Nanocrystals for large Stokes shift-based optosensing

The influence of Stokes shift in optosensing was discussed. Then, the current status of large Stokes shift-based optosensing was reviewed here.     

Nanocrystals for large Stokes shift-based optosensing

Stokes shift is an important feature of fluorescence, which reveals the energy loss between the excitation and the emission. For most fluorescent materials(e.g., organic dyes and proteins), the large overlap between the absorption and emission spectra endow them a small Stokes shift that induced reabsorption by fluorophore itself. Although the self-absorption can be effectively reduced due to the emergence of fluorescent nanomaterials, fluorescence attenuation is still observed in aggregated or concentrated nanocrystals, causing reduced sensitivity of biosensors. Therefore, increasing the Stokes shift can effectively improve the performance of nano-agents based biosensing. In this critical review, through understanding the Stokes shift from the viewpoint of self-absorption, the influence of Stokes shift on fluorescence properties are discussed. Based on the principle of changing the Stokes shift of fluorescent nanomaterials, we described the methods for constructing various optically large Stokes shift-based nanomaterials, and the application of these nanocrystals in biosensing is especially concerned in this review.     

New insights on the photophysical behavior of PRODAN in anionic and cationic reverse micelles: from which state or states does it emit?

6-propionyl-2-(N,N-dimethyl)aminonaphtahalene, PRODAN, is widely used as a fluorescent molecular probe because of its significant Stokes shift in polar solvents. It is an aromatic compound with intramolecular charge-transfer states (ICT) that can be particularly useful as a sensor. The nature of the emissive states has not yet been established despite the detailed experimental and theoretical investigations done on this fluorophore. In this work, we performed absorption, steady-state, time-resolved fluorescence (TRES) and time-resolved area normalized emission (TRANES) spectroscopies on the molecular probe PRODAN in the anionic water/sodium 1,4-bis-2-ethylhexylsulfosuccinate (AOT)/n-heptane and the cationic water/benzyl-n-hexadecyl dimethylammonium chloride (BHDC)/benzene reverse micelles (RMs). The experiments were done by varying the surfactant concentrations at a fixed molar ratio (W = [H2O]/[Surfactant]) and changing the water content at a constant surfactant concentration. The results obtained varying the surfactant concentration at W = 0 show a bathochromic shift and an increase in the intensity of the PRODAN emission band due to the PRODAN partition process between the external solvent and the RMs interface. The partition constants, Kp, are quantified from the changes in the PRODAN emission spectra and the steady-state anisotropy () with the surfactant concentration in both RMs. The Kp value is larger in the BHDC than the AOT RMs, probably due to the interaction between the cationic polar head of the surfactant and the aromatic ring of PRODAN. The partition process is confirmed with the TRES experiments, where the data fit to a continuous model, and with the time-resolved area normalized emission spectroscopy (TRANES) spectra, where only one isoemissive point is detected. On the other hand, the emission spectra at W = 10 and 20 show a dual fluorescence with a new band that emerges in the low-energy region of the spectra, a band that was previously assigned to the PRODAN emission from the water pool of RMs. Our studies demonstrate that this band is due to the emission from an ICT state of the molecular probe PRODAN located at the interface of the RMs. These results are also confirmed by the lifetime measurements, the TRES experiments where the results fit to a two-state model, and the time-resolved area normalized emission spectroscopy (TRANES) spectra where three or two isoemissive points are detected in the AOT and BHDC RMs, respectively. In the AOT RMs, Kp values obtained at W = 10 and 20 are almost independent of the water content; the values are higher for the BHDC RMs due to the higher micropolarity of this interface.     

An indole-linked C8-deoxyguanosine nucleoside acts as a fluorescent reporter of Watson-Crick versus Hoogsteen base pairing

Pyrrole- and indole-linked C(8)-deoxyguanosine nucleosides act as fluorescent reporters of H-bonding specificity. Their fluorescence is quenched upon Watson-Crick H-bonding to dC, while Hoogsteen H-bonding to G enhances emission intensity. The indole-linked probe is ～ 10-fold brighter and shows promise as a fluorescent reporter of Hoogsteen base pairing.     

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.     

Biosynthesis of a fluorescent protein with extreme pseudo-Stokes shift by introducing a genetically encoded non-natural amino acid outside the fluorophore

A novel kind of fluorescent protein relying on the intramolecular interplay between two different fluorophores, one of chemical origin and one of biological origin, was developed. The fluorescent non-natural amino acid l-(7-hydroxycoumarin-4-yl)ethylglycine was site-specifically incorporated into the recombinant enhanced cyan fluorescent protein (eCFP) at a permissible surface position ～20 ? away from the protein fluorophore using amber suppression in Escherichia coli with an engineered cognate Methanococcus jannaschii tRNA synthetase. The resulting eCFP(Cou) exhibited almost quantitative intramolecular Fo?rster resonance energy transfer (FRET) between its two fluorophores, showing brilliant cyan emission at 476 nm upon excitation in the near-UV at 365 nm (a wavelength easily accessible via conventional laboratory UV sources), in contrast to its natural counterpart. Thus, this fluorescent protein with unprecedented spectroscopic properties reveals an extreme apparent Stokes shift of ～110 nm between the absorption wavelength of the coumaryl group and the emission wavelength of eCFP.     

Photophysical characters of rationally designed hetero-ring-expanded guanine analogues and effect of cytosine pairing

We present the results of the CIS and TDB3LYP calculations of the optical absorption and emission spectra of some newly designed guanine (G) analogues and their Watson-Crick base pairs. Compared with natural G, the onset absorption peaks of these newly designed analogues are red-shifted, while the fluorescence peaks are blue-shifted. In general, the first excited singlet states (pipi*) of these analogues are nonplanar for all bases considered here. But, the Stokes shifts for the designed G-analogues are much smaller than that of natural G, suggesting that they have stronger molecular rigidity and higher fluorescence quantum yields than those of natural G. The first excited states of these Watson-Crick base pairs essentially originate from those of their isolated purine moieties, as demonstrated from the S1 geometries of their Watson-Crick base pairs. For G and its analogues, A1 and A2 (they are ring-expanded with one-bond intercalation at the C5 site), the pairing with cytosine reduces the oscillator strengths of both the first absorption peak (by 27%-60%) and the fluorescent emission (by 19%-23%), while for the analogues A3, A4, and xG in which G is ring-expanded with a two-bond intercalation at the C5 site, the pairing, in contrast, increases the oscillator strengths of both the first absorption peak (by 11%-15%) and the fluorescent emission (by 3%-20%). These observations indicate that the pairing with cytosine can quench the fluorescence for G, A1, and A2 but enhance the fluorescence quantum yields for A3, A4, and xG. The significant shifts induced by ring-expansion in the ring-expanded G with a two-bond intercalation at the C5 site reveal a possibility for their fluorescent detections.     

High-performance fluorescent particles prepared via miniemulsion polymerization

Highly fluorescent polymer particles were prepared with Eu beta-diketonates complex as a fluorophore by miniemulsion polymerization technique. Eu beta-diketonates complex has a long decay time, a large Stokes shift, and very narrow emission bands in comparison with other organic fluorescent compounds. Aqueous miniemulsion was prepared by mixing monomer, crosslinker, hydrophobe, and Eu beta-diketonates complex and then putting the mixture into an aqueous solution of surfactant, followed by ultrasonication. An aqueous solution of initiator was added to the miniemulsion to obtain fluorescent polymer particles, which were monodispersed without aggregation. Particle size was decreased to deca-nano scale by increasing the amount of surfactant. Fluorescent intensity was increased by using Eu beta-complex coordinated with additional ligand. Further fluorescence quantum yields and fluorescent properties in the presence of DNA were investigated to the confirm superiority of Eu beta-diketonates complexes in polymer particles.     

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.     

Determination of redox potentials for the Watson-Crick base pairs, DNA nucleosides, and relevant nucleoside analogues

Redox potentials for the DNA nucleobases and nucleosides, various relevant nucleoside analogues, Watson-Crick base pairs, and seven organic dyes are presented based on DFT/B3LYP/6-31++G(d,p) and B3YLP/6-311+G(2df,p)//B3LYP/6-31+G* levels of calculations. The values are determined from an experimentally calibrated set of equations that correlate the vertical ionization (electron affinity) energy of 20 organic molecules with their experimental reversible oxidation (reduction) potential. Our results are in good agreement with those estimated experimentally for the DNA nucleosides in acetonitrile solutions (Seidel et al. J. Phys. Chem. 1996, 100, 5541). We have found that nucleosides with anti conformation exhibit lower oxidation potentials than the corresponding syn conformers. The lowering in the oxidation potential is due to the formation of an intramolecular hydrogen bonding interaction between the 5'-OH group of the sugar and the N3 of the purine bases or C2=O of the pyrimidine bases in the syn conformation. Pairing of adenine or guanine with its complementary pyrimidine base decreases its oxidation potential by 0.15 or 0.28 V, respectively. The calculated energy difference between the oxidation potential for the G.C base pair and that of the guanine base is in good agreement with the experimental value estimated recently (0.34 V: Caruso, T.; et al. J. Am. Chem. Soc. 2005, 127, 15040). The complete and consistent set of reversible redox values determined in this work for the DNA constituents is expected to be of considerable value to those studying charge and electronic energy transfer in DNA.     

An example of how to use AOT reverse micelle interfaces to control a photoinduced intramolecular charge-transfer process

6-Propionyl-2-(N,N-dimethyl)aminonaphtahalene, PRODAN, is widely used as a fluorescent molecular probe due to its significant Stokes shift in polar solvents. It is an aromatic compound with intramolecular charge-transfer (ICT) states which can be particularly useful as sensors. In this work, we performed absorption, steady-state, time-resolved fluorescence (TRES), and time-resolved area normalized emission (TRANES) spectroscopies on PRODAN dissolved in nonaqueous reverse micelles. The reverse micelles are composed of polar solvents/sodium 1,4-bis-2-ethylhexylsulfosuccinate (AOT)/n-heptane. Sequestered polar solvents included ethylene glycol (EG), propylene glycol (PG), glycerol (GY), formamide (FA), dimethylformamide (DMF), and dimethylacetamide (DMA). The experiments were performed with varying surfactant concentrations at a fixed molar ratio W(S) = [polar solvent]/[AOT]. In every reverse micelle studied, the results show that PRODAN undergoes a partition process between the external solvent and the reverse micelle interface. The partition constants, K(p), are quantified from the changes in the PRODAN emission and/or absorption spectra with the surfactant concentration. The K(p) values depend strongly on the encapsulated polar solvent and correlate quite well with the AOT reverse micelle interface's zones where PRODAN can exist and emits. Thus, the partition toward the reverse micelle interface is strongly favored in DMF and DMA containing micelles where the PRODAN emission comes only from an ICT state. For GY/AOT reverse micelles, the K(p) value is the lowest and only emission from the local excited (LE) state is observed. On the other hand, for EG/AOT, PG/AOT, and water/AOT reverse micelles, the K(p) values are practically the same and emission from both states (LE and ICT) is simultaneously detected. We show here that it is possible to control the PRODAN state emission by simply changing the properties of the AOT reverse micelle interfaces by choosing the appropriate polar solvent to make the reverse micelle media. Indeed, we present experimental evidence with the answer to the long time question about from which state does PRODAN emit, a process that can be controlled using the unique reverse micelle interfaces properties.     

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.     

Fluorescent pyrimidopyrimidoindole nucleosides: control of photophysical characterizations by substituent effects

10-(2-Deoxy-beta-D-ribofuranosyl)pyrimido[4',5':4,5]pyrimido[1,6-a]indole-6,9(7H)-dione (dCPPI) and its derivatives were synthesized via the Suzuki-Miyaura coupling reaction of 5-iododeoxycytidine with 5-substituted N-Boc-indole-2-borates and characterized by UV-vis and fluorescence spectroscopy. The new fluorescent nucleosides showed rather large Stokes shifts (116-139 nm) in an aqueous buffer. The fluorescent intensities were dependent on the nature of the substituents on the indole rings. The electron-withdrawing groups increased the fluorescent intensity while the electron-donating groups having lone pairs decreased it. Among the substituted dCPPI derivatives tested, the trimethylammonium derivative of dCPPI was found to emit the brightest fluorescent light. The solvatochromism of dCPPI and its derivatives was also studied. Some of the dCPPI derivatives showed interesting solvent-dependent fluorescence enhancement and could be useful as new fluorescent structural probes for nucleic acids. The Lippert-Mataga analyses of the Stokes shift were also carried out to obtain estimated values of the dipole moment of the excited states of some of the derivatives.     

A PHOTOPHYSICAL STUDY OF SOLVATOCHROMIC PROBE 6-PROPIONYL-Z(N,N-DIMETHYLAMINO)NAPHTHALENE (PRODAN) IN SOLUTION

A photophysical study of 6-propionyl-2-( N,N -dimethylamino)naphthalene (PRODAN) in room-temperature solutions under various conditions is reported. The results show no unusual photophysical properties, except for an extremely large solvatochromic shift of PRODAN fluorescence spectrum. The previously reported extra blue emission band for PRODAN in an aqueous solution is identified to be due entirely to trace water-soluble impurities in the sample. The excited-state dipole moment of PRODAN is determined based on solvatochromic results using a known twisted intramolecular charge transfer (TICT) molecule p -( N,N -diethylamino)ethylbenzoate (DEAEB) as a reference to probe specific solute-solvent interactions. The possibility of TICT state formation in PRODAN is discussed, and a solvation equilibrium mechanism is proposed to account for the photophysical behavior of PRODAN.     

Pyrene-labeled base-discriminating fluorescent DNA probes for homogeneous SNP typing

This paper describes the design of novel base-discriminating fluorescent (BDF) nucleobases and their application to single nucleotide polymorphism (SNP) typing. We devised novel BDF nucleosides, (Py)U and (Py)C, which contain a pyrenecarboxamide chromophore connected by a propargyl linker. The fluorescence spectrum of the duplex containing a (Py)U/A base pair showed a strong emission at 397 nm on 327 nm excitation. In contrast, the fluorescence of duplexes containing (Py)U/N base pairs (N = C, G, or T) was considerably weaker. The proposed structure of the duplex containing a matched (Py)U/A base pair suggests that the high polarity near the pyrenecarboxamide group is responsible for the strong A-selective fluorescence emission. Moreover, the fluorescence of the duplex containing a (Py)U/A base pair was not quenched by a flanking C/G base pair. The fluorescence properties are quite different from previous BDF nucleobases, where fluorescence is quenchable by flanking C/G base pairs. The duplex containing the C derivative, (Py)C, selectively emitted fluorescence when the base opposite (Py)C was G. The drastic change of fluorescence intensity by the nature of the complementary base is extremely useful for SNP typing. (Py)U- and (Py)C-containing oligodeoxynucleotides acted as effective reporter probes for homogeneous SNP typing of DNA samples containing c-Ha-ras and BRCA2 SNP sites.     

Fluorescent and thermal properties of siloxane-polyurethanes based on 1,8-naphthalimide

A series of fluorescent siloxane-polyurethanes(HPMS-PUs) containing an amino-functionalized,1 8-naphthalimide,fluorescent monomer(AABD) as a chain extender were synthesized.The properties of the HPMS-PUs were investigated by UV–vis and fluorescence spectroscopies,thermogravimetric analysis and thermal migration behavior.The maximum absorption and emission wavelengths of HPMS-PUs showed a red shift of about 4 nm and a blue shift of about 9 nm,respectively,compared to those of AABD.The Stokes shifts of AABD and HPMS-PU2 were 3514 and 2931 cm 1,respectively.The quantum yield of HPMS-PU2 was 0.79,which was six times higher than that of AABD.Concentration self-quenching was observed in both AABD and HPMS-PUs.The fluorescence of HPMS-PUs was quite stable with respect to both temperature and fluorescence quencher effects.The thermal stability of HPMS-PUs increased with AABD content.The fluorophore units in the HPMS-PUs did not readily migrate.     

Ultrafast repair of irradiated DNA: nonadiabatic ab initio simulations of the guanine-cytosine photocycle

Nonadiabatic first-principles molecular dynamics simulations have been performed of the photoexcited Watson-Crick guanine-cytosine (GC) DNA base pair in the gas phase and in aqueous solution. An excited state coupled proton-electron transfer (CPET) from G to C along the central hydrogen bond is observed upon excitation of the pipi* state initially localized on G. In the resulting charge transfer state a conical intersection between the excited state and the ground state is easily accessible. Therefore radiationless decay is fast, of the order of 100 fs, followed by a rapid CPET back reaction retrieving the initial Watson-Crick structure. A detailed analysis of the mechanism of nonradiative decay suggests a biexponential behavior in which out-of-plane motion plays a special role for the longer decay component.     

Spectroscopic Study of New Fluorescent Probes

Abstract— Various newly synthesized substances containing the same chromophore as PRODAN were subjected to a spectroscopic study. The new substances, ω-[6-( N -meth-yl- N -alkylamino)naphthoyl]alcanoic acids (MANA), possess polar groups and alkyl chains of variable length that make them potentially useful as fluorescent probes in membrane studies. This paper reports on their spectroscopic properties in various pure solvents. Their Stokes shifts are given and related to different physicochemical properties of the solvents. A theoretical study of the behavior of the new substances is also presented.     

Absorption and fluorescence emission spectroscopic characters of naphtho‐homologated yy‐DNA bases and effect of methanol solution and base pairing

A comprehensive theoretical study of electronic transitions of naphtho‐homologated base analogs, namely, yy‐T , yy‐C , yy‐A , and yy‐G , was performed. The nature of the low‐lying excited states is discussed, and the results are compared with those from experiment and also with those of y‐bases. Geometrical characteristics of the lowest excited singlet ππ* and nπ* states were explored using the CIS method, and the effects of methanol solution and paring with their complementary natural bases on the relevant absorption and emission spectra of these modified bases were examined. The calculated excitation and emission energies agree well with the measured data, where experimental results are available. In methanol solution, the fluorescence from yy‐A and yy‐G would be expected to occur around 539 and 562 nm, respectively, suggesting that yy‐A is a green‐colored fluorophore, whereas yy‐G is a yellow‐colored fluorophore. The methanol solution was found to red‐shift both the absorption and emission maxima of yy‐A , yy‐T , and yy‐C , but blue‐shift those for yy‐G . Generally, though base pairing has no significant effects on the absorption and fluorescence maxima of yy‐A , yy‐C , and yy‐T , it blue‐shifts those for yy‐G . © 2009 Wiley Periodicals, Inc. J Comput Chem 2010