Synthesis and fluorescence study of 7-azaindole in DNA oligonucleotides replacing a purine base

The fluorescence spectroscopy of 7-azaindole (7aIn) incorporated in DNA oligonucleotides is investigated. Incorporation of 7aIn into DNA oligonucleotides is accomplished through standard solid-phase phosphoramidite chemistry. Fluorescence emission of the 7aIn chromophore shifts slightly to the red (from 386 nm to 388 nm) upon glycosylation at the N-1 position, but its relative fluorescence quantum yield increases 23 times, from 0.023 to 0.53. Upon incorporation into DNA, the fluorescence emission of 7aIn is greatly quenched with fluorescence quantum yields of 0.020 and 0.016 in single and double strand DNA, respectively. The fluorescence emission for 7aIn in DNA oligonucleotides shifts to the blue with an emission maximum at 379 nm. Both the strong fluorescence quenching and the blue shift of the emission spectrum signify that 7aIn is stacked with neighboring DNA bases in both single and double strand DNA. As the duplex DNA melts due to temperature increase, the fluorescence of the 7aIn chromophore increases, indicating the transition from the less fluorescent duplex DNA to the more fluorescent single strand DNA. Since this fluorescent 7aIn is a structural analog of purine, its fluorescence property may be utilized as a probe for studying nucleic acid structure and dynamics.     

Quantification of Photosensitized Singlet Oxygen Production by a Fluorescent Protein

Fluorescent proteins are increasingly becoming actuators in a range of cell biology techniques. One of those techniques is chromophore‐assisted laser inactivation (CALI), which is employed to specifically inactivate the function of target proteins or organelles by producing photochemical damage. CALI is achieved by the irradiation of dyes that are able to produce reactive oxygen species (ROS). The combination of CALI and the labelling specificity that fluorescent proteins provide is useful to avoid uncontrolled photodamage, although the inactivation mechanisms by ROS are dependent on the fluorescent protein and are not fully understood. Herein, we present a quantitative study of the ability of the red fluorescent protein TagRFP to produce ROS, in particular singlet oxygen (¹O₂). TagRFP is able to photosensitize ¹O₂ with an estimated quantum yield of 0.004. This is the first estimation of a quantum yield of ¹O₂ production value for a GFP‐like protein. We also find that TagRFP has a short triplet lifetime compared to EGFP, which reflects relatively high oxygen accessibility to the chromophore. The insight into the structural and photophysical properties of TagRFP has implications in improving fluorescent proteins for fluorescence microscopy and CALI.     

Fluorescent proteins as biomarkers and biosensors: throwing color lights on molecular and cellular processes

Green fluorescent protein (GFP) from jellyfish Aequorea victoria is the most extensively studied and widely used in cell biology protein. GFP-like proteins constitute a fast growing family as several naturally occurring GFP-like proteins have been discovered and enhanced mutants of Aequorea GFP have been created. These mutants differ from wild-type GFP by conformational stability, quantum yield, spectroscopic properties (positions of absorption and fluorescence spectra) and by photochemical properties. GFP-like proteins are very diverse, as they can be not only green, but also blue, orange-red, far-red, cyan, and yellow. They also can have dual-color fluorescence (e.g., green and red) or be non-fluorescent. Some of them possess kindling property, some are photoactivatable, and some are photoswitchable. This review is an attempt to characterize the main color groups of GFP-like proteins, describe their structure and mechanisms of chromophore formation, systemize data on their conformational stability and summarize the main trends of their utilization as markers and biosensors in cell and molecular biology.     

Analogues of uracil nucleosides with intrinsic fluorescence (NIF-analogues): synthesis and photophysical properties

Uridine cannot be utilized as fluorescent probe due to its extremely low quantum yield. For improving the uracil fluorescence characteristics we extended the natural chromophore at the C5 position by coupling substituted aromatic rings directly or via an alkenyl or alkynyl linker to create fluorophores. Extension of the uracil base was achieved by treating 5-I-uridine with the appropriate boronic acid under the Suzuki coupling conditions. Analogues containing an alkynyl linker were obtained from 5-I-uridine and the suitable boronic acid in a Sonogashira coupling reaction. The uracil fluorescent analogues proposed here were designed to satisfy the following requirements: a minimal chemical modification at a position not involved in base-pairing, resulting in relatively long absorption and emission wavelengths and high quantum yield. 5-((4-Methoxy-phenyl)-trans-vinyl)-2'-deoxy-uridine, 6b, was found to be a promising fluorescent probe. Probe 6b exhibits a quantum yield that is 3000-fold larger than that of the natural chromophore (Φ 0.12), maximum emission (478 nm) which is 170 nm red shifted as compared to uridine, and a Stokes shift of 143 nm. In addition, since probe 6b adopts the anti conformation and S sugar puckering favored by B-DNA, it makes a promising nucleoside analogue to be incorporated in an oligonucleotide probe for detection of genetic material.     

Spectral Versatility of Single Reef Coral Fluorescent Proteins Detected by Spectrally‐Resolved Single Molecule Spectroscopy

We use spectrally‐resolved room temperature single molecule spectroscopy to yield insights into the occurrence and dynamics of spectral forms of single tetramers of DsRed and its variants DsRed2, Fluorescent Timer, DsRed_N42H and AG4. The red‐emitting chromophore in DsRed and all studied variants readily converts into a high quantum efficiency super‐red emitting form. We propose the existence of two super‐red forms of different quantum efficiencies. The observed emission from the green‐emitting chromophore is consistent with bulk spectroscopy. We further observe distinct new spectral forms from each variant, which we attribute to a photoinduced chemical reaction leading to a truncated form of the red‐emitting chromophore analogous to the chromophore in the visible fluorescent protein zFP538. Our results have implications for the accurate interpretation of biological and biochemical processes illuminated by fluorescent proteins as well as for choosing appropriate experimental configurations.     

Self-restricted oxazolone GFP chromophore for construction of reaction-based fluorescent probe toward dopamine

The β-barrel provides a confined environment for chromophores of the green fluorescent protein (GFP) family, defining their emission profiles by the chromophore/β-barrel interactions. Here, we describe the generation of self-restricted oxazolone GFP chromophore (GFPc) for construction of reaction-based fluorescent probe toward dopamine by mimicking the confinement effect of the β-barrel. Through standard synthetic method, the first self-restricted GFPc oxazolone analogue (MBDO) and the conventional pyrenyl-based chromophore (PDO) were prepared respectively. Under the same condition, MBDO shows much better emission response with fluorescent quantum yield (QY) over one order of magnitude higher than that of PDO due to the generation of the self-restricted effect. And, the fluorescent QY of MBDO reaches above 30% in dimethyl sulfoxide, which is the largest ever recorded for unlocked GFPc analogues in highly polar solvents. Moreover, theoretical calculations further reveal that the enhanced emission of MBDO is due to the inhibition of conformational motions around the exocyclic CC bonds. Combination the enhanced emission and the reactivity of the lactone, MBDO is applied to construct reaction-based fluorescent probe toward dopamine via a ring-opening reaction of the lactone. Prospectively, the destruction of the oxazolone would break the effective conjugated structure of the chromophore, which can decrease the corresponding fluorescence. This work puts forward a novel approach to generate highly emissive GFPc oxazolone analogue, which can be used to fabricate reaction-based fluorescent probe toward dopamine, potentially promoting the biochemical applications using synthetic GFP chromophore analogues.     

Singlet Oxygen-mediated Photobleaching of the Prosthetic Group in Hemoglobins and C-Phycocyanin

Proteins bearing colored prosthetic groups, such as the heme group in hemoglobin or the bilin group in c-phycocyanin, quench singlet oxygen by interactions at the apoprotein and the prosthetic group levels. In both proteins, chemical modification of the chromophore constitutes only a minor reaction pathway. While total deactivation of singlet oxygen takes place with rate constants of 4.0 x 10(9) and 4.2 x 10(8) M-1 s-1 for hemoglobin and phycocyanin, respectively, the bleaching of the chromophore takes place with rate constants of 3.2 x 10(6) and approximately 1 x 10(7) M-1 s-1. Irradiation of phycocyanin with red light bleaches the chromophore with low yields (approximately 0.8 x 10(-4)). Part of this bleaching is mediated by singlet oxygen produced by the irradiation of the bilin group. The low relevance of the singlet oxygen pathway is compatible with a low quantum yield (approximately 10(-3)) of free singlet oxygen production after irradiation of the protein.     

Synthesis of fluorescent diarylethenes having a 2,4,5-triphenylimidazole chromophore

Diarylethenes 1a-4a, having a fluorescent 2,4,5-triphenylimidazole chromophore in the aryl group, were synthesized. Upon excitation of the triphenylimidazole chromophore with 366 nm, 1a-4a underwent photocyclization reactions, and the solutions containing 1a-4a changed color from colorless to red-purple or to blue. The colors disappeared by irradiation with visible (lambda > 480 nm) light. The fluorescence intensity of the solutions also reversibly changed with the photochromic reactions. The fluorescence quantum yields of 1a, 2a, 3a, and 4a were determined to be 4.6, 7.7, 9.1, and 8.4%, respectively. The fluorescence quantum yields decreased with the increase in photocyclization quantum yields.     

Linkages Make a Difference in the Photoluminescence of Covalent Organic Frameworks

Covalent organic frameworks (COFs) with structural designability and tunability of photophysical properties enable them to be a promising class of organic luminescent materials by incorporating well-designed fluorescent units directly into the periodic skeletons. The photophysical properties of COFs are mainly affected by the structural features, which determine the conjugation degree, charge delocalization ability, and exciton dynamics of COFs. To understand the relationship between COF structures and their photophysical properties, two COFs with the same pyrene chromophore units but different linkages (imine or vinylene) were designed and synthesized. Interestingly, different linkages endow COFs with huge differences in solid-state photoluminescence quantum yield (PLQY) for imine- and vinylene-linked pyrene-based COFs, which possess PLQY values of 0.34 % and 15.43 %, respectively. The femtosecond-transient absorption spectra and time-dependent density functional theory reveal the different charge-transfer pathways in imine- and vinylene-linked COFs, which influence the exciton relaxation way and fluorescence intensity. In addition, an effective white-light device was obtained by coating the vinylene-linked COF on a light-emitting diode strip.     

Fluorescent dimers of rhodamine 6G in concentrated ethylene glycol solution

Aggregation of rhodamine 6G in concentrated ethylene glycol solutions is studied as a function of temperature. The measurements of absorption and fluorescence spectra evidence that the system of interest consists of two fluorescent species: monomers and dimers. Strong overlaps between all absorption and fluorescence bands in this system enable forward and reverse energy transport between monomers and dimers. The quantitative analysis of the effect of nonradiative energy transport (NET) on the fluorescence spectra as well as on the fluorescence quantum yields of monomers and dimers explains the temperature and concentration regularities observed. In particular, it is shown that in the concentrated solution the calculated monomer quantum yield is underrated compared to that measured, if the reverse NET is neglected. The lack of information on the value of the dimer quantum yield does not allow for full analysis of the forward and reverse NET in the system. However, it is shown that if that quantum yield is determined as the best fit parameter, an excellent agreement between the experimental and calculated values is obtained.     

Photoconversion in the red fluorescent protein from the sea anemone Entacmaea quadricolor: is cis-trans isomerization involved?

Proteins from the family of the green fluorescent protein (GFP) are presently extensively used in molecular and cellular biology. Recent studies suggest that isomerization of the chromophore occurs upon excitation and is involved in nonradiative deactivation. Using Raman spectroscopy, we report on photoinduced cis-trans isomerization in the red fluorescent protein eqFP611 from the sea anemone Entacmaea quadricolor. The crystal structure of eqFP611 shows that the chemical structure of the chromophore, p-hydroxybenzylidene-imidazolinone with an extended -conjugated system, is nearly identical to the chromophore of other red fluorescent proteins such as DsRed and HcRed. However, the chromophore of eqFP611 has a trans configuration whereas the chromophore of DsRed has a cis configuration. Upon irradiation with 532-nm light, the absorption of eqFP611 peaking at 559 nm diminished, and concomitantly a drastic decrease in the quantum yield of fluorescence as well as more complex decay kinetics was observed. Upon irradiation, changes in the Raman spectrum of eqFP611 were observed, and the relative intensities and peak positions of the irradiated eqFP611 showed striking similarity with the peaks in the Raman spectrum of DsRed. These observations are tentatively interpreted as trans-to-cis isomerization of the chromophore taking place upon irradiation together with the opening of new, nonradiative pathways.     

Fluorescence quantum yield and photochemistry of bacteriophytochrome constructs

Bacteriophytochromes (Bphs) are red-light photoreceptor proteins with a photosensory core that consists of three distinct domains, PAS, GAF and PHY, and covalently binds biliverdin (BV) to a conserved cysteine in the PAS domain. In a recent development, PAS-GAF variants were engineered for use as a near-infrared fluorescent marker in mammalian tissues (Tsien and co-workers, Science, 2009, 324, 804-807). Here, we report the fluorescence quantum yield and photochemistry of two highly-related Bphs from Rps. palustris, RpBphP2 (P2) and RpBphP3 (P3) with distinct photoconversion and fluorescence properties. We applied ultrafast spectroscopy to wild type P3 and P2 PAS-GAF proteins and their P3 D216A, Y272F and P2 D202A PAS-GAF-PHY mutant proteins. In these mutants hydrogen-bond interactions between a conserved aspartate (Asp) which connects the BV chromophore with the PHY domains are disrupted. The excited-state lifetime of the truncated P3 and P2 PAS-GAF proteins was significantly longer than in their PAS-GAF-PHY counterparts that constitute the full photosensory core. Mutation of the conserved Asp to Ala in the PAS-GAF-PHY protein had a similar but larger effect. The fluorescence quantum yields of the P3 D216A and Y272F mutants were 0.066, higher than that of wild type P3 (0.043) and similar to the engineered Bph of Tsien and co-workers. We conclude that elimination of a key hydrogen-bond interaction between Asp and a conserved Arg in the PHY domain is responsible for the excited-state lifetime increase in all Bph variants studied here. H/D exchange resulted in a 1.4-1.7 fold increase of excited-state lifetime. The results support a reaction model in which deactivation of the BV chromophore proceeds via excited-state proton transfer from the BV pyrrole nitrogens to the backbone of the conserved Asp or to a bound water. This work may aid in rational structure- and mechanism-based conversion of constructs based on P3 and other BPhs into efficient near-IR, deep tissue, fluorescent markers.     

Spectral properties of substituted coumarins in solution and polymer matrices

The absorption and fluorescence spectra of substituted coumarins (2-oxo-2H-chromenes) were investigated in solvents and in polymer matrices. The substitutions involved were: (1) by groups with varying electron donating ability such as CH?, OCH? and N(CH?)?, mainly, but not exclusively, in positions 7 and (2), by either CHO or 4-PhNHCONHN=CH- in position 3. While the spectra of non-substituted coumarin-3-carbaldehyde has absorptions at approximately 305 and 350 nm, substitution at position 7 leads to remarkable changes in the shape of the absorption spectrum and shifts the absorption to a longer wavelength. Similarly, the replacement of the formyl group with a semicarbazide group substantially influences the shape of the absorption spectrum, and coumarins which have only N(CH?)? in position 7 experience small changes. These changes are associated with the increasing intramolecular charge transfer (ICT) character and increasing conjugation length of the chromophoric system, respectively, in the studied molecules. The fluorescence is almost negligible for derivatives which have H in this position. With increasing electron donating ability, and the possibility of a positive mesomeric (+M) effect of the substituent in position 7 of the coumarin moiety, the fluorescence increases, and this increase is most intense when N(CH?)? substitutes in this position, for both 3-substituted derivatives. Spectral measurements of the studied coumarins in polymer matrices revealed that the absorption and fluorescence maxima lay within the maxima for solvents, and that coumarins yield more intense fluorescence in polymer matrices than when they are in solution. The quantum yield of derivatives which have a dimethylamino group in position 7 in polymer matrices approaches 1, and the fluorescence lifetime is within the range of 0.5-4 ns. The high quantum yield of 7-dimethylamino derivatives qualifies them as laser dyes which have k(F) higher than k(nr) in the given medium. This is caused by stiffening of the coumarin structure in polar polymer matrices, such as PMMA and PVC, due to higher micro-viscosity than in solution and intermolecular dipole-dipole interaction between chromophore (dopant) and matrix.     

The enhanced green fluorescent protein as a tool for the analysis of protein dynamics and localization: local fluorescence study at the single-molecule level

The green fluorescent protein (GFP) has emerged, in recent years, as a powerful reporter molecule for monitoring gene expression, protein localization and protein-protein interaction. Several mutant variants are now available differing in absorption, emission spectra and quantum yield. Here we present a detailed study of the fluorescence properties of the Phe-64-->Leu, Ser-65-->Thr mutant down to the single molecule level in order to assess its use in quantitative fluorescence microscopy and single-protein trafficking. This enhanced GFP (EGFP) is being used extensively as it offers higher-intensity emission after blue-light excitation with respect to wild-type GFP. By means of fluorescence spectroscopy we demonstrate the absence of the neutral form of the chromophore and the lack of photobleaching recovery after ultraviolet light irradiation. Furthermore, we show that the EGFP spectral properties from isolated to densely packed molecules are highly conserved. From these experiments EGFP emerges as an ideal molecule for quantitative studies of intra and intercellular tagged-protein dynamics and fluorescence-activated cell sorting, but not for monitoring single-protein trafficking over extended periods of time.     

Hydrogen Bond Fluctuations Control Photochromism in a Reversibly Photo‐Switchable Fluorescent Protein

Reversibly switchable fluorescent proteins (RSFPs) are essential for high‐resolution microscopy of biological samples, but the reason why these proteins are photochromic is still poorly understood. To address this problem, we performed molecular dynamics simulations of the fast switching Met159Thr mutant of the RSFP Dronpa. Our simulations revealed a ground state structural heterogeneity in the chromophore pocket that consists of three populations with one, two, or three hydrogen bonds to the phenolate moiety of the chromophore. By means of non‐adiabatic quantum mechanics/molecular dynamics simulations, we demonstrated that the subpopulation with a single hydrogen bond is responsible for off‐switching through photo‐isomerization of the chromophore, whereas two or more hydrogen bonds inhibit the isomerization and promote fluorescence instead. While rational design of new RSFPs has so far focused on structure alone, our results suggest that structural heterogeneity must be considered as well.     

TRANSFER OF EXCITATION ENERGY BETWEEN PORPHYRIN CENTERS OF A COVALENTLY-LINKED DIMER*

Abstract— Three covalently-linked porphyrin hybrid dimers were synthesized, each containing a metallotetraarylporphyrin [Zn(II), Cu(II), or Ni(II)], and a free base tetraarylporphyrin. Transfer of singlet excitation energy from the metalloporphyrin center to the free base porphyrin center was determined by measuring fluorescence properties. The Zn hybrid dimer displayed excellent intramolecular transfer of energy ( 85%) from the excited singlet state of the Zn(II) chromophore to the free base chromophore. No evidence for such transfer of the excited singlet state energy was found in the Ni(II) or Cu(II) analogues. From our experimental data, the fluorescence quantum yield of the Zn hybrid dimer was the same as for the free base monomer porphyrin (0.11; Seybold and Gouterman, 1969). Thus, the covalent attachment of another fluorescent porphyrin center effectively doubled the antenna size without decreasing the quantum yield even though the fluorescence quantum yield of the Zn(II) containing monomer was substantially less (0.03, according to Seybold and Gouterman, 1969) than that of the free base porphyrin. The donor-acceptor distance and the rate constant for energy transfer were calculated using the Forster equation. Assuming random orientation, a donor-acceptor distance of 15 Å was calculated with an associated rate constant (k_ci) for energy transfer of 1.9 ± 10₉ s_–1.     

Modulation of fluorescence through coassembly of molecules in organic nanostructures

This paper describes the fluorescence of bimolecular coassemblies that form one-dimensional nanostructures. One molecule is a fluorescent peptide amphiphile containing its branched stilbene chromophore covalently linked to the hydrophilic end of the amphiphile, and the second molecule is a shorter, nonfluorescent peptide amphiphile of complementary charge. Using circular dichroism we observe that mixing both molecules results in coassemblies that exhibit a beta-sheet signature in the peptide region indicative of these types of nanostructures. The nature of the coassembly is dependent on the molar ratio of each component, and the changing CD spectra suggest the formation of domains along the length of the nanofibers with decreasing concentrations of the fluorescent component. In coassemblies with dilute concentrations of the fluorophore, we observe an increase in fluorescence intensity and quantum yield, as well as chiral transfer to the achiral segment of the fluorescent peptide amphiphile. The coassemblies studied containing a fluorescent component at a low molar ratio exhibit fluorescence resonance energy transfer to fluorescent acceptors in solution. When the nonfluorescent peptide amphiphile component is designed to bind the important bioactive polysaccharide heparin, a selective transfer of energy is observed between fluorescein-tagged heparin and the coassemblies in both dilute solution and in macroscopic gels.     

硅掺杂碳量子点荧光猝灭法测定水样中铜(Ⅱ)

3-氨丙基三甲氧基硅烷(APTMS)与戊二醛(GA)混合前驱物合成的硅掺杂碳量子点(SDCQDs),其最大吸收、激发和发射波长分别为259,245,395 nm,量子产率为13.60%,XPS谱图表明碳量子点掺杂Si,且富含甲亚胺基团和硅氧键。Cu~(2+)对碳量子点荧光产生猝灭作用,依据Cu~(2+)浓度与碳量子点荧光强度猝灭率的相关性,建立碳量子点荧光探针测定水样中Cu~(2+)的分析方法,其它金属离子对Cu~(2+)干扰程度较小,回收率为91.4%~100.8%,检出限为0.13μmol/L,相对标准偏差为0.20%~0.92%。     

Are the Fluorescent Properties of the Cyan Fluorescent Protein Sensitive to Conditions of Oxidative Stress?

The modifications induced by reactive oxygen species (ROS) on fluorescent proteins (FPs) may have important implications for live cell fluorescence imaging. Using quantitative γ-radiolysis, we have studied the ROS-induced biochemical and photophysical perturbations on recombinant cyan fluorescent protein (CFP). After oxidation by the ˙OH radical, the protein displays a modified RP-HPLC elution profile, while the CFP fluorescence undergoes pronounced decreases in intensity and lifetime, without changes in its excitation and emission spectra. Meanwhile, the Förster resonant energy transfer (FRET) between the single W⁵⁷ and the chromophore remains unperturbed. These results rule out a direct oxidation of the CFP chromophore and of W⁵⁷ as well as major changes in the protein 3D structure, but show that new fluorescent forms associated to a higher level of dynamic quenching have been generated. Thus, strict in situ controls are required when CFP is to be used for FRET studies in situations of oxidative activity, or under strong illumination.     

Charge-transfer interactions in a multichromophoric hexaarylbenzene containing pyrene and triarylamines

Two different hexaarylbenzenes with three pyrene and three triarylamine substituents in different positions (trigonal symmetric and asymmetric arrangement) were synthesized, and their charge-transfer states were investigated by optical spectroscopy. In these multichromophoric systems triarylamine acts as the electron donor and pyrene as the electron acceptor. A reference chromophore with only one donor-acceptor pair was also investigated. All these chromophores form charge-transfer states upon photoexcitation which relax with a moderate fluorescence quantum yield to the ground state. The compounds do not differ significantly concerning most of their fluorescence properties, which shows that the fluorescent charge-transfer state is very similar in all chromophores. This observation indicates symmetry breaking for the symmetric chromophore within fluorescence lifetime of several tens of ns. This interpretation was substantiated by fluorescence excitation anisotropy measurements in a sucrose octaacetate matrix.