Single-Molecule FRET Study of DNA G-Quadruplex

ＩｎｔｒｏｄｕｃｔｉｏｎＴｅｌｏｍｅｒｅｓａｒｅｔｈｅｅｎｄｒｅｇｉｏｎｓｏｆｃｈｒｏｍｏｓｏｍｅｓｃｏｎｓｉｓｔｉｎｇｏｆＤＮＡａｎｄａｓｓｏｃｉａｔｅｄｐｒｏｔｅｉｎ .Ｔｈｅｔｅｌｏｍ ｅｒｉｃＤＮＡｃｏｎｔａｉｎｓＧ ｒｉｃｈｒｅｐｅａｔｓｏｆＤＮＡｓｅｑｕｅｎｃｅｓ .ＴｈｉｓＧ ｒｉｃｈｏｖｅｒｈａｎｇｃａｎｆｏｒｍａｓｔａｂｌｅ ｇｕａｎｉｎｅ ｑｕａｄｒｕｐｌｅｘｉｎｖｉｔｒｏｕｎｄｅｒ ｐｈｙｓｉｏｌｏｇｉｃａｌｃｏｎｄｉ ｔｉｏｎｓ[1,2 ] .Ｉｔｉｓｎｏｗｗｅｌｌ ｅｓｔａｂｌｉｓｈｅｄｔ…     

Fluorescence resonance energy transfer (FRET) in chemistry and biology: Non-F?rster distance dependence of the FRET rate

Fluorescence resonance energy transfer (FRET) is a popular tool to study equilibrium and dynamical properties of polymers and biopolymers in condensed phases and is now widely used in conjunction with single molecule spectroscopy. In the data analysis, one usually employs the F?rster expression which predicts (l/R ⁶) distance dependence of the energy transfer rate. However, critical analysis shows that this e_xpression can be of rather limited validity in many cases. We demonstrate this by explicitly considering a donor-acceptor system, polyfluorene (PF₆)-tetraphenylporphyrin (TPP), where the size of both donor and acceptor is comparable to the distance separating them. In such cases, one may expect much weaker distance (as l/R ² or even weaker) dependence. We have also considered the case of energy transfer from a dye to a nanoparticle. Here we find l/R ⁴ distance dependence at large separations, completely different from F?rster. We also discuss recent application of FRET to study polymer conformational dynamics. Dedicated to Prof J Gopalakrishnan on his 62nd birthday.     

Modulation of FRET efficiency by donor-acceptor ratio in co-condensed fluorophore-silica nanoconjugates

Förster resonance energy transfer (FRET) in nanocomposites is an important step in many applications. In order to maximize the amount of energy transferred from donor, D, to an acceptor, A, it is essential to minimize self-quenching of the donor. In the present work, fluorescein (D) and rhodamine B (A) are covalently bound into silica nanoshells (C-dye-SNS) with varying D:A ratio where the amount of A has been held constant. The total number of dye molecules is varied from 24 to 140 per nanoshell keeping the number of A molecules at ~13 ​± ​2 molecules per particle. In these conditions, FRET is found to be governed by the D:A ratio. An energy transfer process associated with maximum efficiency of 77% with time constant of 130 ps has been observed in these nanoconjugates. Fast fluorescence decays for D and corresponding risetime for A are observed in the present systems, unlike in those with high concentration of D and A (~1000 molecules/nanoshell). Thus, the presently used dye concentrations are found to be more appropriate than the higher concentration used earlier.     

Coumarin Modified Rhodamine Derivative： Fluorescent Chemosensor Selectively Recognizing Al^3＋ and Ca^2＋

A fluorescent probe with a coumarin moiety bound to rhodamine 6G hydrazide（l） was synthesized. Its sensing behavior toward various metal ions was investigated with fluorescence methods. Compound I displays different fluorescence emission responses to Al^3＋ and Ca^2＋ at the same excitation wavelength in the visible light region, while no changes occur after the addition of other metal ions. The binding ratios of the complexs of 1-Al^3＋ and 1-Ca^2＋ are both 2：1 according to the Job plot and high resolution mass spectrometer（HRMS） experiments. Moreover, emission spectrum of 1-Ca^2＋ complex and absorption spectrum of the rbodamine dyes overlap largely. When Al^3＋ was added to the 1-Ca2＋ system, calcium in complex 1-Ca2＋ can be displaced by Al^3＋, resulting in the output of another ratiometric sensing signal, which demonstrates that the 1-Ca^2＋ complex can be served as a new and effective fluorescence resonance energy transfer（FRET） donor for rhodamine derivatives.     

Aptamer-quantum dots and teicoplanin-gold nanoparticles constructed FRET sensor for sensitive detection of Staphylococcus aureus

The detection of bacterial pathogen such as Staphylococcus aureus(S.aureus) is essential for the regulation of food hygiene and disease diagnosis.Herein,we developed a simple one-step fluorescence resonance energy transfer(FRET)-based sensor for specific and sensitive detection of S.aureus in food and serum samples,in which aptamer-modified quantum dots(aptamer-QDs) was employed as the energy donor and antibiotic of teicoplanin functionalized-gold nanoparticles(Teico-AuNPs) was chosen as the energy acceptor.Within 1 h,the FRET-based sensor showed a linear range of from 10 cfu/mL to 5 × 10~8 cfu/mL,with the low limit of detection(LOD,2 cfu/mL) for S.aureus in buffer.When further applied to assay S.aureus in real samples,the FRET-based sensor showed good recoveries ranging from 84.5% to 110.0%,with relative standard derivations(RSDs) of 0.01%-0.44% and a LOD of 100 cfu/mL in milk,orange juice and human serum.     

Rational Design of Ratiometric Fe3+ Fluorescent Probes Based on FRET Mechanism

As the most abundant transition metal element in mammals, iron(Fe) plays a vital role in life activities. It is of great significance to study the variation of Fe³⁺ level in living organisms. In virtue of the advantages of high sensitivity, good selectivity and low damage to living systems, the fluorescence detection of Fe³⁺ has attracted much attention. Compared with the intensity-based fluorescent probe, the ratiometric fluorescent probe has less interference of environmental and can realize quantitative detection. In this study, four ratiometric Fe³⁺ fluorescent probes, R1, R2, R3 and R4_, were designed and synthesized using fluorescence resonance energy transfer(FRET) mechanism to achieve quantitative detection of Fe³⁺. In the FRET systems, 1,8-naphthalimide fluorophore derivatives were adopted as donors while rhodamine B derivatives were selected as receptors. The connection sites of the donor and acceptor in R3 and R4 are different from those in R1 and R2. All the four probes showed good response and selectivity to Fe³⁺. The energy transfer efficiencies of R3 and R4 were obviously higher than those of R1 and R2. This work provided a promising strategy for the development of fluorescent ratiometic Fe³⁺sensors.     

Application of a Highly Robust and Efficient Fluorescence‐Resonance‐Energy‐Transfer (FRET) System in DNA

We report a feasibility study for the application of our newly developed highly efficient and robust fluorescence‐resonance‐energy‐transfer (FRET) system to DNA. A 2′‐oligodeoxynucleotide, 12 , equipped with a quinolinone derivative as donor and a (bathophenanthroline)ruthenium(II) complex as acceptor and having a single uridine as potential cleavage site under basic conditions revealed an intensive FRET, which almost vanished after cleavage of the oligonucleotide under basic conditions (Fig. 7). Furthermore, in the arrangement of a molecular beacon (MB) DNA (see 13 ), a significant decrease of the FRET was observed after hybridization to a target sequence (Fig. 9). Due to the long decay times of the fluorescence of the Ru‐complex, the system allows for highly sensitive time‐gated measurements.     

A new nanobiosensor for glucose with high sensitivity and selectivity in serum based on fluorescence resonance Energy transfer (FRET) between CdTe quantum dots and Au nanoparticles

A novel assembled nanobiosensor QDs-ConA-beta-CDs-AuNPs was designed for the direct determination of glucose in serum with high sensitivity and selectivity. The sensing approach is based on fluorescence resonance energy transfer (FRET) between CdTe quantum dots (QDs) as an energy donor and gold nanoparticles (AuNPs) as an energy acceptor. The specific combination of concanavalin A (ConA)-conjugated QDs and thiolated beta-cyclodextrins (beta-SH-CDs)-modified AuNPs assembles a hyperefficient FRET nanobiosensor. In the presence of glucose, the AuNPs-beta-CDs segment of the nanobiosensor is displaced by glucose which competes with beta-CDs on the binding sites of ConA, resulting in the fluorescence recovery of the quenched QDs. Experimental results show that the increase in fluorescence intensity is proportional to the concentration of glucose within the range of 0.10-50 muM under the optimized experimental conditions. In addition, the nanobiosensor has high sensitivity with a detection limit as low as 50 nM, and has excellent selectivity for glucose over other sugars and most biological species present in serum. The nanobiosensor was applied directly to determine glucose in normal adult human serum, and the recovery and precision of the method were satisfactory. The unique combination of high sensitivity and good selectivity of this biosensor indicates its potential for the clinical determination of glucose directly and simply in serum, and provides the possibility to detect low levels of glucose in single cells or bacterial cultures. Moreover, the designed nanobiosensor achieves direct detection in biological samples, suggesting the use of nanobiotechnology-based assembled sensors for direct analytical applications in vivo or in vitro.     

Liposomal FRET Assay Identifies Potent Drug-Like Inhibitors of the Ceramide Transport Protein (CERT)

Ceramide transfer protein (CERT) mediates non-vesicular transfer of ceramide from endoplasmic reticulum to Golgi apparatus and thus catalyzes the rate-limiting step of sphingomyelin biosynthesis. Usually, CERT ligands are evaluated in tedious binding assays or non-homogenous transfer assays using radiolabeled ceramides. Herein, a facile and sensitive assay for CERT, based on Förster resonance energy transfer (FRET), is presented. To this end, we mixed donor and acceptor vesicles, each containing a different fluorescent ceramide species. By CERT-mediated transfer of fluorescent ceramide, a FRET system was established, which allows readout in 96-well plate format, despite the high hydrophobicity of the components. Screening of a 2 000 compound library resulted in two new potent CERT inhibitors. One is approved for use in humans and one is approved for use in animals. Evaluation of cellular activity by quantitative mass spectrometry and confocal microscopy showed inhibition of ceramide trafficking and sphingomyelin biosynthesis.     

A New Robust and Highly Sensitive FRET Donor–Acceptor Pair: Synthesis,Characterization, and Application in a Thrombin Assay

The synthesis of a new, robust fluorescence‐resonance‐energy‐transfer (FRET) system is described. Its donor chromophore is derived from an N‐allyl‐substituted quinolinone attached to 4‐bromophenylalanine via Heck cross‐coupling. The resulting Fmoc‐protected derivative 11 was used as building block in solid‐phase peptide synthesis (SPPS). As FRET acceptor, a sulfonylated ruthenium(II)–bathophenanthroline complex with a peripheral COOH function was prepared for covalent attachment to target molecules. The UV/VIS absorption and emission spectra of peptides bearing only the donor (D) or acceptor (A) dye showed a good overlap of the emission band of the donor with the absorption band of the acceptor. The fluorescence spectra of a peptide bearing both dyes revealed an additional emission after excitation of the donor, which is due to indirect excitation of the acceptor via FRET. The long fluorescence lifetime of the Ru^II complex (0.53 μs) makes it well‐suited for time‐resolved measurements. As a first application of this new FRET system, the peptide 18 , with the recognition sequence for the protease thrombin, flanked by the two dyes, was synthesized and successfully cleaved by the enzyme. The change in the ratio of the fluorescence intensities could be determined.     

Characterization of the Mode of Incorporation of Lipophilic Compounds in Solid Dispersions at the Nanoscale Using Fluorescence Resonance Energy Transfer (FRET)

Summary: Efficient engineering of solid dispersions stagnates by the current inability to establish the mode of drug distribution on a molecular level at a low drug load. This study describes the application of fluorescence resonance energy transfer (FRET) to characterize the mode of incorporation of dispersed lipophilic molecules in a solid matrix. Two different lipophilic fluorophores (donor and acceptor) were used as model substances and were incorporated in polyvinylpyrrolidone to form solid dispersions using two different production processes: lyophilization and fusion. The efficiency of the resonance energy transfer from donor to acceptor was measured by confocal microscopy. We show that the method can be used to compare the modes of drug incorporation of solid dispersions at the nanoscale.

Absorption and emission spectra of Bodipy R6G (donor) and Bodipy 650/665 (acceptor).     

酶促开环聚合合成双亲性H型嵌段共聚物及其自组装

通过固定化酶Novozyme435（NV435）催化聚乙二醇（PEG）开环聚合己内酯（CL）得到端基带有羟基的ABA型三嵌段聚合物,用2,2-二氯代乙酰氯将聚合物的端羟基功能化形成H型大分子引发剂,在CuCl／HMTETA体系中引发4-乙烯基吡啶（4VP）进行原子转移自由基聚合反应（ATRP）,得到了具有两亲性的H型五嵌段聚合物（PVP）2-b—PCL-b．PEG-PCL-（PVP）2,用红外光谱（FT IR）,核磁共振（^1H NMR）,凝胶渗透色谱（GPC）对其结构与分子量及其分子量分布进行了表征,结果表明：H型五嵌段聚合物分子量46121g／mol,分子量分布1．30．并利用动态光散射（DLS）和原子力显微镜（AFM）对聚合物在水溶液中的自组装行为进行了研究,H型嵌段聚合物的胶束呈球形结构,平均直径为70nm左右．     

Building‐Block Approach for the Straightforward Incorporation of a New FRET (Fluorescence‐Resonance‐Energy Transfer) System into Synthetic DNA

The synthesis of the two new phosphoramidites 5 and 8 bearing a carbostyril (=quinolin‐2(1H)‐one) chromophore used as donor entity in our recently developed new FRET (fluorescence‐resonance‐energy transfer) system is described (Schemes 1 and 2) The high stability of the chromophore to basic conditions enables the incorporation of the phosphoramidites directly into DNA during solid‐phase synthesis (Schemes 3 and 4). Since this is also possible for the (bathophenanthroline)ruthenium(II) complex used as acceptor (Scheme 4, Steps d and e), the whole labelling procedure to insert the FRET system into synthetic DNA is straightforward and represents a major improvement to our previous strategy.     

Verification and Biophysical Characterization of a New Three‐Color Förster Resonance‐Energy‐Transfer (FRET) System in DNA

We report on a new three‐color FRET system consisting of three fluorescent dyes, i.e., of a carbostyril (=quinolin‐2(1H)‐one)‐derived donor D, a (bathophenanthroline)ruthenium complex as a relay chromophore A₁, and a Cy dye as A₂ (FRET=Förster resonance‐energy‐transfer) (cf. Fig. 1). With their widely matching spectroscopic properties (cf. Fig. 2), the combination of these dyes yielded excellent FRET efficiencies. Furthermore, fluorescence lifetime measurements revealed that the long fluorescence lifetime of the Ru complex was transferred to the Cy dye offering the possibility to measure the whole system in a time‐resolved mode. The FRET system was established on double‐stranded DNA (cf. Fig. 3) but it should also be generally applicable to other biomolecules.     

Overcoming Kinetic Limitations of Electron Injection in the Dye Solar Cell via Coadsorption and FRET

A new, extremely simple concept for the use of energy transfer as a means to the enhancement of light absorption and current generation in the dye solar cell (DSC) is presented. This model study is based upon a carboxy‐functionalized 4‐aminonaphthalimide dye (carboxy‐fluorol) as donor, and (NBu₄)₂[Ru(dcbpy)₂(NCS)₂] (N719) as acceptor chromophores. A set of three different devices is assembled containing either exclusively carboxy‐fluorol or N719, or a mixture of both. This set of transparent devices is characterized via IV‐measurements under AM1.5G and monochromatic illumination and their light‐harvesting and external quantum efficiencies (LHE and EQE, respectively) are determined as well. It is shown that the device containing only the donor chromophore has a marginal power conversion efficiency, thus indicating that carboxy‐fluorol is a poor sensitizer for the DSC. Cyclovoltametric measurements show that the poor sensitization ability arises from the kinetic inhibition of electron injection into the TiO₂ conduction band. Comparing the spectral properties of the DSCs assembled presently, however, demonstrates that light absorbed by carboxy‐fluorol is almost quantitatively contributing to the photocurrent if N719 is present as an additional sensitizer. In this case, N719 acts as a catalyst for the sensitization of TiO₂ by carboxy‐fluorol in addition to being a photosensitizer. Evaluation of the maximum output power under blue illumination shows that the introduction of an energy‐donor moiety via coadsorption, leads to a significant increase in the monochromatic maximum output power. This result demonstrates that energy transfer between coadsorbed chromophores could be useful for the generation of current in dye‐sensitized solar cells.