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1.  Differential Tuning of the Electron Transfer Parameters in 1,3,5-Triarylpyrazolines: A Rational Design Approach for Optimizing the Contrast Ratio of Fluorescent Probes 
Journal of the American Chemical Society  2008;130(39):13023-13032.
A large class of cation-responsive fluorescent sensors utilizes a donor-spacer-acceptor (D-A) molecular framework that can modulate the fluorescence emission intensity through a fast photoinduced intramolecular electron transfer (PET) process. The emission enhancement upon binding of the analyte defines the contrast ratio of the probe, a key property that is particularly relevant in fluorescence microscopy imaging applications. Due to their unusual electronic structure, 1,3,5-triaryl-pyrazoline fluorophores allow for the differential tuning of the excited state energy ΔE00 and the fluorophore acceptor potential E(A/A−), both of which are critical parameters that define the ET thermodynamics and thus the contrast ratio. By systematically varying the number and attachment positions of fluoro-substituents on the fluorophore π-system, ΔE00 can be adjusted over a broad range (0.4 eV) without significantly altering the acceptor potential E(A/A−). Experimentally measured D-A coupling and reorganization energies were used to draw a potential map for identifying the optimal ET driving force that is expected to give a maximum fluorescence enhancement for a given change in donor potential upon binding of the analyte. The rational design strategy was tested by optimizing the fluorescence response of a pH sensitive probe, thus yielding a maximum emission enhancement factor of 400 upon acidification. Furthermore, quantum chemical calculations were used to reproduce the experimental trends of reduction potentials, excited state energies, and ET driving forces within the framework of linear free energy relationships (LFER). Such LFERs should be suitable to semi-empirically predict ET driving forces with an average unsigned error of 0.03 eV, consequently allowing for the computational prescreening of substituent combinations to best match the donor potential of a given cation receptor. Within the scaffold of the triarylpyrazoline platform, the outlined differential tuning of the electron transfer parameters should be applicable to a broad range of cation receptors for designing PET sensors with maximized contrast ratios.
doi:10.1021/ja803074y
PMCID: PMC3199570  PMID: 18767839
2.  Electronically Tuned 1,3,5-Triarylpyrazolines as Cu(I)-Selective Fluorescent Probes† 
Organic & biomolecular chemistry  2009;8(2):363-370.
We have prepared and characterized a Cu(I)-responsive fluorescent probe, constructed using a large tetradentate, 16-membered thiazacrown ligand ([16]aneNS3) and 1,3,5-triaryl-substituted pyrazoline fluorophores. The fluorescence contrast ratio upon analyte binding, which is mainly governed by changes of the photoinduced electron transfer (PET) driving force between the ligand and fluorophore, was systematically optimized by increasing the electron withdrawing character of the 1-aryl-ring, yielding a maximum 50-fold fluorescence enhancement upon saturation with Cu(I) in methanol and a greater than 300-fold enhancement upon protonation with trifluoroacetic acid. The observed fluorescence increase was selective towards Cu(I) over a broad range of mono- and divalent transition metal cations. Previously established Hammett LFERs proved to be a valuable tool to predict two of the PET key parameters, the acceptor potential E(A/A−) and the excited state energy ΔE00, and thus to identify a set of pyrazolines that would best match the thermodynamic requirements imposed by the donor potential E(D+/D) of the thiazacrown receptor. The described approach should be applicable for rationally designing high-contrast pyrazoline-based PET probes selective towards other metal cations.
doi:10.1039/b918311f
PMCID: PMC3164304  PMID: 20066271
3.  Impacts of quantum dots in molecular detection and bioimaging of cancer 
BioImpacts : BI  2014;4(3):149-166.
Introduction: A number of assays have so far been exploited for detection of cancer biomarkers in various malignancies. However, the expression of cancer biomarker(s) appears to be extremely low, therefore accurate detection demands sensitive optical imaging probes. While optical detection using conventional fluorophores often fail due to photobleaching problems, quantum dots (QDs) offer stable optical imaging in vitro and in vivo.
Methods: In this review, we briefly overview the impacts of QDs in biology and its applications in bioimaging of malignancies. We will also delineate the existing obstacles for early detection of cancer and the intensifying use of QDs in advancement of diagnostic devices.
Results: Of the QDs, unlike the II-VI type QDs (e.g., cadmium (Cd), selenium (Se) or tellurium (Te)) that possess inherent cytotoxicity, the I-III-VI 2 type QDs (e.g., AgInS2, CuInS2, ZnS-AgInS2) appear to be less toxic bioimaging agents with better control of band-gap energies. As highly-sensitive bioimaging probes, advanced hybrid QDs (e.g., QD-QD, fluorochrome-QD conjugates used for sensing through fluorescence resonance energy transfer (FRET), quenching, and barcoding techniques) have also been harnessed for the detection of biomarkers and the monitoring of delivery of drugs/genes to the target sites. Antibody-QD (Ab-QD) and aptamer- QD (Ap-QD) bioconjugates, once target the relevant biomarker, can provide highly stable photoluminescence (PL) at the target sites. In addition to their potential as nanobiosensors, the bioconjugates of QDs with homing devices have successfully been used for the development of smart nanosystems (NSs) providing targeted bioimaging and photodynamic therapy (PDT).
Conclusion: Having possessed great deal of photonic characteristics, QDs can be used for development of seamless multifunctional nanomedicines, theranostics and nanobiosensors.
doi:10.15171/bi.2014.008
PMCID: PMC4204040  PMID: 25337468
Bioimaging; Bioconjugates; Cancer; Multimodal nanomedicines; Quantum dots; Theranostics
4.  Fluorescent Sensing of Fluoride in Cellular System 
Theranostics  2015;5(2):173-187.
Fluoride ions have the important roles in a lot of physiological activities related with biological and medical system, such as water fluoridation, caries treatment, and bone disease treatment. Great efforts have been made to develop new methods and strategies for F- detection in the past decades. Traditional methods for the detection of F- including ion chromatography, ion-selective electrodes, and spectroscopic techniques have the limitations in the biomedicine research. The fluorescent probes for F- are very promising that overcome some drawbacks of traditional fluoride detection methods. These probes exhibit high selectivity, high sensitivity as well as quick response to the detection of fluoride anions. The review commences with a brief description of photophysical mechanisms for fluorescent probes for fluoride, including photo induced electron transfer (PET), intramolecular charge transfer (ICT), fluorescence resonance energy transfer (FRET), and excited-state intramolecular proton transfer (ESIPT). Followed by a discussion about common dyes for fluorescent fluoride probes, such as anthracene, naphalimide, pyrene, BODIPY, fluorescein, rhodamine, resorufin, coumarin, cyanine, and near-infrared (NIR) dyes. We divide the fluorescent probes for fluoride in cellular application systems into nine groups, for example, type of hydrogen bonds, type of cleavage of Si-O bonds, type of Si-O bond cleavage and cylization reactions, etc. We also review the recent reported carriers in the delivery of fluorescent fluoride probes. Seventy-four typical fluorescent fluoride probes are listed and compared in detail, including quantum yield, reaction medium, excitation and emission wavelengths, linear detection range, selectivity for F-, mechanism, and analytical applications. Finally, we discuss the future challenges of the application of fluorescent fluoride probes in cellular system and in vivo. We wish that more and more excellent fluorescent fluoride probes will be developed and applied in the biomedicine field in the future.
doi:10.7150/thno.9860
PMCID: PMC4279002  PMID: 25553106
fluoride; fluorescent probes; fluorophores; cell, in vivo.
5.  Kinetically Controlled Photoinduced Electron Transfer Switching in Cu(I)-Responsive Fluorescent Probes 
Copper(I)-responsive fluorescent probes based on photoinduced electron transfer (PET) switching consistently display incomplete recovery of emission upon Cu(I) binding compared to the corresponding isolated fluorophores, raising the question of whether Cu(I) might engage in adverse quenching pathways. To address this question, we performed detailed photophysical studies on a series of Cu(I)-responsive fluorescent probes that are based on a 16-membered thiazacrown receptor ([16]aneNS3) tethered to 1,3,5-triarylpyrazoline-fluorophores. The fluorescence enhancement upon Cu(I) binding, which is mainly governed by changes in the photoinduced electron transfer (PET) driving force between the ligand and fluorophore, was systematically optimized by increasing the electron withdrawing character of the 1-aryl-ring, yielding a maximum 29-fold fluorescence enhancement upon saturation with Cu(I) in methanol and a greater than 500-fold enhancement upon protonation with trifluoroacetic acid. Time-resolved fluorescence decay data for the Cu(I)-saturated probe indicated the presence of three distinct emissive species in methanol. Contrary to the notion that Cu(I) might engage in reductive electron transfer quenching, femtosecond time-resolved pump-probe experiments provided no evidence for formation of a transient Cu(II) species upon photoexcitation. Variable temperature 1H NMR experiments revealed a dynamic equilibrium between the tetradentate NS3-coordinated Cu(I) complex and a ternary complex involving coordination of a solvent molecule, an observation that was further supported by quantum chemical calculations. The combined photophysical, electrochemical, and solution chemistry experiments demonstrate that electron transfer from Cu(I) does not compete with radiative deactivation of the excited fluorophore, and hence, that the Cu(I)-induced fluorescence switching is kinetically controlled.
doi:10.1021/ja908326z
PMCID: PMC3199569  PMID: 20020716
copper; fluorescent probes; photoinduced intramolecular electron transfer; PET; Marcus theory; pyrazoline fluorophores
6.  Bioimaging Probes for Reactive Oxygen Species and Reactive Nitrogen Species 
Reactive oxygen species (ROS) play key roles in many pathogenic processes, including carcinogenesis, inflammation, ischemia-reperfusion injury and signal transduction. Also, reactive nitrogen species (RNS) cause various biological events such as neurodegenerative disorders. Sensitive and specific detection methods for ROS and RNS in biological samples should be useful for elucidation of biological events both in vitro and in vivo. Fluorescent probes based on small organic molecules have become indispensable tools in modern biology because they provide dynamic information concerning the localization and quantity of biological molecules of interest, without the need of genetic engineering of the sample. In this review, we recount some recent achievements in the field of small molecular fluorescent probes. First, the probes for nitric oxide and peroxynitrite as RNS are introduced and the probes of hydroxyl radical, hydrogen peroxide, hypochlorous and singlet oxygen as ROS are discussed, based on the fluorescence off/on switching mechanisms including photoinduced electron transfer and spirocyclization processes, and with some applications for in vitro and in vivo systems.
doi:10.3164/jcbn.R09-66
PMCID: PMC2735621  PMID: 19794917
bioimaging probe; reactive oxygen species; reactive nitrogen species; fluorescence; photoinduced electron transfer
7.  Target-cancer cell specific activatable fluorescence imaging Probes: Rational Design and in vivo Applications 
Accounts of chemical research  2010;44(2):83-90.
CONSPECTUS
Conventional imaging methods, such as angiography, computed tomography, magnetic resonance imaging and radionuclide imaging, rely on contrast agents (iodine, gadolinium, radioisotopes) that are “always on”. While these agents have proven clinically useful, they are not sufficiently sensitive because of the inadequate target to background ratio. A unique aspect of optical imaging is that fluorescence probes can be designed to be activatable, i.e. only “turned on” under certain conditions. These probes can be designed to emit signal only after binding a target tissue, greatly increasing sensitivity and specificity in the detection of disease. There are two basic types of activatable fluorescence probes; 1) conventional enzymatically activatable probes, which exist in the quenched state until activated by enzymatic cleavage mostly outside of the cells, and 2) newly designed target-cell specific activatable probes, which are quenched until activated in targeted cells by endolysosomal processing that results when the probe binds specific cell-surface receptors and is subsequently internalized. Herein, we present a review of the rational design and in vivo applications of target-cell specific activatable probes. Designing these probes based on their photo-chemical (e.g. activation strategy), pharmacological (e.g. biodistribution), and biological (e.g. target specificity) properties has recently allowed the rational design and synthesis of target-cell specific activatable fluorescence imaging probes, which can be conjugated to a wide variety of targeting molecules. Several different photo-chemical mechanisms have been utilized, each of which offers a unique capability for probe design. These include: self-quenching, homo- and hetero-fluorescence resonance energy transfer (FRET), H-dimer formation and photon-induced electron transfer (PeT). In addition, the repertoire is further expanded by the option for reversibility or irreversibility of the signal emitted using the aforementioned mechanisms. Given the wide range of photochemical mechanisms and properties, target-cell specific activatable probes possess considerable flexibility and can be adapted to specific diagnostic needs. Herein, we summarize the chemical, pharmacological, and biological basis of target-cell specific activatable imaging probes and discuss methods to successfully design such target-cell specific activatable probes for in vivo cancer imaging.
doi:10.1021/ar1000633
PMCID: PMC3040277  PMID: 21062101
8.  Predicting the photoinduced electron transfer thermodynamics in polyfluorinated 1,3,5-triarylpyrazolines based on multiple linear free energy relationships† 
Organic & biomolecular chemistry  2009;7(8):1536-1546.
The photophysical properties of 1,3,5-triarylpyrazolines are strongly influenced by the nature and position of substituents attached to the aryl-rings, rendering this fluorophore platform well suited for the design of fluorescent probes utilizing a photoinduced electron transfer (PET) switching mechanism. To explore the tunability of two key parameters that govern the PET thermodynamics, the excited state energy ΔE00 and acceptor potential E(A/A−), a library of polyfluoro-substituted 1,3-diaryl-5-phenyl-pyrazolines was synthesized and characterized. The observed trends for the PET parameters were effectively captured through multiple Hammett linear free energy relationships (LFER) using a set of independent substituent constants for each of the two aryl rings. Given the lack of experimental Hammett constants for polyfluoro substituted aromatics, theoretically derived constants based on the electrostatic potential at the nucleus (EPN) of carbon atoms were employed as quantum chemical descriptors. The performance of the LFER was evaluated with a set of compounds that were not included in the training set, yielding a mean unsigned error of 0.05 eV for the prediction of the combined PET parameters. The outlined LFER approach should be well suited to design and optimize the performance of cation-responsive 1,3,5-triarylpyrazolines.
doi:10.1039/b821042j
PMCID: PMC3171193  PMID: 19343239
9.  rsEGFP2 enables fast RESOLFT nanoscopy of living cells 
eLife  2012;1:e00248.
The super-resolution microscopy called RESOLFT relying on fluorophore switching between longlived states, stands out by its coordinate-targeted sequential sample interrogation using low light levels. While RESOLFT has been shown to discern nanostructures in living cells, the reversibly photoswitchable green fluorescent protein (rsEGFP) employed in these experiments was switched rather slowly and recording lasted tens of minutes. We now report on the generation of rsEGFP2 providing faster switching and the use of this protein to demonstrate 25–250 times faster recordings.
DOI: http://dx.doi.org/10.7554/eLife.00248.001
eLife digest
For decades it was assumed that the diffraction of light meant that optical microscopy could not resolve features that were smaller than about the half the wavelength of the light being used to create an image. However, various ‘super-resolution’ methods have allowed researchers to overcome this diffraction limit for fluorescence imaging, which is the most popular form of microscopy used in the life sciences. This approach involves tagging the biomolecules of interest with fluorescent molecules, such as green fluorescent protein (GFP), so that they can be identified in cells. An excitation laser then drives the fluorescent molecule, which is also known as a fluorophore, into an excited state: after a short time, the fluorophore can return to its ground state by releasing a fluorescence photon. Images of the sample are built up by detecting these photons.
In STED super-resolution microscopy a second laser is used to instantly send the molecules from their excited or ‘on’ states back to their ground or ‘off’ states before any fluorescence can occur. The second laser beam is usually shaped like a doughnut, with a small region of low light intensity surrounded by a region of much higher intensity. STED microscopy is able to beat the diffraction limit because the second laser turns all the fluorophores ‘off’ except those in the small sub-wavelength region at the centre of the doughnut. The image is build up by scanning both lasers over the sample so that the small region in which the fluorophores are ‘on’ probes the entire cell.
RESOLFT is a similar technique that employs fluorescent molecules with ‘on’ and ‘off’ times that are much longer than those used in STED microscopy. In particular, RESOLFT uses fluorescent molecules that can be rapidly switched back and forth between long-lived ‘on’ and ‘off’ states many times by the two lasers. The fact that both these states are long-lived states means that RESOLFT requires much lower laser intensities than STED, which makes it attractive for imaging biological samples over large areas or long times.
RESOLFT demonstrated its suitability for bioimaging for the first time last year, with a protein called rsEGFP (reversibly switchable enhanced GFP) being employed as the fluorophore. However, the time needed to switch this protein between the ‘on state’ and the ‘off state’ was relatively long, and it took about an hour to record a typical image. Now, Grotjohann et al. have modified this protein to make a new fluorophore called rsEGFP2 with a shorter switching time, and have used it to image various structures—including Vimentin, a protein that forms part of the cytoskeleton in many cells, and organelles called peroxisomes—inside live mammalian cells. They were able to record these images some 25–250 times faster than would have been possible with previous RESOLFT approaches. The combination of RESOLFT and rsEGFP2 should allow researchers to image a wide variety of structures and processes in living cells that have not been imaged before.
DOI: http://dx.doi.org/10.7554/eLife.00248.002
doi:10.7554/eLife.00248
PMCID: PMC3534202  PMID: 23330067
confocal microscopy; fluorescent probes; GFP; nanoscopy; superresolution; live-cell imaging; None
10.  High-contrast fluorescence sensing of aqueous Cu(I) with triaryl-pyrazoline probes: Dissecting the roles of ligand donor strength and excited state proton transfer 
Cu(I)-responsive fluorescent probes based on a photoinduced electron transfer (PET) mechanism generally show incomplete fluorescence recovery relative to the intrinsic quantum yield of the fluorescence reporter. Previous studies on probes with an N-aryl thiazacrown Cu(I)-receptor revealed that the recovery is compromised by incomplete Cu(I)-N coordination and resultant ternary complex formation with solvent molecules. Building upon a strategy that successfully increased the fluorescence contrast and quantum yield of Cu(I) probes in methanol, we integrated the arylamine PET donor into the backbone of a hydrophilic thiazacrown ligand with a sulfonated triarylpyrazoline as a water-soluble fluorescence reporter. This approach was not only expected to disfavor ternary complex formation in aqueous solution but also to maximize PET switching through a synergistic Cu(I)-induced conformational change. The resulting water-soluble probe 1 gave a strong 57-fold fluorescence enhancement upon saturation with Cu(I) with high selectivity over other cations, including Cu(II), Hg(II), and Cd(II); however, the recovery quantum yield did not improve over probes with the original N-aryl thiazacrown design. Concluding from detailed photophysical data, including responses to acidification, solvent isotope effects, quantum yields, and time-resolved fluorescence decay profiles, the fluorescence contrast of 1 is compromised by inadequate coordination of Cu(I) to the weakly basic arylamine nitrogen of the PET donor and by fluorescence quenching via two distinct excited state proton transfer pathways operating under neutral and acidic conditions.
doi:10.1039/c2dt31985c
PMCID: PMC3755598  PMID: 23169532
11.  Electronic structural dependence of the photophysical properties of fluorescent heteroditopic ligands – implications in designing molecular fluorescent indicators† 
Organic & biomolecular chemistry  2010;8(23):5431-5441.
Two fluorescent heteroditopic ligands (2a and 2b) for zinc ion were synthesized and studied. The efficiencies of two photophysical processes, intramolecular charge transfer (ICT) and photoinduced electron transfer (PET), determine the magnitudes of emission bathochromic shift and enhancement, respectively, when a heteroditopic ligand forms mono- or dizinc complexes. The electron-rich 2b is characterized by a high degree of ICT in the excited state with little propensity for PET, which is manifested in a large bathochromic shift of emission upon Zn2+ coordination without enhancement in fluorescence quantum yield. The electron-poor 2a displays the opposite photophysical consequence where Zn2+ binding results in greatly enhanced emission without significant spectral shift. The electronic structural effects on the relative efficiencies of ICT and PET in 2a and 2b as well as the impact of Zn2+-coordination are probed using experimental and computational approaches. This study reveals that the delicate balance between various photophysical pathways (e.g. ICT and PET) engineered in a heteroditopic ligand is sensitively dependent on the electronic structure of the ligand, i.e. whether the fluorophore is electron-rich or poor, whether it possesses a donor–acceptor type of structure, and where the metal binding occurs.
doi:10.1039/c0ob00482k
PMCID: PMC3530201  PMID: 20882250
12.  Facile synthesis of fluorescent Au/Ce nanoclusters for high-sensitive bioimaging 
Background
Tumor-target fluorescence bioimaging is an important means of early diagnosis, metal nanoclusters have been used as an excellent fluorescent probe for marking tumor cells due to their targeted absorption. We have developed a new strategy for facile synthesis of Au/Ce nanoclusters (NCs) by doping trivalent cerium ion into seed crystal growth process of gold. Au/Ce NCs have bright fluorescence which could be used as fluorescent probe for bioimaging.
Results
In this study, we synthesized fluorescent Au/Ce NCs through two-step hydrothermal reaction. The concentration range of 25–350 μM, Au/Ce NCs have no obvious cell cytotoxicity effect on HeLa, HepG2 and L02 cells. Furthermore, normal cells (L02) have no obvious absorption of Au/Ce NCs. Characterization of synthesized Au/Ce NCs was done by using TEM, EDS and XPS. Then these prepared Au/Ce NCs were applied for in vitro/in vivo tumor-target bioimaging due to its prolonged fluorescence lifetime and bright luminescence properties.
Conclusions
The glutathione stabilized Au/Ce NCs synthesized through hydrothermal reaction possess stable and bright fluorescence that can be readily utilized for high sensitive fluorescence probe. Our results suggest that Au/Ce NCs are useful candidate for in vitro/in vivo tumor bioimaging in potential clinical application.
doi:10.1186/s12951-015-0071-y
PMCID: PMC4320607  PMID: 25643754
Fluorescence bioimaging; Au/Ce nanoclusters; Probe; Tumor
13.  Enhancing Photoinduced Electron Transfer Efficiency of Fluorescent pH-Probes with Halogenated Phenols 
Analytical Chemistry  2014;86(18):9293-9300.
Photoinduced electron transfer (PET), which causes pH-dependent quenching of fluorescent dyes, is more effectively introduced by phenolic groups than by amino groups which have been much more commonly used so far. That is demonstrated by fluorescence measurements involving several classes of fluorophores. Electrochemical measurements show that PET in several amino-modified dyes is thermodynamically favorable, even though it was not experimentally found, underlining the importance of kinetic aspects to the process. Consequently, the attachment of phenolic groups allows for fast and simple preparation of a wide selection of fluorescent pH-probes with tailor-made spectral properties, sensitive ranges, and individual advantages, so that a large number of applications can be realized. Fluorophores carrying phenolic groups may also be used for sensing analytes other than pH or molecular switching and signaling.
doi:10.1021/ac502513g
PMCID: PMC4165219  PMID: 25126834
14.  Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection 
Tetrahedron  2007;63(17):3591-3600.
We report the design, synthesis and characterization of binary oligonucleotide probes for mRNA detection. The probes were designed to avoid common problems found in standard binary probes such as direct excitation of the acceptor fluorophore and overlap between the donor and acceptor emission spectra. Two different probes were constructed that contained an array of either two or three dyes and that were characterized using steady-state fluorescence spectroscopy, time-resolved fluorescence spectroscopy and fluorescence depolarization measurements. The three-dye binary probe (BP-3d) consists of a Fam fluorophore which acts as a donor, collecting light and transferring it as energy to Tamra, which subsequently transfers energy to Cy5 when the two probes are hybridized to mRNA. This design allows the use of 488 nm excitation, which avoids the direct excitation of Cy5 and at the same time provides a good fluorescence resonance energy transfer (FRET) efficiency. The two-dye binary probe system (BP-2d) was constructed of Alexa488 and Cy5 fluorophores. Although the overlap between the fluorescence of Alexa488 and the absorption of Cy5 is relatively low, FRET still occurs due to their close physical proximity when the probes are hybridized to mRNA. This framework also decreases the direct excitation of Cy5 and reduces the fluorescence overlap between the donor and the acceptor. Picosecond time-resolved spectroscopy showed a reduction in the fluorescence lifetime of donor fluorophores after the formation of the hybrid between the probes and target mRNA. Interestingly, BP-2d in the presence of mRNA shows a slow rise in the fluorescence decay of Cy5 due to a relatively low FRET rate, which together with the reduction in the Alexa488 lifetime provides a way to improve the signal to background ratio using time-resolved fluorescence spectra (TRES). In addition, fluorescence depolarization measurements showed complete depolarization of the acceptor dyes (Cy5) for both BP-3d (due to sequential FRET steps) and BP-2d (due to the relatively low FRET rate) in the presence of the mRNA target.
doi:10.1016/j.tet.2006.08.109
PMCID: PMC2775546  PMID: 19907676
Binary probes; fluorescence; energy transfer; FRET; time-resolved emission spectra (TRES); Cy5; Alexa488; Fam; Tamra; mRNA
15.  Polyfluorophore Excimers and Exciplexes as FRET Donors in DNA 
Bioconjugate chemistry  2009;20(12):2371-2380.
We describe studies aimed at testing whether oligomeric exciplex- and excimer fluorophores conjugated to DNA have the potential to act as donors for energy transfer by the Förster mechanism. Oligodeoxyfluorosides (ODFs) are composed of stacked, electronically interacting fluorophores replacing the bases on a DNA scaffold. The monomer chromophores in the twenty tetramer-length ODFs studied here include pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and a nonfluorescent spacer (S); these are conjugated in varied combinations at the 3’ end of a 14mer DNA probe sequence. In the absence of an acceptor chromophore, many of the ODF-DNAs show broad, unstructured long-wavelength emission peaks characteristic of excimer and exciplex excited states, similar to what has been observed for unconjugated ODFs. Although such delocalized excited states have been widely studied, we know of no prior report of their use in FRET. We tested the ability of the twenty ODFs to donate energy to Cy5 and TAMRA dyes conjugated to a complementary strand of DNA, with these acceptors oriented either at the near or far end of the ODF-conjugated probes. Results showed that a number of the ODF fluorophores exhibited relatively efficient energy transfer characteristic of the Förster mechanism, as judged by drops in donor emission quantum yield and fluorescence lifetime, accompanied by increases in intensity of acceptor emission bands. Excimer/exciplex bands in the donors were selectively quenched while shorter-wavelength monomer emission stayed relatively constant, consistent with the notion that the delocalized excited states, rather than individual fluorophores, are the donors. Interestingly, only specific sequences of ODFs were able to act as donors, while others did not, even though their emission wavelengths were similar. The new FRET donors possess large Stokes shifts, which can be beneficial for multiple applications. In addition, all ODFs can be excited at a single wavelength; thus, ODFs may be candidates as “universal FRET donors”, thus allowing multicolor FRET of multiple species to be carried out with one excitation.
doi:10.1021/bc9003926
PMCID: PMC2795122  PMID: 19916519
excimer; exciplex; pyrene; perylene; benzopyrene; Förster; cyanine
16.  New Two-photon Absorbing Probe with Efficient Superfluorescent Properties 
The journal of physical chemistry. B  2010;114(44):14087-14095.
The synthesis, linear photophysical and photochemical parameters, two-photon absorption (2PA), and superfluorescence properties of 2,2′-(5,5′-(9,9-didecyl-9H-fluorene-2,7-diyl)bis(ethyne-2,1-diyl)bis(thiophene-5,2-diyl))dibenzo[d]thiazole (1) were investigated, suggesting its potential as an efficient fluorescent probe for bioimaging applications. The steady-state absorption, fluorescence, and excitation anisotropy spectra of 1 were measured in several organic solvents and aqueous media. Probe 1 exhibited high fluorescence quantum yield (∼ 0.7-0.8) and photochemical stability (photobleaching quantum yield ∼ (3 - 7)·10-6). The 2PA spectra were determined over a broad spectral range (640-920 nm) using a standard two-photon induced fluorescence method under femtosecond excitation. A well-defined two-photon allowed absorption band at 680-720 nm with corresponding 2PA cross sections δ2PA ≈ 800-900 GM was observed. The use of probe 1 in bioimaging was shown via one- and two-photon fluorescence imaging of HCT-116 cells. An amplification of the stimulated emission of 1 was demonstrated in organic solvents and thin polystyrene films, which potentially can be used for the development of new fluorescent labels with increased spectral brightness.
doi:10.1021/jp107343k
PMCID: PMC3008650  PMID: 20949957
17.  High-contrast Cu(I)-selective fluorescent probes based on synergistic electronic and conformational switching 
The design of fluorescent probes for the detection of redox-active transition metals such as Cu(I/II) is challenging due to potentially interfering metal-induced non-radiative deactivation pathways. By using a ligand architecture with a built-in conformational switch that maximizes the change in donor potential upon metal binding and an electronically decoupled tunable pyrazoline fluorophore as acceptor, we systematically optimized the photoinduced electron transfer (PET) switching behavior of a series of Cu(I)-selective probes and achieved an excellent fluorescence enhancement of greater than 200-fold. Crystal structure analysis combined with NMR solution studies revealed significant conformational changes of the ligand framework upon Cu(I) coordination. The photophysical data are consistent with a kinetically controlled PET reaction involving only the ligand moiety, despite the fact that Cu(I)-mediated reductive quenching would be thermodynamically preferred. The study demonstrates that high-contrast ratios can be achieved even for redox-active metal cations, providing that the metal-initiated quenching pathways are kinetically unfavorable.
doi:10.1039/C1SC00024A
PMCID: PMC3176711  PMID: 21949587
18.  Biocompatible near-infrared fluorescent nanoparticles for macro and microscopic in vivo functional bioimaging 
Biomedical Optics Express  2014;5(11):4076-4088.
Near-infrared (NIR) imaging technology has been widely used for biomedical research and applications, since it can achieve deep penetration in biological tissues due to less absorption and scattering of NIR light. In our research, polymer nanoparticles with NIR fluorophores doped were synthesized. The morphology, absorption/emission features and chemical stability of the fluorescent nanoparticles were characterized, separately. NIR fluorescent nanoparticles were then utilized as bright optical probes for macro in vivo imaging of mice, including sentinel lymph node (SLN) mapping, as well as distribution and excretion monitoring of nanoparticles in animal body. Furthermore, we applied the NIR fluorescent nanoparticles in in vivo microscopic bioimaging via a confocal microscope. Under the 635 nm-CW excitation, the blood vessel architecture in the ear and the brain of mice, which were administered with nanoparticles, was visualized very clearly. The imaging depth of our one-photon microscopy, which was assisted with NIR fluorescent nanoprobes, can reach as deep as 500 μm. Our experiments show that NIR fluorescent nanoparticles have great potentials in various deep-tissue imaging applications.
doi:10.1364/BOE.5.004076
PMCID: PMC4242039  PMID: 25426331
(160.2540) Fluorescent and luminescent materials; (160.4236) Nanomaterials; (300.6170) Spectra; (170.3880) Medical and biological imaging; (170.2655) Functional monitoring and imaging; (180.1790) Confocal microscopy
19.  Nucleic acid-based fluorescent probes and their analytical potential 
Analytical and Bioanalytical Chemistry  2010;399(9):3157-3176.
It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.
FigureHybridization with a nucleic acid target or affinity interactions with a nonnucleic acid target generate changes in the fluorescence characteristics of a nucleic acid-based fluorescent probe
doi:10.1007/s00216-010-4304-5
PMCID: PMC3044240  PMID: 21046088
Bioanalytical methods; Bioassays; Biosensors; Chemical sensors; Fluorescence/luminescence; Nucleic acids (DNA, RNA)
20.  Computational Studies on Response and Binding Selectivity of Fluorescence Sensors 
Using a computational strategy based on density functional theory calculations, we successfully designed a fluorescent sensor for detecting Zn2+ [J. Phys. Chem. B 2006, 110, 22991-22994]. In this work, we report our further studies on the computational design protocol for developing Photoinduced Electron Transfer (PET) fluorescence sensors. This protocol was applied to design a PET fluorescence sensor for Zn2+ ions, which consists of anthracene as the fluorophore connected to pyridine as the receptor through dimethylethanamine as the linker. B3LYP and time-dependent B3LYP calculations were performed with the basis set 6-31G(d,p), 6-31+G(d,p), 6-311G(d,p), and 6-311+G(d,p). The calculated HOMO and LUMO energies of the fluorophore and receptor using all four basis sets show that the relative energy levels remain unchanged. This indicates that any of these basis sets can be used in calculating the relative molecular orbital (MO) energy levels. Furthermore, the relative MO energies of the independent fluorophore and receptor are not altered when they are linked together, which suggests that one can calculate the MO energies of these components separately and use them as the MO energies of the free sensor. These are promising outcomes for the computational design of sensors, though more case studies are needed to further confirm these conclusions. The binding selectivity studies indicate that the predicted sensor can be used for Zn2+ even in the presence of the divalent cation, Ca2+.
doi:10.1021/jp908368k
PMCID: PMC2859673  PMID: 20039659
21.  Bioorthogonal chemistry: strategies and recent development 
The use of covalent chemistry to track biomolecules in their native environment—a focus of bioorthogonal chemistry—has received considerable interests recently among chemical biologists and organic chemists alike. To facilitate wider adoption of bioorthogonal chemistry in biomedical research, a central effort in the last few years has been focused on the optimization of a few known bioorthogonal reactions, particularly with respective to reaction kinetics improvement, novel genetic encoding systems, and fluorogenic reactions for bioimaging. During these optimizations, three strategies have emerged, including the use of ring strain for substrate activation in the cycloaddition reactions, the discovery of new ligands and privileged substrates for accelerated metal-catalysed reactions, and the design of substrates with pre-fluorophore structures for rapid “turn-on” fluorescence after selective bioorthogonal reactions. In addition, new bioorthogonal reactions based on either modified or completely unprecedented reactant pairs have been reported. Finally, increasing attention has been directed toward the development of mutually exclusive bioorthogonal reactions and their applications in multiple labeling of a biomolecule in cell culture. In this feature article, we wish to present the recent progress in bioorthogonal reactions through the selected examples that highlight the above-mentioned strategies. Considering increasing sophistication in bioorthogonal chemistry development, we strive to project several exciting opportunities where bioorthogonal chemistry can make a unique contribution to biology in near future.
doi:10.1039/c3cc44272a
PMCID: PMC3847904  PMID: 24145483
22.  Theranostic Nanoshells: From Probe Design to Imaging and Treatment of Cancer 
Accounts of chemical research  2011;44(10):936-946.
CONSPECTUS
Recent advances in theranostics have expanded our ability to design and construct multifunctional nanoparticles that will ultimately allow us to image and treat diseases in a single clinical procedure. Theranostic nanoparticles, combining targeting, therapeutic and diagnostic functions within a single nanoscale complex, have emerged as a result of this confluence of nanoscience and biomedicine. The theranostic capabilities of gold nanoshells -spherical, silica core, gold shell nanoparticles- have attracted tremendous attention over the past decade as nanoshells have emerged as a promising tool for cancer therapy and bioimaging enhancement. This account examines the design and synthesis of nanoshell-based theranostic agents, their plasmon-derived optical properties and their corresponding applications. Nanoshells illuminated with resonant light are either strong optical absorbers or scatterers, properties which give rise to their unique capabilities. In this account, we discuss the underlying physical principles contributing to the photothermal response of nanoshells. We elucidate the photophysics of nanoshell-induced fluorescence enhancement of weak near-infrared fluorophores. We then describe the application of nanoshells as a contrast agent for optical coherence tomography of breast carcinoma cells in vivo. We also examine the recent progress of nanoshells as a multimodal theranostic probe for near-infrared fluorescence and magnetic resonance imaging (MRI) combined with photothermal ablation of cancer cells. The design and preparation of nanoshell complexes is discussed, and their ability to enhance the photoluminescence of fluorophores while incorporating MR contrast is described. We show the theranostic potential of the multimodal nanoshells in vivo for imaging subcutaneous breast cancer tumors in animal models and their biodistribution in various tissues.
We then discuss the potential of nanoshells as light-triggered gene therapy vectors. The plasmonic properties of nanoshells make them highly effective as light controlled delivery vectors, adding temporal control to the spatial control characteristic of nanoparticle-based gene therapy approaches. We describe the fabrication of DNA-conjugated nanoshell complexes and compare the efficiency of light-induced and thermally-induced DNA release of DNA. We examine light-triggered release of DAPI (4',6-diamidino-2-phenylindole) molecules, which bind reversibly to double-stranded DNA, to visualize intracellular light-induced release. Finally, we look at future prospects of nanoshell-based theranostics, the potential impact and near-term challenges of theranostic nanomedicine in the next decade.
doi:10.1021/ar200023x
PMCID: PMC3888233  PMID: 21612199
23.  In vivo Biodistribution and Clearance Studies using Multimodal ORMOSIL Nanoparticles 
ACS nano  2010;4(2):699-708.
Successful translation of the use of nanoparticles from laboratories to clinics requires exhaustive and elaborate studies involving the biodistribution, clearance and biocompatibility of nanoparticles for in vivo biomedical applications. We report here the use of multimodal organically modified silica (ORMOSIL) nanoparticles for in vivo bioimaging, biodistribution, clearance and toxicity studies. We have synthesized ORMOSIL nanoparticles with diameters of 20-25 nm, conjugated with near infra-red (NIR) fluorophores and radiolabelled them with 124I, for optical and PET imaging in vivo. The biodistribution of the non targeted nanoparticles was studied in non-tumored nude mice by optical fluorescence imaging, as well by measuring the radioactivity from harvested organs. Biodistribution studies showed a greater accumulation of nanoparticles in liver, spleen and stomach than in kidney, heart and lungs. The clearance studies carried out over a period of 15 days indicated hepatobiliary excretion of the nanoparticles. Selected tissues were analyzed for any potential toxicity by histological analysis, which confirmed the absence of any adverse effect or any other abnormalities in the tissues. The results demonstrate that these multimodal nanoparticles have potentially ideal attributes for use as biocompatible probes for in vivo imaging.
doi:10.1021/nn901146y
PMCID: PMC2827663  PMID: 20088598
ORMOSIL Nanoparticles; optical and PET Imaging; NIR fluorophore; 124I radiolabeling; Biodistribution; clearance and toxicity
24.  Rational design, synthesis and characterization of highly fluorescent optical switches for high-contrast optical lock-in detection (OLID) imaging microscopy in living cells 
Bioorganic & medicinal chemistry  2010;19(3):1030-1040.
A major challenge in cell biology is to elucidate molecular mechanisms that underlie the spatio-temporal control of cellular processes. These studies require microscope imaging techniques and associated optical probes that provide high-contrast and high-resolution images of specific proteins and their complexes. Auto-fluorescence however, can severely compromise image contrast and represents a fundamental limitation for imaging proteins within living cells. We have previously shown that optical switch probes and optical lock-in detection (OLID) image microscopy improve image contrast in high background environments. Here, we present the design, synthesis and characterization of amino- reactive and cell permeable optical switches that integrate the highly fluorescent fluorophore, tetramethylrhodamine (TMR) and spironaphthoxazine (NISO), a highly efficient optical switch. The NISO moiety in TMR-NISO undergoes rapid and reversible, excited-state driven transitions between a colorless spiro (SP)-state and a colored merocyanine (MC)-state in response to irradiation with 365 nm and >530 nm light. In the MC-state, the TMR (donor) emission is almost completely extinguished by Förster resonance energy transfer (FRET) to the MC probe (acceptor), whereas in the colorless SP-state, the quantum yield for TMR fluorescence is maximal. Irradiation of TMR-NISO with a defined sequence of 365 nm and 546 nm manipulates the levels of SP and MC with concomitant modulation of FRET efficiency and the TMR fluorescence signal. High fidelity optical switching of TMR fluorescence is shown for TMR-NISO probes in vitro and for membrane permeable TMR-NISO within living cells.
doi:10.1016/j.bmc.2010.07.015
PMCID: PMC2997889  PMID: 20674372
Optical switch; FRET; Spironaphthoxazine; NISO; Tetramethylrhodamine; Fluorescence
25.  Multicolored pH-Tunable and Activatable Fluorescence Nanoplatform Responsive to Physiologic pH Stimuli 
Tunable, ultra-pH responsive fluorescent nanoparticles with multichromatic emissions are highly valuable in a variety of biological studies, such as endocytic trafficking, endosome/lysosome maturation, and pH regulation in subcellular organelles. Small differences (e.g., <1 pH unit) and yet finely regulated physiological pH inside different endocytic compartments present a huge challenge to the design of such a system. Herein, we report a general strategy to produce pH-tunable, highly activatable multicolored fluorescent nanoparticles using commonly available pH-insensitive dyes with emission wavelengths from green to near IR range. pH-induced micellization is the primary driving force of fluorescence activation between the ON (unimer) and OFF (micelle) states. Among three possible photochemical mechanisms, homo Förster resonance energy transfer (homo-FRET) was found to be the most facile strategy to render ultra-pH response over the H-dimer and photoinduced electron transfer (PeT) mechanisms. Based on this insight, we selected several fluorophores with small Stoke shifts (<40 nm) and established a panel of multicolored nanoparticles with wide emission range (500-820 nm) and different pH transitions. Each nanoparticle maintained the sharp pH response (ON/OFF <0.25 pH unit) with corresponding pH transition point at pH 5.2, 6.4, 6.9 and 7.2. Incubation of a mixture of multicolored nanoparticles with human H2009 lung cancer cells demonstrated sequential activation of the nanoparticles inside endocytic compartments directly correlating with their pH transitions. This multicolored, pH-tunable nanoplatform offers many exciting opportunities for the study of many important cell physiological processes such as pH regulation and endocytic trafficking of subcellular organelles.
doi:10.1021/ja300176w
PMCID: PMC3427786  PMID: 22524413

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