Activity-Based Genetically Encoded Fluorescent and Luminescent Probes for Detecting Formaldehyde in Living Cells

Formaldehyde (FA) is endogenously produced in living systems through a variety of biological processes and has been implicated in many pathological conditions. Detection tools for biological FA are therefore of great interest. Reported here are novel activity-based genetically encoded fluorescent and luminescent probes for detecting FA in aqueous solutions and living mammalian cells. A FA-reactive lysine analogue, PrAK, was site-specifically incorporated into the essential lysine sites of enhanced green fluorescent protein (EGFP) and firefly luciferase (fLuc) to afford fluorescent and luminescent FA probes, respectively. FA selectively reacts with PrAK residues on EGFP and fLuc through a 2-aza-Cope rearrangement, resulting in fluorescence and luminescence turn-on responses, respectively, to FA selectively over potentially interfering reactive species in aqueous buffer. Moreover, the genetically encoded probes are capable of visualizing FA at physiologically relevant levels in living mammalian cells by fluorescence and luminescence imaging, demonstrating their potential as new tools to explore FA biology.     

Activity‐Based Genetically Encoded Fluorescent and Luminescent Probes for Detecting Formaldehyde in Living Cells

Formaldehyde (FA) is endogenously produced in living systems through a variety of biological processes and has been implicated in many pathological conditions. Detection tools for biological FA are therefore of great interest. Reported here are novel activity‐based genetically encoded fluorescent and luminescent probes for detecting FA in aqueous solutions and living mammalian cells. A FA‐reactive lysine analogue, PrAK, was site‐specifically incorporated into the essential lysine sites of enhanced green fluorescent protein (EGFP) and firefly luciferase (fLuc) to afford fluorescent and luminescent FA probes, respectively. FA selectively reacts with PrAK residues on EGFP and fLuc through a 2‐aza‐Cope rearrangement, resulting in fluorescence and luminescence turn‐on responses, respectively, to FA selectively over potentially interfering reactive species in aqueous buffer. Moreover, the genetically encoded probes are capable of visualizing FA at physiologically relevant levels in living mammalian cells by fluorescence and luminescence imaging, demonstrating their potential as new tools to explore FA biology.     

FRET in a Synthetic Flavin‐ and Bilin‐binding Protein

The last decade has seen development and application of a large number of novel fluorescence‐based techniques that have revolutionized fluorescence microscopy in life sciences. Preferred tags for such applications are genetically encoded fluorescent proteins (FP), mostly derivatives of the green fluorescent protein (GFP). Combinations of FPs with wavelength‐separated absorption/fluorescence properties serve as excellent tools for molecular interaction studies, for example, protein–protein complexes or enzyme–substrate interactions, based on the FRET phenomenon (Förster resonance energy transfer). However, alternatives are requested for experimental conditions where FP proteins or FP couples are not or less efficiently applicable. We here report as a “proof of principle” a specially designed, non‐naturally occurring protein (LG1) carrying a combination of a flavin‐binding LOV‐ and a photochromic bilin‐binding GAF domain and demonstrate a FRET process between both chromophores.     

Properties of the bimodal fluorescent protein produced by Photobacterium phosphoreum

A fluorescent protein isolated from the deep-sea luminous bacterium Photobacterium phosphoreum strain bmFP has been purified, cloned and sequenced. The protein is 96.5% identical in amino acid sequence to FP390, the weakly fluorescent flavoprotein encoded by the luxF gene characteristic of Photobacterium species. Similar to FP390, bmFP is a dimer of two homologous subunits binding four FMN-myristate chromophores but has the distinctive feature of emitting a bimodal fluorescence with maxima at about 488 and 517 nm, hence the name bmFP. For both bands of this fluorescence, the excitation spectrum exhibits a peak at 336 nm, not corresponding to its flavin-like absorption spectrum. Heating of bmFP in urea resulted in a decrease in the intensity of the 488 nm band along with the appearance of a new fluorescence peaking at 423 nm, partially reversible upon the removal of the urea. Upon complete denaturation, either by heat or guanidium chloride at 65 degrees C, fluorescence characteristic of both free flavin and this 423 nm species appears. It is speculated that chromophores in different states of protonation, associated with a single protein, are responsible for the unusual spectral properties of bmFP.     

DNAzyme-Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells

Genetically encoded fluorescent proteins (FPs) have been used for metal ion detection. However, their applications are restricted to a limited number of metal ions owing to the lack of available metal-binding proteins or peptides that can be fused to FPs and the difficulty in transforming the binding of metal ions into a change of fluorescent signal. We report herein the use of Mg²⁺-specific 10–23 or Zn²⁺-specific 8–17 RNA-cleaving DNAzymes to regulate the expression of FPs as a new class of ratiometric fluorescent sensors for metal ions. Specifically, we demonstrate the use of DNAzymes to suppress the expression of Clover2, a variant of the green FP (GFP), by cleaving the mRNA of Clover2, while the expression of Ruby2, a mutant of the red FP (RFP), is not affected. The Mg²⁺ or Zn²⁺ in HeLa cells can be detected using both confocal imaging and flow cytometry. Since a wide variety of metal-specific DNAzymes can be obtained, this method can likely be applied to imaging many other metal ions, expanding the range of the current genetically encoded fluorescent protein-based sensors.     

Salmonella-host cell interactions, changes in host cell architecture, and destruction of prostate tumor cells with genetically altered Salmonella.

Increasingly, genetically modified Salmonella are being explored as a novel treatment for cancer because Salmonella preferentially replicate within tumors and destroy cancer cells without causing the septic shock that is typically associated with wild-type S. typhimurium infections. However, the mechanisms by which genetically modified Salmonella strains preferentially invade cancer cells have not yet been addressed in cellular detail. Here we present data that show S. typhimurium strains VNP20009, LT2, and CRC1674 invasion of PC-3M prostate cancer cells. S. typhimurium-infected PC-3M human prostate cancer cells were analyzed with immunofluorescence microscopy and transmission electron microscopy (TEM) at various times after inoculation. We analyzed microfilaments, microtubules, and DNA with fluorescence and immunofluorescence microscopy. 3T3 Phi-Yellow-mitochondria mouse 3T3 cells were used to study the effects of Salmonella infestation on mitochondria distribution in live cells. Our TEM results show gradual destruction of mitochondria within the PC-3M prostate cancer cells with complete loss of cristae at 8 h after inoculation. The fluorescence intensity in YFP-mitochondria-transfected mouse 3T3 cells decreased, which indicates loss of mitochondria structure. Interestingly, the nucleus does not appear affected by Salmonella within 8 h. Our data demonstrate that genetically modified S. typhimurium destroy PC-3M prostate cancer cells, perhaps by preferential destruction of mitochondria.     

A novel single frequency stabilized Fabry-Perot laser diode at 1590 nm for gas sensing

A novel single frequency stabilized Fabry-Perot (SFP) laser diode with an emission wavelength of lambda = 1590 nm for H2S gas sensing is reported. Sculpting of the multi-mode spectral distribution of a FP laser to achieve single frequency emission is carried out using post growth photolitographic processing of the device. The resulting longitudinal-mode controlled FP laser has a stabilized single frequency emission with a side mode suppression ratio (SMSR) of 40 dB. The application of this device to spectroscopic based H2S sensing is demonstrated by targeting absorption lines in the wavelength range 1588 < or = lambda < or = 1591 nm. Using wavelength modulation spectroscopy (WMS), a low detection limit of 120 ppm x m x Hz(-1/2) was estimated while targeting the absorption line at 1590.08 nm. These initial results demonstrate the potential of the stabilized FP laser diode at this wavelength as a tunable, single frequency source for spectroscopic based gas sensing.     

DNAzyme‐Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells

Genetically encoded fluorescent proteins (FPs) have been used for metal ion detection. However, their applications are restricted to a limited number of metal ions owing to the lack of available metal‐binding proteins or peptides that can be fused to FPs and the difficulty in transforming the binding of metal ions into a change of fluorescent signal. We report herein the use of Mg²⁺‐specific 10–23 or Zn²⁺‐specific 8–17 RNA‐cleaving DNAzymes to regulate the expression of FPs as a new class of ratiometric fluorescent sensors for metal ions. Specifically, we demonstrate the use of DNAzymes to suppress the expression of Clover2, a variant of the green FP (GFP), by cleaving the mRNA of Clover2, while the expression of Ruby2, a mutant of the red FP (RFP), is not affected. The Mg²⁺ or Zn²⁺ in HeLa cells can be detected using both confocal imaging and flow cytometry. Since a wide variety of metal‐specific DNAzymes can be obtained, this method can likely be applied to imaging many other metal ions, expanding the range of the current genetically encoded fluorescent protein‐based sensors.     

Identification of a chemical substructure that is immobilized to ferrite nanoparticles (FP)

Despite the wide utility of ferrite nanoparticles (FP), a methodology to conjugate heterologous molecules to FP is still limited and characterization of small molecule-conjugated FP is not well known. Here, we describe what kinds of proteins and amino acids are selectively immobilized onto FP when FP is synthesized in the presence of these molecules. Two-dimentional gel electrophoresis (2D SDS-PAGE) showed that proteins with low pI value were selectively bound to FP. Quantitative analyses using HPLC suggested that L-aspartic acid (Asp) and L-cysteine (Cys) were bound to FP selectively among natural amino acids examined. Additional analysis of compounds-conjugated FP revealed that selective binding of Asp to FP was attributed with its molecular structure. It was found that the substructure of amino acid-bound to FP specifically was composed of a defined chelation of two carboxyl groups separated by two carbon atoms as deduced from FT-IR measurement. Thus, we concluded that molecules possessing two carboxyl groups separated by two carbons were bound to FP spontaneously and selectively, which might enable the attachment of free functional groups onto the FP surface if their molecules have functional groups other than carboxyl groups. The resulting complex might be applicable as a chemical tag to immobilize various molecules onto FP.     

Novel 6-formylpterin derivatives: chemical synthesis and O2 to ROS conversion activities

6-Formylpterin (6FP) has been demonstrated to have strong neuroprotective effects against transient ischemia-reperfusion injury in gerbils. Also it has been shown that in rats, 6FP protected retinal neurons even when it was administered after the ischemic insult. Since there is a significant need for such a compound that effectively suppresses the events caused by the lack of oxygen supply, 6FP has attracted further investigation. Unfortunately, however, 6FP is hardly soluble in water at neutral pH and in organic solvents because of its self-assembling ability. Although a several mM solution of 6FP is available in alkaline water, it is unstable. In the present study, a novel chemical derivatization of 6FP has been developed which maintains the formyl group on the 6-position of 6FP, which is essential for the physiological activities of 6FP, and increases solubility in water and organic solvents. In the method, the 2- and 3-positions of 6FP were modified by a three component coupling reaction: 6FP was subjected to the reaction with acid chloride and N,N-dimethylformamide. The derivatives synthesized here, 2-(N,N-dimethylaminomethyleneamino)-6-formyl-3-pivaloylpteridine-4-one 1, 2-(N,N-dimethylaminomethyleneamino)-6-formyl-3-isobutyrylpteridine-4-one 2, and 2-(N,N-dimethylaminomethyleneamino)-6-formyl-3-o-toluoylpteridine-4-one 3, showed high solubility in water (1.0-5.6 mM) and organic solvents. The O(2) conversion property has also been determined for the derivative 1. Using an oxygen electrode, it has been found that O(2) is consumed in the presence of 1 and NADH at around pH 7.4 and that the rate of O(2) consumption is enhanced by UV-A irradiation. Electron paramagnetic resonance (EPR) analysis coupled with DMPO spin trapping has also revealed that in the presence of NADH, 1 converts O(2) to O(2)(-), which is further reduced to OH. By UV-A illumination in the analogous systems, (1)O(2) formation was observed. These results are similar to those reported previously for 6FP.     

Selective functionalization of a genetically encoded alkene-containing protein via "photoclick chemistry" in bacterial cells

We report a tetrazole-based, photoclick chemistry that can be employed to selectively functionalize an alkene genetically encoded in a protein inside E. coli cells. The reaction involved the treatment of E. coli cells with cell-permeable tetrazoles followed by a brief photo irradiation at 302 nm (4 min) and an overnight incubation at 4 degrees C. This in vivo alkene functionalization procedure was simple, straightforward, and nontoxic to E. coli cells. Additionally, fluorescent adducts were formed, facilitating the monitoring of the reaction in vivo. This reaction should offer a new tool for the study of alkene-containing proteins in living systems.     

Molecular and ionic complexes of pyrrolidinofullerene bearing chelating 3-pyridyl units

Molecular and ionic complexes of cis-2',5'-di(pyridin-3-yl)pyrrolidino[3',4':1,9](C(60)-I(h))[5,6]fullerene DP3FP with chlorobenzene (C(6)H(5)Cl), manganese(II) tetraphenylporphyrin (Mn(II)TPP) and tetrakis(dimethylamino)ethylene (TDAE) have been obtained for the first time. X-ray single crystal structure determination for the crystalline DP3FP·C(6)H(5)Cl (1) solvate proved unambiguously its molecular structure with the cis-arrangement of chelating 3-pyridyl groups. It has been demonstrated that DP3FP easily forms self-assembled photoactive complexes with metallated porphyrins. For example, the formation of a 1 : 1 complex between DP3FP and zinc (II) tetraphenylporphyrin (Zn(II)TPP) in cyclohexane solution (2) was evidenced using absorption spectroscopy. A successful X-ray single crystal structure determination was performed for a self-assembled triad composed of a DP3FP molecule linked with two Mn(II)TPP molecules in {DP3FP·(Mn(II)TPP)(2)}·(C(6)H(4)Cl(2))(3) (3). A strong organic donor TDAE reduces DP3FP to the radical anion state thus forming an ionic complex (TDAE˙(+))·(DP3FP˙(-))·(C(6)H(4)Cl(2))(1.6) (4). Optical, electronic and magnetic properties of 4 were investigated in detail. The performed studies strongly suggest that pyrrolidinofullerene DP3FP can be used as a building block in the design of various organic materials with advanced optoelectronic and/or magnetic properties.     

A cellular FRET-based sensor for beta-O-GlcNAc, a dynamic carbohydrate modification involved in signaling

beta-O-N-Acetyl-d-glucosamine (O-GlcNAc) is a dynamic carbohydrate modification that is involved in cell signaling and has been implicated in a variety of disease states, including Alzheimer's and type-II diabetes. Despite the importance of this modification, little is known about the spatial and temporal localization of O-GlcNAc during signaling. This is due to the lack of methods for the study of O-GlcNAc in living cell systems. Herein we report the first genetically encoded FRET-based sensor for the detection of O-GlcNAc dynamics in live mammalian cells.     

Highly selective, naked-eye and fluorescent "off-on" probe for detection of histidine/histidine-rich proteins and its application in living cell imaging

A highly selective colorimetric and fluorescence enhanced probe S1 (M2@Cu) for histidine and histidine-rich proteins has been developed. In neutral aqueous ethanol solution, probe S1 can selectively detect histidine out of twenty DNA encoded amino acids by showing a color change from brownish red to light green, and with a fluorescence enhancement up to 99-fold at 537 nm, simultaneously.     

High-throughput examination of fluorescence resonance energy transfer-detected metal-ion response in mammalian cells

Fluorescence resonance energy transfer (FRET)-based genetically encoded metal-ion sensors are important tools for studying metal-ion dynamics in live cells. We present a time-resolved microfluidic flow cytometer capable of characterizing the FRET-based dynamic response of metal-ion sensors in mammalian cells at a throughput of 15 cells/s with a time window encompassing a few milliseconds to a few seconds after mixing of cells with exogenous ligands. We have used the instrument to examine the cellular heterogeneity of Zn(2+) and Ca(2+) sensor FRET response amplitudes and demonstrated that the cluster maps of the Zn(2+) sensor FRET changes resolve multiple subpopulations. We have also measured the in vivo sensor response kinetics induced by changes in Zn(2+) and Ca(2+) concentrations. We observed an ～30 fold difference between the extracellular and intracellular sensors.     

Cis-trans photoisomerization of fluorescent-protein chromophores

Photochromic variants of fluorescent proteins are opening the way to a number of opportunities for high-sensitivity regioselective studies in the cellular environment and may even lead to applications in information and communication technology. Yet, the detailed photophysical processes at the basis of photoswitching have not been fully clarified. In this paper, we used synthetic FP chromophores to clarify the photophysical processes associated with the photochromic behavior. In particular, we investigated the spectral modification of synthetic chromophore analogues of wild-type green fluorescent protein (GFP), Y66F GFP (BFPF), and Y66W GFP (CFP) upon irradiation in solutions of different polarities. We found that the cis-trans photoisomerization mechanism can be induced in all the chromophores. The structural assignments were carried out both by NMR measurements and DFT calculations. Remarkably, we determined for the first time the spectra of neutral trans isomers in different solvents. Finally, we calculated the photoconversion quantum yields by absorption measurements under continuous illumination at different times and by a nanosecond laser-flash photolysis method. Our results indicate that cis-trans photoisomerization is a general mechanism of FP chromophores whose efficiency is modulated by the detailed mutant-specific protein environment.     

Constructing Photoactivatable Protein with Genetically Encoded Photocaged Glutamic Acid

Genetically replacing an essential residue with the corresponding photocaged analogues via genetic code expansion (GCE) constitutes a useful and unique strategy to directly and effectively generate photoactivatable proteins. However, the application of this strategy is severely hampered by the limited number of encoded photocaged proteinogenic amino acids. Herein, we report the genetic incorporation of photocaged glutamic acid analogues in E. coli and mammalian cells and demonstrate their use in constructing photoactivatable variants of various fluorescent proteins and SpyCatcher. We believe genetically encoded photocaged Glu would significantly promote the design and application of photoactivatable proteins in many areas.     

新型支化侧链偶氮聚电解质的合成与性能研究

通过后重氮偶合的方法合成了一种含支化侧链偶氮苯生色团的聚电解质 (PBANT AC) .用IR、NMR、DSC、UV和元素分析等手段对聚合物的结构和性能进行了表征 .研究发现 ,在不同比例的水和四氢呋喃混合溶剂中PBANT AC的紫外 可见光光谱有很大的差别 .这种差别反映了PBANT AC分子中的偶氮苯生色团的不同聚集状态 .通过静电吸附逐层自组装的方法将PBANT AC分子组装成多层膜 .在 488nm的偏振Ar+ 激光的照射下 ,聚合物薄膜中的偶氮苯生色团可发生光致取向 ,取向有序度约 0 0 5 .偶氮苯生色团的顺反异构化反应使H 聚集体在光照后发生解聚集     

Bond selection in the photoisomerization reaction of anionic green fluorescent protein and kindling fluorescent protein chromophore models

The chromophores of the most widely known fluorescent proteins (FPs) are derivatives of a core p-hydroxybenzylidene-imidazolinon-5-one (HBI) motif, which usually occurs as a phenolate anion. Double bond photoisomerization of the exocyclic bridge of HBI is widely held to be an important internal conversion mechanism for FP chromophores. Herein we describe the ground and excited-state electronic structures and potential energy surfaces of two model chromophores: 4- p-hydroxybenzylidiene-1,2-dimethyl-imidazolin-5-one anion (HBDI), representing green FPs (GFPs), and 2-acetyl-4-hydroxybenylidene-1-methyl-imidazolin-5-one anion (AHBMI), representing kindling FPs (KFPs). These chromophores differ by a single substitution, but we observe qualitative differences in the potential energy surfaces which indicate inversion of bond selection in the photoisomerization reaction. Bond selection is also modulated by whether the reaction proceeds from a Z or an E conformation. These configurations correspond to fluorescent and nonfluorescent states of structurally characterized FPs, including some which can be reversibly switched by specific illumination regimes. We explain the difference in bond selectivity via substituent stabilization effects on a common set of charge-localized chemical structures. Different combinations of these structures give rise to both optically active (planar) and twisted intramolecular charge-transfer (TICT) states of the molecules. We offer a prediction of the gas-phase absorption of AHBMI, which has not yet been measured. We offer a hypothesis to explain the unusual fluorescence of AHBMI in DMF solution, as well as an experimental proposal to test our hypothesis.     

几个荧光蛋白发色团双光子吸收性质的理论研究

实验测得的荧光蛋白的单、双光子吸收光谱在低频和高频区域都表现出明显不同的特征。为了揭示这些不同点的起源和研究荧光蛋白的构–效关系,我们详细研究了三种荧光蛋白发色团(一种增强型蓝绿色荧光蛋白的中性发色团和两种红色荧光蛋白的阴离子发色团)的单、双光子吸收特性,分别计算了纯的和振动分辨的电子谱。计算结果表明：光谱线形与计算采用的交换相关密度泛函及谱截面计算所采用的近似关系密切;如果在计算光谱截面时,我们利用长程修正的交换相关泛函CAM-B3LYP来计算几何和电子结构参数,然后把Franck-Condon (FC)效应和包含Herzberg-Teller (HT)效果的电-声耦合效应都考虑进去,理论计算的光谱与实验测定的光谱可以很好地符合;对于两种离子态的发色团,HT电-声耦合效应使得对应于基态到第一激发态跃迁的双光子吸收最强峰相对于单光子吸收的最强峰发生了蓝移,但HT电-声耦合效应对高频的双光子吸收谱没有太大的影响;分子内电荷转移是导致高频区的双光子吸收明显强于单光子吸收的主要原因。