Synthesis and fluorescence properties of dimethylaminonaphthalene-deoxyuridine conjugates as polarity-sensitive probes

The design of probes for monitoring various structures and dynamics of DNA and its surroundings is an important step in understanding biological events accompanying interbiomolecular interaction. We have developed novel fluorescent nucleosides in which the uracil base and the fluorophore are tethered by rigid linkers. They show unique absorption and fluorescence emission spectra. Nucleoside 2 is a fluorophore with high CT character and the fluorescence is very sensitive to solvent polarity. Nucleoside 3 shows absorption and emission maxima with longer wavelength due to extension of the DAN-conjugate system. These fluorophore-deoxyuridine conjugates with unique fluorescence properties would work as reporter probes sensitive to the change in microenvironment around specific sites of DNA.     

Photoinduced intramolecular charge transfer and S2 fluorescence in thiophene-pi-conjugated donor-acceptor systems: experimental and TDDFT studies

Experimental and theoretical methods were used to study newly synthesized thiophene-pi-conjugated donor-acceptor compounds, which were found to exhibit efficient intramolecular charge-transfer emission in polar solvents with relatively large Stokes shifts and strong solvatochromism. To gain insight into the solvatochromic behavior of these compounds, the dependence of the spectra on solvent polarity was studied on the basis of Lippert-Mataga models. We found that intramolecular charge transfer in these donor-acceptor systems is significantly dependent on the electron-withdrawing substituents at the thienyl 2-position. The dependence of the absorption and emission spectra of these compounds in methanol on the concentration of trifluoroacetic acid was used to confirm intramolecular charge-transfer emission. Moreover, the calculated absorption and emission energies, which are in accordance with the experimental values, suggested that fluorescence can be emitted from different geometric conformations. In addition, a novel S(2) fluorescence phenomenon for some of these compounds was also be observed. The fluorescence excitation spectra were used to confirm the S(2) fluorescence. We demonstrate that S(2) fluorescence can be explained by the calculated energy gap between the S(2) and S(1) states of these molecules. Furthermore, nonlinear optical behavior of the thiophene-pi-conjugated compound with diethylcyanomethylphosphonate substituents was predicted in theory.     

Phenylene alkylene dendrons with site-specific incorporated fluorescent pyrene probes

This report deals with the synthesis and the spectroscopic properties of two second generation (G2) dendrons with site-specific incorporated phenyl pyrene derivatives as solvatochromic fluorescent probes. The generations that do not carry the probe are equipped with volume dummies, pyrene moieties that do not show a solvatochromic effect. Two complementary G2 phenylene alkylene dendrons were synthesized using Suzuki-Miyaura cross coupling. Most of the reactions used in the 10-step sequence generating the target compounds proceeded in good yields. The incorporated probes can be selectively photoexcited and show solvatochromic shifts that are of the same magnitude as for the free probes in a homogeneous solvent environment. In addition to the charge-transfer fluorescence, a broad emission band is observed that is assigned to an intramolecular exciplex formation between the aryl pyrene chromophores.     

Solvent and Media Effects on the Photophysics of Naphthoxazole Derivatives

The photophysical properties of 2‐phenyl‐naphtho[1,2‐d][1,3]oxazole, 2(4‐N,N‐dimethylaminophenyl)naphtho[1,2‐d][1,3]oxazole and 2(4‐N,N‐diphenylaminophenyl) naphtho[1,2‐d][1,3]oxazole were studied in a series of solvents. UV–Vis absorption spectra are insensitive to solvent polarity whereas the fluorescence spectra in the same solvent set show an important solvatochromic effect leading to large Stokes shifts. Linear solvation energy relationships were employed to correlate the position of fluorescence spectra maxima with microscopic empirical solvent parameters. This study indicates that important intramolecular charge transfer takes place during the excitation process. In addition, an analysis of the solvatochromic behavior of the UV–Vis absorption and fluorescence spectra in terms of the Lippert–Mataga equation shows a large increase in the excited‐state dipole moment, which is also compatible with the formation of an intramolecular charge‐transfer excited state. We propose both naphthoxazole derivatives as suitable fluorescent probes to determine physicochemical microproperties in several systems and as dyes in dye lasers; consequence of their high fluorescence quantum yields in most solvents, their large molar absorption coefficients, with fluorescence lifetimes in the range 1–3 ns as well as their high photostability.     

Synthesis and Photophysical Properties of a Series of Cyclopenta[b]naphthalene Solvatochromic Fluorophores

The synthesis and photophysical properties of a series of naphthalene-containing solvatochromic fluorophores are described within. These novel fluorophores are prepared using a microwave-assisted dehydrogenative Diels-Alder reaction of styrene, followed by a palladium-catalyzed cross coupling reaction to install an electron donating amine group. The new fluorophores are structurally related to Prodan. Photophysical properties of the new fluorophores were studied and intriguing solvatochromic behavior was observed. For most of these fluorophores, high quantum yields (60-99%) were observed in methylene chloride in addition to large Stokes shifts (95-226 nm) in this same solvent. As the solvent polarity increased, so did the observed Stokes shift with one derivative displaying a Stokes shift of ～300 nm in ethanol. All fluorophore emission maxima, and nearly all absorption maxima were significantly red-shifted when compared to Prodan. Shifting the absorption and emission maxima of a fluorophore into the visible region increases its utility in biological applications. Moreover, the cyclopentane portion of the fluorophore structure provides an attachment point for biomolecules that will minimize disruptions of the photophysical properties.     

Spectral properties and orientation of voltage-sensitive dyes in lipid membranes

Voltage-sensitive dyes are frequently used for probing variations in the electric potential across cell membranes. The dyes respond by changing their spectral properties: measured as shifts of wavelength of absorption or emission maxima or as changes of absorption or fluorescence intensity. Although such probes have been studied and used for decades, the mechanism behind their voltage sensitivity is still obscure. We ask whether the voltage response is due to electrochromism as a result of direct field interaction on the chromophore or to solvatochromism, which is the focus of this study, as result of changed environment or molecular alignment in the membrane. The spectral properties of three styryl dyes, di-4-ANEPPS, di-8-ANEPPS, and RH421, were investigated in solvents of varying polarity and in model membranes using spectroscopy. Using quantum mechanical calculations, the spectral dependence of monomer and dimer ANEPPS on solvent properties was modeled. Also, the kinetics of binding to lipid membranes and the binding geometry of the probe molecules were found relevant to address. The spectral properties of all three probes were found to be highly sensitive to the local environment, and the probes are oriented nearly parallel with the membrane normal. Slow binding kinetics and scattering in absorption spectra indicate, especially for di-8-ANEPPS, involvement of aggregation. On the basis of the experimental spectra and time-dependent density functional theory calculations, we find that aggregate formation may contribute to the blue-shifts seen for the dyes in decanol and when bound to membrane models. In conclusion, solvatochromic and other intermolecular interactions effects also need to be included when considering electrochromic response voltage-sensitive dyes.     

Fluorescence of size-expanded DNA bases: reporting on DNA sequence and structure with an unnatural genetic set

We recently described the synthesis and helix assembly properties of expanded DNA (xDNA), which contains base pairs 2.4 A larger than natural DNA pairs. This designed genetic set is under study with the goals of mimicking the functions of the natural DNA-based genetic system and of developing useful research tools. Here, we study the fluorescence properties of the four expanded bases of xDNA (xA, xC, xG, xT) and evaluate how their emission varies with changes in oligomer length, composition, and hybridization. Experiments were carried out with short oligomers of xDNA nucleosides conjugated to a DNA oligonucleotide, and we investigated the effects of hybridizing these fluorescent oligomers to short complementary DNAs with varied bases opposite the xDNA bases. As monomer nucleosides, the xDNA bases absorb light in two bands: one at approximately 260 nm (similar to DNA) and one at longer wavelength ( approximately 330 nm). All are efficient violet-blue fluorophores with emission maxima at approximately 380-410 nm and quantum yields (Phifl) of 0.30-0.52. Short homo-oligomers of the xDNA bases (length 1-4 monomers) showed moderate self-quenching except xC, which showed enhancement of Phifl with increasing length. Interestingly, multimers of xA emitted at longer wavelengths (520 nm) as an apparent excimer. Hybridization of an oligonucleotide to the DNA adjacent to the xDNA bases (with the xDNA portion overhanging) resulted in no change in fluorescence. However, addition of one, two, or more DNA bases in these duplexes opposite the xDNA portion resulted in a number of significant fluorescence responses, including wavelength shifts, enhancements, or quenching. The strongest responses were the enhancement of (xG)n emission by hybridization of one or more adenines opposite them, and the quenching of (xT)n and (xC)n emission by guanines opposite. The data suggest multiple ways in which the xDNA bases, both alone and in oligomers, may be useful as tools in biophysical analysis and biotechnological applications.     

Sensing metal ions with DNA building blocks: fluorescent pyridobenzimidazole nucleosides

We describe novel fluorescent N-deoxyribosides (1 and 2) having 2-pyrido-2-benzimidazole and 2-quino-2-benzimidazole as aglycones. The compounds were prepared from the previously unknown heterocyclic precursors and Hoffer's chlorosugar, yielding alpha anomers as the chief products. X-ray crystal structures confirmed the geometry and showed that the pyridine and benzimidazole ring systems deviated from coplanarity in the solid state by 154 degrees and 140 degrees , respectively. In methanol compounds 1 and 2 had absorption maxima at 360 and 370 nm, respectively, and emission maxima at 494 and 539 nm. Experiments revealed varied fluorescence responses of the nucleosides to a panel of 17 monovalent, divalent, and trivalent metal ions in methanol. One or both of the nucleosides showed significant changes with 10 of the metal ions. The most pronounced spectral changes for ligand-nucleoside 1 included red shifts in fluorescence (Au(+), Au(3+)), strong quenching (Cu(2+), Ni(2+), Pt(2+)), and substantial enhancements in emission intensity coupled with red shifts (Ag(+), Cd(2+), Zn(2+)). The greatest spectral changes for ligand-nucleoside 2 included a red shift in fluorescence (Ag(+)), a blue shift (Cd(2+)), strong quenching (Pd(2+), Pt(2+)), and substantial enhancements in emission intensity coupled with a blue shift (Zn(2+)). The compounds could be readily incorporated into oligodeoxynucleotides, where an initial study revealed that they retained sensitivity to metal ions in aqueous solution and demonstrated possible cooperative sensing behavior with several ions. The two free nucleosides alone can act as differential sensors for multiple metal ions, and they are potentially useful monomers for contributing metal ion sensing capability to DNAs.     

Solvatochromism and prototropism of diaminodiphenyl sulphones and 2-aminodiphenyl sulphone: a comparative study by electronic spectra

A comparative study of absorption and fluorescence maxima of 4,4′-diaminodiphenyl sulphone (4DADPS), 3,3′-diaminodiphenyl sulphone (3DADPS) and 2-aminodiphenyl sulphone (2ADPS) in different solvents reveals that (i) solvatochromic shifts are found to be mainly due to interaction of solvents with amino group, (ii) in any one solvent the net solvatochromic shifts of two amino groups are less than that of one amino group, (iii) fluorescence shift from cyclohexane to water is a maximum for 4DADPS and a minimum for 2ADPS and (iv) 4DADPS and 3DADPS possess more twisted intramolecular charge transfer character than 2ADPS. The excited-state acidity constants, determined by fluorimetric titration and Förster cycle methods, have been reported and discussed.     

Novel Nucleoside Analogues with Fluorophores Replacing the DNA Base

We describe the preparation and fluorescence properties of a set of new nucleosides in which a known hydrocarbon or oligothiophene fluorophore replaces the DNA base at C(1) of the deoxyribose moiety (see 3a – f ). These compounds are potentially useful as probes in the study of the structure and dynamics of nucleic acids and their complexes with proteins. In addition, they may find use as fluorescent labels for nucleic-acid-based biomedical diagnostics methods. The fluorophores conjugated to deoxyribose at C(1) in the α-D -form include terphenyl, stilbene, terthiophene, benzoterthiophene, and pyrene. Also included is a non-fluorescent spacer in which cyclohexene replaces the DNA base. The nucleosides are derived from brominated fluorophore precursors and Hoffer's 2-deoxy-3,5-di-O-(p-toluoyl)-D -ribofuranosyl chloride. The emission maxima of the free nucleosides range from 345 to 536 nm. Also described are the 5′-(dimethoxytrityl) 3′-O-phosphoramidite derivatives 5a – f , suitable for incorporation into oligonucleotides by automated synthesizers.     

Structure and fluorescence properties of merocyanine dyes derived from dimethylbarbituric acid

The fluorescence properties of positively and negatively solvatochromic di-, tetra-, and hexamethinemerocyanines derived from 1,3-dimethylbarbituric acid in solvents of various polarities were studied. The range of solvatofluorochromic effect for these compounds is narrower than the range of solvatochromic effect. Extension of the polymethine chain of these compounds causes in the fluorescence spectra, in contrast to the absorption spectra, an increase in vinylene shifts, a decrease in deviations, and band narrowing. The electronic structure of the merocyanines was analyzed by the AM1 method. Transitions between the ideal states (neutral polyene, polymethine, and charged polyene) were examined. The electronic structure of the merocyanines in the excited state was found to approach the cyanine limit. Its attainment accounts for a sharp increase in the quantum yields of the fluorescence and a decrease in the Stokes shifts in going to higher vinylogs, and also with an increase in the solvent polarity for positively solvatochromic merocyanines and with its decrease for the negatively solvatochromic derivatives.     

PRODAN-conjugated DNA: synthesis and photochemical properties

A solvatochromic fluorophore, PRODAN, has been used as a microenvironment-sensitive reporter. Based on the chemistry of PRODAN, we designed and synthesized four novel fluorescent nucleosides, PDNX (X = U, C, A, and G), to which a PRODAN fluorophore was attached at pyrimidine C5 or purine C8. The fluorescent nucleosides sensitively varied the Stokes shift values depending on the orientational polarizability of the solvent. The PDNX incorporated into DNA also changed the Stokes shift values depending on the DNA structure. In particular, the excitation spectrum of the PDNX-containing duplex shifted to a longer wavelength and gave a smaller Stokes shift value when the base opposite PDNX could form a Watson-Crick base pair with PDNX. A lower energy excitation of PDNX-containing DNA resulted in a strong fluorescence emission selective to the Watson-Crick pairing base. This unique photochemical character was applicable to the efficient typing of single-nucleotide polymorphisms of genes.     

New highly fluorescent ketocyanine polarity probes

The syntheses and spectral properties of three new and highly fluorescent solvent polarity probes are described. They are found to be extremely sensitive to solvent polarity in that spectral red shifts in both absorption and fluorescence spectra occur upon increasing solvent polarity. Excitation and emission data of the dyes in a set of different polar solvents are given. The emission data are compared with the standard ET^N values of solvent polarity and a linear correlation is obtained over a wide range. The origin of the unusual solvatochromic properties is discussed in terms of the resonance structures of this new group of molecular probes. Their outstanding features include high spectral sensitivity to polarity, high molar absorptivities, high fluorescence quantum yields, longwave excitation and emission, insignificant quenching by oxygen, and a sufficient stability in aqueous solution. Therefore, the new probes are considered to be advantageous over other polarity probes used so far in probing biochemical and biological systems.     

Anthraquinone as a redox label for DNA: synthesis, enzymatic incorporation, and electrochemistry of anthraquinone-modified nucleosides, nucleotides, and DNA

Modified 2'-deoxynucleosides and deoxynucleoside triphosphates (dNTPs) bearing anthraquinone (AQ) attached through an acetylene or propargylcarbamoyl linker at the 5-position of pyrimidine (C) or at the 7-position of 7-deazaadenine were prepared by Sonogashira cross-coupling of halogenated dNTPs with 2-ethynylanthraquinone or 2-(2-propynylcarbamoyl)anthraquinone. Polymerase incorporations of the AQ-labeled dNTPs into DNA by primer extension with KOD XL polymerase have been successfully developed. The electrochemical properties of the AQ-labeled nucleosides, nucleotides, and DNA were studied by cyclic and square-wave voltammetry, which show a distinct reversible couple of peaks around -0.4 V that make the AQ a suitable redox label for DNA.     

Hemicyanine-linked pyrimidine mimics as solvatochromic fluorophores with visible excitation wavelengths

The design of solvatochromic fluorescent nucleosides with visible excitation wavelengths is a goal towards the generation of modified oligonucleotides for fluorimetry-based molecular imaging. Herein, two hemicyanine-linked C5-2′-deoxyuridine nucleosides (PyI-dU and APPy-dU) have been synthesized by first generating hemicyanine-alkyne precursors that were attached via the alkyne moiety to 5-iodo-2′-deoxyuridine (5-I-dU) by Sonogashira coupling. The photophysical properties of the hemicyanine-linked dU probes have been characterized and compared to the corresponding properties of the hemicyanine-alkyne precursors. The nucleoside probe PyI-dU exhibits optical features that mimic the properties of the free hemicyanine-alkyne precursor, while the APPy-dU probe displays more favorable optical properties (longer excitation wavelength, brighter emission in water) than its precursor that is ascribed to π-stacking interactions between the hemicyanine dye with the dU nucleobase. Overall, probe APPy-dU is a superior solvatochromic fluorophore than PyI-dU suggesting its greater utility for fluorescent imaging applications.     

Solvatochromic study of 1,2-dihydroxyanthraquinone in neat and binary solvent mixtures

Preferential solvation of a solvatochromic probe has been studied in binary mixtures comprising of a non-protic and a protic solvent. The non-protic solvents employed are carbon tetrachloride (CCl(4)), acetonitrile (AcN) and N,N-dimethyl formamide (DMF) and the protic solvents are methanol (MeOH) and ethanol (EtOH). The probe molecule exhibits different spectroscopic characteristics depending upon the properties of the solubilizing media. The observed spectral features provide an indication of the microenvironment immediately surrounding the probe. Solvatochromic shifts of the ground and excited states of the probe were analysed by monitoring the charge transfer absorption band and the fluorescence emission spectra in terms of the solute-solvent and solvent-solvent interactions. Fluorescence emission spectra show the dual emission due to excited state proton transfer nature of the probe molecule. The effect of solvent and the excitation energy on dual emission are also studied. The observed magnitude of the Stokes shift in the above solvents has been used to deduce experimentally the dipole moment ratio of the probe molecule for the excited state to the ground state. The dipole moment of excited state is higher than the ground state.     

A Theoretical Study of the UV/Visible Absorption and Emission Solvatochromic Properties of Solvent‐Sensitive Dyes

Using the density‐functional vertical self‐consistent reaction field (VSCRF) solvation model, incorporated with the conductor‐like screening model (COSMO) and the self‐consistent reaction field (SCRF) methods, we have studied the solvatochromic shifts of both the absorption and emission bands of four solvent‐sensitive dyes in different solutions. The dye molecules studied here are: S‐TBA merocyanine, Abdel‐Halim's merocyanine, the rigidified aminocoumarin C153, and Nile red. These dyes were selected because they exemplify different structural features likely to impact the solvent‐sensitive fluorescence of “push‐pull”, or merocyanine, fluorophores. All trends of the blue or red shifts were correctly predicted, comparing with the experimental observations. Explicit H‐bonding interactions were also considered in several protic solutions like H₂O, methanol and ethanol, showing that including explicit H‐bonding solvent molecule(s) in the calculations is important to obtain the correct order of the excitation and emission energies. The geometries, electronic structures, dipole moments, and intra‐ and intermolecular charge transfers of the dyes in different solvents are also discussed.     

Effect of substituents on the fluorescence and absorption spectra of coumarins

The absorption and fluorescence emission of substituted coumarins have been studied in different solvents. It is observed that the substituents alter both the absorption and fluorescence emission maxima. These shifts are discussed in terms of the change in mobility of π-electrons caused by the nature and position of the substituent group in the parent compound.     

Photoinduced intramolecular charge transfer to meta position of benzene ring in 6-aminophthalides

Substitution of non-fluorescent phthalide (Pd) with amino group at meta (6) position in relation to the electron-accepting part of the lactone ring completely changes Pd photophysics: a new long-wavelength absorption band arises and the molecule becomes highly fluorescent. The experimental data and the analysis of vertical electronic transitions with TDDFT method indicate that the first absorption band in 6-aminophthalides (6-APds) comprises a single CT transition to the S1 state. Almost equal absorption and emission transition dipole moments indicate that S0 <--> S1 transition in all 6-APds is not affected by any mixing with other electronic states, the excited-state vibrational relaxation is not accompanied by significant conformational changes and the Stokes shifts reflect mainly solvation energetics of these molecules. Excited state dipole moments obtained from solvatochromic plots and from CASSCF calculations confirm large charge displacement from amino group towards the meta position of the benzene ring upon excitation of 6-APds to S1 state. Long fluorescence lifetimes and high fluorescence quantum yields demonstrate efficient and stable excited state charge separation in 6-APds. Taken together with sensitivity of 6-APds to polarity and proticity of the environment these properties make them good candidates for fluorescent probes of long-time scale molecular dynamics.     

Highly fluorescent conjugated pyrenes in nucleic acid probes: (phenylethynyl)pyrenecarbonyl-functionalized locked nucleic acids

In recent years, fluorescently labeled oligonucleotides have become a widely used tool in diagnostics, DNA sequencing, and nanotechnology. The recently developed (phenylethynyl)pyrenes are attractive dyes for nucleic acid labeling, with the advantages of long-wave emission relative to the parent pyrene, high fluorescence quantum yields, and the ability to form excimers. Herein, the synthesis of six (phenylethynyl)pyrene-functionalized locked nucleic acid (LNA) monomers M(1)-M(6) and their incorporation into DNA oligomers is described. Multilabeled duplexes display higher thermal stabilities than singly modified analogues. An increase in the number of phenylethynyl substituents attached to the pyrene results in decreased binding affinity towards complementary DNA and RNA and remarkable bathochromic shifts of absorption/emission maxima relative to the parent pyrene fluorochrome. This bathochromic shift leads to the bright fluorescence colors of the probes, which differ drastically from the blue emission of unsubstituted pyrene. The formation of intra- and interstrand excimers was observed for duplexes that have monomers M(1)-M(6) in both complementary strands and in numerous single-stranded probes. If more phenylethynyl groups are inserted, the detected excimer signals become more intense. In addition, (phenylethynyl)pyrenecarbonyl-LNA monomers M(4), M(5), and M(6) proved highly useful for the detection of single mismatches in DNA/RNA targets.