Luminescence spectroscopic studies of trimethinecyanines substituted in polymethine chain with nucleic acids and proteins

The series of symmetrical beta-substituted and alpha,gamma-substituted trimethinecyanine dyes were studied for their absorption and fluorescent characteristics in unbound state and in the presence of nucleic acids and proteins. It was shown that beta-substituted and alpha,gamma-bridged trimethinecyanines containing extended heterocyclic systems or N-phenyl as well as N-cyclohexyl substituents demonstrate increased affinity to proteins. At the same time the presence of both N-phenyl and N-cyclohexyl substituents leads to the decrease of the dye fluorescence intensity in complexes with nucleic acids. For trimethinecyanines similarly to unsymmetrical monomethines the presence of N-omega-hydroxy alkyl substituents results in the increase of fluorescence intensity of dye-DNA complex and the emission decrease of dye-RNA complex.     

Interaction of cyanine dyes with nucleic acids. XVIII. Formation of the carbocyanine dye J-aggregates in nucleic acid grooves.

Spectral properties of carbocyanine dye 3-methyl-2-[3-methyl-2-(3-methyl-2,3-dihydro-1,3-benzothiazole-2-iliden)-1- butenyl]-1,3-benzothiazole-3-il iodide (Cyan betaiPr) in water solution, as well as in the presence of different types of double stranded DNA have been studied. While in water solution of 'free' dye Cyan betaiPr stays mainly in monomeric form, in the presence of DNA the dye molecules form J-aggregates. The molecular structure of these J-aggregates causes the Davydov splitting of their absorption band, corresponding to the first electronic transition. A study of site-specificity showed that in the presence of poly (dA/dT) the majority of Cyan betaiPr molecules form J-aggregates, while in the presence of poly (dGC/dGC) dye molecules stay mainly in monomeric form and in presence of chicken erythrocytes DNA both J-aggregate and monomeric forms of dye are present. We suppose that Cyan betaiPr molecules aggregate in DNA groove, which serves as a template for J-aggregate forming. An increase of ionic strength of solution leads to the release of dye molecules from DNA grooves and prevents J-aggregates formation.     

Interaction of cyanine dyes with nucleic acids. XVII. Towards an aggregation of cyanine dyes in solutions as a factor facilitating nucleic acid detection

Spectral properties of newly synthesized cyanine dyes, namely 1-[6-(4-[6-[2,6-dimethyl-4-(3-methyl-2,3-dihydro-1,3-benzothiazol- 2-ylidenmethyl)-1-pyridiniumyl]hexanoyl]piperazino)-6- oxohexyl]-2,6-dimethyl-4-(3-ethyl-2,3-dihydro-1,3-benzothiazol+ ++-2-ylidenmethyl)pyridinium (K-6) (bichromophoric dye) and 1-[5-di(3-[5-[2,6-dimethyl-4-(3-methyl-2,3-dihydro-1,3-benzothiazol++ +-2-ylidenmethyl)-1-pyridiniumyl]pentylcarboxamido]pro pyl) carbamoylpentyl]-2,6-dimethyl-4-(3-methyl-2,3-dihydro-1,3-benzo thiazol-2-ylidenmethyl) pyridinium (K-T) (trichromophoric dye) in solutions in the presence of and without deoxyribonucleic acid (DNA) were studied within a wide concentration range. It has been established that absorption, as well as fluorescence of investigated dye solutions, without DNA are mainly determined by H-aggregates of dye molecules. On the contrary, the fluorescence of dye solutions in the presence of DNA gives an intrinsic dye molecular fluorescence. H-aggregates are broken because of binding dye molecules with DNA. It has been suggested that both K-T and K-6 molecules bind mainly with DNA via the interaction of two chromophores. As the ratio of the number of dye molecules to that of DNA base pairs increases with an increase in dye concentration, a formation of dye molecule H-aggregates on DNA molecules are observed. Such aggregates have a different structure than those formed in the solutions without DNA. On the grounds of the data obtained, it is concluded that it is possible to use a dye aggregation capable of obtaining higher values for fluorescence enhancement of the DNA stains.     

Study of the noncovalent interaction of squarylium dyes with serum albumins

The noncovalent interaction of zwitterionic indolium squarylium dyes (hydrophilic and hydrophobic) and a structurally analogous ionic indodicarbocyanine (hydrophilic) dye with serum albumins was studied by spectral and fluorescent methods. It has been found that the hydrophilic squarylium dye with sulfonate groups most efficiently interacts with albumins, which is probably due to the double negative charge of the dye molecule at the expense of the sulfonate groups and the possibility to form hydrogen bonds with albumin. The hydrophobic squarylium dye, as well as the hydrophilic indodicarbocyanine dye without the squarylium fragment in its structure, bind with albumins much weaker than the structurally relevant hydro- philic squarylium dye. The properties of the latter dye permit us to recommend it for using as a spectral and fluorescent probe for serum albumins in extracellular media of living organisms.     

Synthesis and application of rhodamine-based fluorescent probe dyes with spacer linker arm

When rhodamine-based fluorescent probe dyes are used to track target molecules they always perturb the behavior of target molecules because of steric hindrance effect. In order to minimize potential steric problems, a kind of rhodamine-based fluorescent probe dye with spacer linker arm was designed and synthesized and its application in immunofluorescence histochemistry was investigated.     

Polymeric fluorescent dyes for labeling of proteins and nucleic acids

In order to increase the sensitivity of fluorescence labeling in biochemical reactions and diagnostic procedures a labeling technique with polymeric fluorescence dyes was established and tested for its applicability. The fluorescence dye is based on the fluorophor coumarine and was covalently linked to the model proteins strepavidine and IgG. The dye was synthesized by radical polymerization of three different types of functional monomers to ensure water solubility, covalent coupling to proteins, and fluorescence. The molecular weight range was between 20 and 200 kDa. Fractions of narrow molecular weight distribution were prepared by gel filtration on Superdex 200. The relationship between size and charge of the different fractions was analyzed by gel electrophoresis. Covalent conjugation to proteins was carried out by formation of a peptide bond between a carboxylic group of the functional monomers and an amino group of the protein mediated by 1-ethyl-3-(3-dimethylamino-propyl)-carbodiimide (EDC). A novel type of gel electrophoresis was developed in order to analyze and optimize the conjugation reaction; the results were in agreement with those from analytical ultracentrifugation with fluorescence detection. Hydrodynamic studies of the uncoupled dye and the protein-dye conjugates exhibited a drastic decrease of Stokes radius of the dye due to the coupling to the protein. Under optimum conditions the fluorescence intensity of a protein-polymeric dye conjugate was enhanced 40-fold compared to a monomeric dye. Biotin binding to the protein streptavidin was not affected significantly by the conjugation with the polymeric dye. At present, the applicability of the polymeric dye in biochemical and diagnostic reactions seems to be limited due to strong but unspecific hydrophobic interactions which might be overcome by using fluoresceine as monomeric dye.     

Interactions of cyanine dyes with nucleic acids. XXIV. Aggregation of monomethine cyanine dyes in presence of DNA and its manifestation in absorption and fluorescence spectra.

Absorption, fluorescence emission and excitation spectra of benzothiazole cyanine dyes--thiazole orange (TO) and 7-methyl-6-(3-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidenmethyl) [1,3] dioxolo [4',5':4,5] benzo [d] [1,3] thiazolium methylmethosulfate (Cyan 13)--were investigated over a wide concentration range. The dyes form aggregates with a 'sandwich'-like structure in water solution. At low dye to DNA concentrations ratios, Cyan 13 and TO monomers appear to interact with the DNA. On increasing the dye to DNA concentrations ratio, free dye molecules aggregate with the DNA-bound ones. The spectra of the free dye aggregates and the aggregates formed on the DNA, are characterized by an anomalously large (more than 100 nm) Stokes shift. This suggests, that the pi-electron systems of the aggregates undergo substantial changes in excited state, compared to those of the monomers. The formation of aggregates consisting of the free and DNA-bound dye molecules can be explained using the half-intercalation model of the interaction of the cyanine dye monomers with the DNA.     

Towards a fluorescent molecular switch for nucleic acid biosensing

A novel fluorescent molecular switch for the detection of nucleic acid hybridization has been explored in relation to the development of a structure that would be amenable for operation when immobilized for solid-phase analyses. The structure was prepared by self-assembly, and used Neutravidin as the central multivalent docking molecule, a newly synthesized biotinylated long-chain linker for intercalating dye that was modified with thiazole orange (TO) at one end, and a biotinylated probe oligonucleotide. Self-assembly of the biotinylated components on adjacent Neutravidin binding sites allowed for physical placement of an oligonucleotide probe molecule next to tethered TO. The TO located at the end of the flexible linker chain was available to intercalate, and could report if a duplex structure was formed by a probe–target interaction by means of fluorescence intensity. Subsequently, regeneration of the single-stranded probe was possible without loss of the intercalator to solution. The switch constructs were assembled in solution and subsequently immobilized onto biotin functionalized optical fibers to complete the sensor design. Solution-phase fluorescence lifetime data showed a biexponential behavior for switch constructs, suggesting intercalation as well as a significant secondary binding mode for the immobilized TO. It was found that the secondary binding mechanism for the dye to DNA could be decreased, thus shifting the dye to intercalative binding modes, by adjusting the solution conditions to a pH below the pI of Neutravidin, and by increasing the ionic strength of the buffer. Preliminary work demonstrated that it was possible to achieve up to a fivefold increase in fluorescence intensity on hybridization to the target.     

Interaction of cyanine dyes with nucleic acids: XXVI. Intercalation of the trimethine cyanine dye cyan 2 into double-stranded DNA: study by spectral luminescence methods

The interaction between double-stranded (ds) DNA and the cyanine dye Cyan 2 has been studied with spectral luminescence methods. Binding constant values have been determined by fluorescence titration and dye distribution in the two-phase system ethyl acetate-water (3.6 x 10(4) and 1.5 x 10(4) M(-1), respectively). Cyan 2 exhibits a small specificity for guanine-cytosine (GC) sequences in total DNA and synthetic polydeoxynucleotides poly(dA/dT) and poly(dGdC/dGdC). The DNA complexes with Cyan 2 are stable at high-ionic strength solution when NaCl is added. The dye molecule complexed with DNA is apparently shielded from the anionic quencher--iodide ion. The negative linear dichroism of the visible absorption band of aligned Cyan 2-DNA complexes indicates that the bound dye lies almost perpendicularly to the DNA helix axis. The linear dichroism of the absorption band at 260 nm suggests a considerable change in the DNA B-form. The results are consistent with an intercalative binding interaction between Cyan 2 and ds DNA.     

2'-Ribose-ferrocene oligonucleotides for electronic detection of nucleic acids

We have synthesized two novel phosphoramidites with a ferrocenyl moiety at the 2'-ribose position linked through a butoxy linker. Using automated DNA/RNA synthesis techniques, oligonucleotides containing ferrocene at various positions were prepared and characterized by HPLC, MALDI-TOF mass spectrometry, and electrochemistry. Thermal stability studies of the ferrocene-modified DNA duplexes revealed that introduction of one or two ferrocenyl complexes does not result in an observed change of the T(m) values of the corresponding DNA duplexes when compared to the nonmodified hybrids. These data indicate that the introduction of a ferrocenyl group at the 2'-position of the ribose ring containing either a purine or pyrimidine base has no effect on the stability of the modified DNA. The electrochemical behavior of the ferrocene-containing DNA was examined by cyclic voltammetry. The modified 2'-ferrocene-oligonucleotides are electrochemically active and can be used as signaling probes for the electronic detection of nucleic acids on bioelectronic sensors.     

Studies on the structural transitions and self-organization behavior of polyacrylic acids with complementary polymers in aqueous solution by laser flash photolysis method using the triplet state of covalently bound phenosafranine

The conformational transition of polyacrylic acids and the formation of interpolymer complexes with synthetic polymers in aqueous solution are investigated using the triplet state of the cationic dye phenosafranine covalently attached to the polymer chain. Laser excitation of the phenosafranine dye covalently bound to polymethacrylic acid at 532 nm shows that the absorption spectrum of the triplet state shifts to red region by 40 nm as compared to that of the free dye in aqueous solution and the triplet state lifetime is enhanced by 20-fold. Laser flash excitation shows that the environment of the triplet state of the dye bound to the polyelectrolyte at pH ?5.5 in aqueous solution is more rigid and less polar resulting in a highly compact globular nature of the polymer. The decay of the triplet state of the dye bound to the polymer is attributed to the quenching of the excited state by the carboxylate groups of polyacrylic acids and to the decay process of the triplet in the tightly coiled polymer environment in the pH range 2.0–5.0. The spectra of the triplet dye molecules bound to the polymer at different degree of ionization of the polyelectrolyte suggest that the structural transition from compact globular structure to stretched rod like structure is cooperative involving a series of structural transitions. The observation of diprotonated triplet state of the PMAA bound dye at higher pH (i.e. pH ∼7.0) reveals the existence of an intermediate structure akin to a micellar segment in PMAA prior to the formation of elongated linear chain. The self-organization of PMAA adduct formation with complementary macromolecules, PVP, PEO and PVA primarily due to hydrogen bonding makes the environment of the dye in the adduct more compact and rigid; in particular poly(vinylpyrrolidone), PVP, has the tendency to form more compact interpolymer complex at pH 4.5 than poly(vinyl alcohol), PVA, and poly(ethylene oxide), PEO as revealed from the laser flash photolysis studies of the polymer bound dye using triplet state of the phenosafranine as the marker.     

Side chain homologation of alanyl peptide nucleic acids: pairing selectivity and stacking

Alanyl peptide nucleic acids (alanyl-PNAs) are oligomers based on a regular peptide backbone with alternating configuration of the amino acids. All side chains are modified by covalently linked nucleobases. Alanyl-PNAs form very rigid, well defined, and linear double strands based on hydrogen bonding of complementary strands, stacking, and solvation. Side chain homology was examined by comparing a methylene linker (alanyl-PNA) with an ethylene linker (homoalanyl-PNA), a trimethylene linker (norvalyl-PNA), and PNA sequences with mixed linker length between nucleobase and backbone. Side chain homology in combination with a linear double strand topology turned out to be valuable in order to selectively manipulate pairing selectivity (pairing mode) and base pair stacking.     

Effect of polymer binding on the spectroscopic properties of stilbene-based fluorescent dyes

Studies utilizing absorption and emission spectrophotometry have been carried out to observe the effect of various polymer substrates on the spectral characteristics of several stilbene-based fluorescent dyes. Poly(vinyl alcohol), cellulose acetate, cellulose fiber, and bovine serum albumin were used as substrates for two common fluorescent whitening agents and for two model compounds. Binding of these molecules to polymers leads to a marked red shift in the absorption spectra and an increase in vibrational structure. These effects are attributed to an increase in molecular planarity induced by the polymer environment. For the case of bovine serum albumin, it is concluded that the dye molecules bind to the protein largely through electrostatic interaction involving the dye sulfonate groups. The spectral characteristics of the dye molecules on wool fibers are interpreted in light of these results.     

The intercalation of ethidium bromide in the chromonic lyotropic phases of drugs and nucleic acids

Chromonic liquid crystalline phases are formed by a variety of drug and dye/water systems. In contrast to conventional lyotropic phases (where micelle formation underlies the mesogenic properties), in chromonic systems the molecules stack in columns. The different chromonic phases are different arrangements of these columns. We have examined the solution of ethidium bromide (EB) in the well-documented chromonic Intal/water system. EB is a widely used nucleic acid stain which changes colour when intercalated into DNA and which becomes fluorescent.

We have charted the changes in the temperature/composition phase diagram of the Intal/water system caused by adding EB. Although there are changes in the position of the phase boundaries, the overall pattern remains qualitatively the same—implying that the host phase is accepting EB as a similar chromonic molecule. The intercalation of EB molecules in the chromonic host phase results in optical effects—a metachromic colour change and fluorescence, similar to those occurring when the dye stains DNA.

These observations strengthen our belief that the central stack of bases in DNA can be regarded as being chromonic in nature.     

Probing binding preferences of DNA and RNA: backbone chirality of thioacetamido-linked nucleic acids and iso-thioacetamido-linked nucleic acids to differentiate DNA versus RNA selective binding

Subtle differences in RNA and DNA duplex geometry could be sensed by the changed stereochemistry at 3'-amino function in the 5-atom thioacetamido linker of thioacetamido-linked nucleic acids and iso-thioacetamido-linked nucleic acids modified oligomers. In contrast to the preferred N-type sugar conformations for either 3'- ribo- or xylo amino nucleosides, predominant S-type sugar conformations were found in the dimers. Although the CD spectral differences for the dimer blocks were found to be identical for those found in phosphodiester linked ribo/xylo dimers, the 5-atom thioactamido linker could reverse the RNA binding selectivity to DNA binding selectivity by the change in configuration at the 3'-amino-substituted sugar.     

Properties of nucleic acid staining dyes used in gel electrophoresis

Nucleic acid staining dyes are used for detecting nucleic acids in electrophoresis gels. Historically, the most common dye used for gel staining is ethidium bromide, however due to its toxicity and mutagenicity other dyes that are safer to the user and the environment are preferred. This Short Communication details the properties of dyes now available and their sensitivity for detection of DNA and their ability to permeate the cell membrane. It was found that GelRed? was the most sensitive and safest dye to use with UV light excitation, and both GelGreen? and Diamond? Nucleic Acid Dye were sensitive and the safer dyes using blue light excitation.     

A 2,7-carbazole-based dicationic salt for fluorescence detection of nucleic acids and two-photon fluorescence imaging of RNA in nucleoli and cytoplasm

A new carbazole-derived dicationic compound, namely 2,7-bis(1-hydroxyethyl-4-vinylpyridinium iodine)-N-ethylcarbazole (2,7-9E-BHVC), with a large two-photon action absorption cross section in nucleic acids has been obtained. Moreover, it possesses the potential of imaging RNA in nucleoli and cytoplasm in two-photon fluorescence microscopy and exhibits good counterstain compatibility with the commercial fluorescent nucleic dye DAPI.     

Complexes of nucleolipid liposomes with single-stranded and double-stranded nucleic acids

We report on the association of anionic liposomes from POP-Ade:POPC (1-palmitoyl-2-oleoyl-phosphatidyladenosine and 1-palmitoyl-2-oleoyl-phosphatidylcholine, respectively) with single- and double-strand nucleic acids, mediated by Ca(2+) bridging. The structural and dynamical features of such complexes are compared with those displayed when the nucleolipid is replaced by POPG (1-palmitoyl-2-oleoyl-sn-phosphatidyl-glycerol), characterized by the same apolar skeleton and negative charge as POP-Ade, but lacking the nucleic polar head. For single-stranded nucleic acids, we demonstrate that specific interactions drive the formation of complexes with nucleolipid liposomes, while no association is present for POPG-based samples. For double-stranded nucleic acids, Ca(2+) bridging promotes association with both liposomal formulations, but the corresponding complexes have different structural features, in terms of size, overall charge and internal liquid-crystalline structure.     

Reactions of excited states of phenoxazin-3-one dyes with amino acids

The interaction with amino acids of the excited states of the N-oxide resazurin and its deoxygenation product resorufin, has been studied in aqueous solution at pH 7.5. Steady-state and time-resolved studies show that the fluorescence is quenched by amino acids. Complexation of the dyes in the ground state with aromatic amino acids was also observed. The singlet quenching is attributed to electron transfer from the amino acids to the excited dye based on the dependence of the bimolecular rate constants with the ionization potential of quenchers. Flash photolysis experiments allowed determination of the quenching rate constants for the triplet deactivation of dyes by several amino acids, as well as the characterization of the transients formed in the process. These data show that the triplet is also deactivated by an electron transfer process. However, the deactivation of the N-oxide dye by tryptophan can be described by a hydrogen atom transfer. The protolytic dissociation constants of the dye radical ions are reported. The irradiation of rezasurin in the presence of amino acids leads to deoxygenation of the dye to give resorufin. This process involves the triplet excited state of resazurin and is efficient only in the presence of amino acids containing the -SH group.     

New asymmetric monomethine cyanine dyes for nucleic-acid labelling: absorption and fluorescence spectral characteristics

Absorption spectra and fluorescence properties of a series of newly synthesized asymmetric monomethine cyanine dyes are studied. The dyes carry one or two positive charges. They are devoid of their own fluorescence in solution and become fluorescent upon binding to nucleic acids only. The fluorescence maxima of the new dyes are localized between 530 and 650 nm. The wavelength and intensity of fluorescence are dependent on molecular structure of the dye, type of nucleic acid and the concentration of both nucleic acid and salts. Some of the dyes are capable of distinguishing between single-stranded and double-stranded (ds) polynucleotides giving fluorescence maxima localized at different wavelengths. Detection threshold for dsDNA for most of the dyes is comparable to that of ethidium bromide. The sensitivity of the dye-dsDNA complexes to NaCl concentrations show that the new dyes interact with dsDNA by both intercalation and electrostatically.