole at site 2 or site 6 have been synthesized and characterized.Studies of absorption spectra,emission spectra and fluorescence lifetime quern hing Indicate that the ground-state interaction between fluorescein and carhazole in dyads is negligible and the intramolecular electron transfer (ET) reactions are mainly of dynamic process.Moreover,the efficiency and raie conslam of lectron transfer reactions in ZFO4 (carbazole linked at site 2'of fluorescein) are larg er than those in 4FOZ (carbazole linked at site 6 of fluorescein) 0 74; KET 11×108S-1),because the mutual orientation of donor and acceptor in ZFO4 is nearly face-to-face,which is more favorable to the process than the shoulder-to-shoulder mutual orientation in 4FOZ.Estimations are also formed of the free energy change of the photomduced electron transfer and the back reactions in the dyads.