In situ hydrodynamic lateral force calibration of AFM colloidal probes

Lateral force microscopy (LFM) is an application of atomic force microscopy (AFM) to sense lateral forces applied to the AFM probe tip. Recent advances in tissue engineering and functional biomaterials have shown a need for the surface characterization of their material and biochemical properties under the application of lateral forces. LFM equipped with colloidal probes of well-defined tip geometries has been a natural fit to address these needs but has remained limited to provide primarily qualitative results. For quantitative measurements, LFM requires the successful determination of the lateral force or torque conversion factor of the probe. Usually, force calibration results obtained in air are used for force measurements in liquids, but refractive index differences between air and liquids induce changes in the conversion factor. Furthermore, in the case of biochemically functionalized tips, damage can occur during calibration because tip-surface contact is inevitable in most calibration methods. Therefore, a nondestructive in situ lateral force calibration is desirable for LFM applications in liquids. Here we present an in situ hydrodynamic lateral force calibration method for AFM colloidal probes. In this method, the laterally scanned substrate surface generated a creeping Couette flow, which deformed the probe under torsion. The spherical geometry of the tip enabled the calculation of tip drag forces, and the lateral torque conversion factor was calibrated from the lateral voltage change and estimated torque. Comparisons with lateral force calibrations performed in air show that the hydrodynamic lateral force calibration method enables quantitative lateral force measurements in liquid using colloidal probes.     

A general strategy to quantify analytes through fluorescence chromaticity and luminosity

To realize a fast, easy-operation and precise way using fluorescence probes to quantify analytes is a goal to facilitate detection, especially in situ. Herein, we are reporting an approach which can be generally employed for the differentiation and quantitation of analytes through fluorescence chromaticity and luminosity. Seven representative fluorescent probes, targeting pH, cysteine, hydrogen sulfide, hydrogen peroxide, palladium and hydrazine, were synthesized and tested. Without utilizing costly instrumentations, portable devices were employed to collect data of photographs from the fluorescence samples in responses to different analytes. Subsequently, the photographic images were digitally processed to generate calibration curves between chromaticity/luminosity verse concentrations after mapping to the CIE 1931 xyY standard color space. Good linear calibration curves and quantitative analysis of unknown samples with low errors through the spectral technology demonstrated the reliability of this method. Thus, we showed the analytical method with a simple and on-site constructible/portable device which is promising for applications in more fluorescence probes.     

A general strategy to quantify analytes through fluorescence chromaticity and luminosity

To realize a fast, easy-operation and precise way using fluorescence probes to quantify analytes is a goal to facilitate detection, especially in situ. Herein, we are reporting an approach which can be generally employed for the differentiation and quantitation of analytes through fluorescence chromaticity and luminosity. Seven representative fluorescent probes, targeting pH, cysteine, hydrogen sulfide, hydrogen peroxide, palladium and hydrazine, were synthesized and tested. Without utilizing costly instrumentations, portable devices were employed to collect data of photographs from the fluorescence samples in responses to different analytes. Subsequently, the photographic images were digitally processed to generate calibration curves between chromaticity/luminosity verse concentrations after mapping to the CIE 1931 xyY standard color space. Good linear calibration curves and quantitative analysis of unknown samples with low errors through the spectral technology demonstrated the reliability of this method. Thus, we showed the analytical method with a simple and on-site constructible/portable device which is promising for applications in more fluorescence probes     

A simple DNA Characterization method using fiber-fluorescence in situ hybridization performed without DNA fragmentation

We performed high-resolution fluorescence imaging of lambda phage DNA molecules hybridized with fluorescent-labeled DNA and peptide nucleic acid probes. In this method, the target DNA and probe were mixed, rapidly denatured and then subjected to liquid hybridization conditions. The hybridized DNA sample was then spotted onto a nontreated glass substrate and subjected to molecular combing. The resultant continuous fluorescence signal of intact lambda DNA shows that the fluorescent-labeled probes bound to the predicted sites but in a pattern that was clearly different to the beads-on-a-string pattern typical for fiber-fluorescence in situ hybridization. The key changes to the conventional method are hybridization of the free target DNA in liquid and lowering the denaturation temperature. The method described here allows the rapid and direct visualization of the specific binding sites of intact DNA molecules without damaging the DNA fibers and causing fragmentation of the fluorescence signal. This technique should be a useful tool in studies of genetics and also large-scale DNA sequencing projects.     

Development of molecular imaging tools to investigate protein functions by chemical probe design

Molecular imaging technologies, which enable the visualization of the behaviors or functions of biomolecules in living systems, have received considerable attention from life scientists. Novel imaging technologies that overcome the limitations of current imaging techniques are desired. In this review, two independent technologies that were recently developed by the authors are described. The first technology is for smart (19)F magnetic resonance imaging (MRI) probes that were developed for in vivo applications. These probes were developed by exploiting paramagnetic relaxation enhancement in order to detect hydrolase activity. With respect to cellular applications, gene expression in cells was visualized using one of the (19)F MRI probes. It was confirmed that this probe design principle is effective for various hydrolases, and broad applications are expected. The second technology is for practical protein labeling. This labeling method is based on a mutant β-lactamase and its specific labeling probes. Since the probe is fluorescence resonance energy transfer (FRET)-based, this labeling method achieves both specific and fluorogenic labeling of target proteins. In addition, derivatization of the probe enabled the labeling of intracellular proteins and the modification of various functional molecules.     

Recent Progress of Small-Molecule Ratiometric Fluorescent Probes for Peroxynitrite in Biological Systems

Peroxynitrite (ONOO⁻) as a major reactive oxygen species plays important roles in cellular signal transduction and homeostatic regulation. Precise detection of ONOO⁻ in biological systems is vital for exploring its physiological and pathological function. Among numerous detection methods, fluorescence imaging technology using fluorescent probes offers some advantages, including simple operation, high sensitivity and selectivity, as well as real-time and nondestructive detection. In particular, ratiometric fluorescent probes, in which the built-in calibration of the two emission bands prevents interference from the biological environment, have been extensively employed to monitor the fluctuation of bioactive species. In this review, we will discuss small-molecule ratiometric fluorescent probes for ONOO⁻ in live cells or in vivo, which involves chemical structures, response mechanisms, and biological applications. Moreover, the challenges and future prospects of ONOO⁻-responsive ratiometric fluorescent probe are also proposed.     

Intracellular protein labeling with prodrug-like probes using a mutant β-lactamase tag

Intracellular protein labeling with small molecular probes that do not require a washing step for the removal of excess probe is greatly desired for real-time investigation of protein dynamics in living cells. Successful labeling of proteins on the cell membrane has been performed using mutant β-lactamase tag (BL-tag) technology. In the present study, intracellular protein labeling with novel cell membrane permeable probes based on β-lactam prodrugs is described. The prodrug-based probes quickly permeated the plasma membranes of living mammalian cells, and efficiently labeled intracellular proteins at low probe concentrations. Because these cell-permeable probes were activated only inside cells, simultaneous discriminative labeling of intracellular and cell surface BL-tag fusion proteins was attained by using cell-permeable and impermeable probes. Thus, this technology enables adequate discrimination of the location of proteins labeled with the same protein tag, in conjunction with different color probes, by dual-color fluorescence. Moreover, the combination of BL-tag technology and the prodrug-based probes enabled the labeling of target proteins without requiring a washing step, owing to the efficient entry of probes into cells and the fast covalent labeling achieved with BL-tag technology after bioactivation. This prodrug-based probe design strategy for BL-tags provides a simple experimental procedure with application to cellular studies with the additional advantage of reduced stress to living cells.     

Measurement of bumetanide in plasma and urine by high-performance liquid chromatography and application to bumetanide disposition.

A high-performance liquid chromatographic method for the measurement of bumetanide in plasma and urine is described. Following precipitation of proteins with acetonitrile, bumetanide was extracted from plasma or urine on a 1-ml bonded-phase C18 column and eluted with acetonitrile. Piretanide dissolved in methanol was used as the internal standard. A C18 Radial Pak column and fluorescence detection (excitation wavelength 228 nm; emission wavelength 418 nm) were used. The mobile phase consisted of methanol-water-glacial acetic acid (66:34:1, v/v) delivered isocratically at a flow-rate of 1.2 ml/min. The lower limit of detection for this method was 5 ng/ml using 0.2 ml of plasma or urine. Nafcillin, but not other semi-synthetic penicillins, was the only commonly used drug that interfered with this assay. No interference from endogenous compounds was detected. For plasma, the inter-assay coefficients of variation of the method were 7.6 and 4.4% for samples containing 10 and 250 ng/ml bumetanide, respectively. The inter-assay coefficients of variation for urine samples containing 10 and 2000 ng/ml were 8.1 and 5.7%, respectively. The calibration curve was linear over the range 5-2000 ng/ml.     

核酸适配体荧光探针在生化分析和生物成像中的研究进展

核酸适配体是指通过体外筛选技术从核酸文库中筛选出来,能够高特异性、高亲和力识别靶标物的寡核苷酸序列,具有靶标类型广泛、合成简单、相对分子质量小、化学稳定性高、易于进行生物化学修饰等优点。 核酸适配体能够通过折叠成特定的二维或三维构型与靶标物特异性结合,加上合适的信号转导机制,为重要靶标物的研究提供理想的分子识别与分子检测探针。 荧光检测技术具有高灵敏、高分辨率、易于实现多元分析等优点。 将核酸适配体的分子识别特性与荧光优异的光学检测性能相结合,在生命科学研究领域有着广泛的应用空间。 本文主要综述了核酸适配体荧光探针常见的分子设计和信号响应方式,及其在细胞成像、亚细胞成像中的应用研究,并对核酸适配体探针目前面临的一些挑战进行了讨论,最后对其未来的发展方向进行了展望。     

A near-infrared fluorescent probe for monitoring fluvastatin-stimulated endogenous H2S production

Most reported fluorescent probes have limitations in practical applications in living systems due to the strong autofluorescence background,construction of probes with near-infrared(NIR) fluorescence emission is an accessible approach for addressing this challenge.We here designed a NIR fluorescent probe for monitoring the endogenous production of H_2S in living cells.The designed probe showed significant NIR fluorescence turn-on response to H_2S with high selectivity,enabling the sensitive detection H_2S.Importantly,the probe could be applied in monitoring the endogenous production of H_2S in raw 264.7 macrophages.This study showed that fluvastatin can promote the activity of cystathionineγ-lyase(CSE) for generation H_2S.     

2-Aminopurine hairpin probes for the detection of ultraviolet-induced DNA damage

Nucleic acid exposure to radiation and chemical insults leads to damage and disease. Thus, detection and understanding DNA damage is important for elucidating molecular mechanisms of disease. However, current methods of DNA damage detection are either time-consuming, destroy the sample, or are too specific to be used for generic detection of damage. In this paper, we develop a fluorescence sensor of 2-aminopurine (2AP), a fluorescent analogue of adenine, incorporated in the loop of a hairpin probe for the quantification of ultraviolet (UV) C-induced nucleic acid damage. Our results show that the selectivity of the 2AP hairpin probe to UV-induced nucleic acid damage is comparable to molecular beacon (MB) probes of DNA damage. The calibration curve for the 2AP hairpin probe shows good linearity (R² = 0.98) with a limit of detection of 17.2 nM. This probe is a simple, fast and economic fluorescence sensor for the quantification of UV-induced damage in DNA.     

High-performance liquid chromatographic method for the determination of pindolol in human plasma

A sensitive, simple and highly reliable high-performance liquid chromatographic method using fluorescence detection is reported for the determination of pindolol in plasma. This method involves a single extraction of pindolol from alkalinized plasma into methyl tert.-butyl ether followed by a back-extraction into dilute hydrochloric acid. Injection of the dilute acid phase directly onto an octyl (LC-8) bonded-phase column provides the final separation, and detection of pindolol is achieved by monitoring the intrinsic fluorescence of pindolol at 315 nm following excitation at 255 nm. The method is sensitive enough to measure with confidence pindolol plasma concentrations of 2 ng/ml using a 2-ml sample. No internal standard is required. This method has been applied to the analysis of 1500 human plasma samples by two different laboratories.     

Monitoring molecular beacon DNA probe hybridization at the single-molecule level

We have monitored the reaction dynamics of the DNA hybridization process on a liquid/solid interface at the single-molecule level by using a hairpin-type molecular beacon DNA probe. Fluorescence images of single DNA probes were recorded by using total internal reflection fluorescence microscopy. The fluorescence signal of single DNA probes during the hybridization to individual complementary DNA probes was monitored over time. Among 400 molecular beacon DNA probes that we tracked, 349 molecular beacons (87.5 %) were hybridized quickly and showed an abrupt fluorescence increase, while 51 probes (12.5 %) reacted slowly, resulting in a gradual fluorescence increase. This ratio stayed about the same when varying the concentrations of cDNA in MB hybridization on the liquid/surface interface. Statistical data of the 51 single-molecule hybridization images showed that there was a multistep hybridization process. Our results also showed that photostability for the dye molecules associated with the double-stranded hybrids was better than that for those with the single-stranded molecular beacon DNA probes. Our results demonstrate the ability to obtain a better understanding of DNA hybridization processes using single-molecule techniques, which will improve biosensor and biochip development where surface-immobilized molecular beacon DNA probes provide unique advantages in signal transduction.     

Fluorescent probes for the stabilization and detection of G-quadruplexes and their prospective applications

This review article discusses the non-covalent interaction of various probe molecules of different structural diversity with G-quadruplex forming Guanine rich DNA sequences, revealing remarkable stimuli responsive fluorescence changes which are appropriate for sensing and other technological applications. Tailor-made probes having quadruplex inducing/stabilizing attachments of well-known dye molecules and its derivatives such as, coumarins, cyanines, thiazole orange, pyrazines, thioflavin T, triphenylmethane, tetraphenylethene, dimethylindole red etc have been employed. These probes express their modulations due to the binding to the topologically distinct G-quadruplexes through structural rigidization, aggregation propensity, binding strengths, tunability and other competitive interactions and are viewed as remarkable changes particularly in their fluorescence features. Based on this concept, several studies have reported the development of label free fluorescence sensor for the selective detection of topology specific G-quadruplexes, therapeutic, early diagnostic of cancer, cation-sensing, trace level detection of an anti-cancer drugs etc. have been accomplished. In vivo imaging is also achieved using a cholesterol attached G-quadruplex forming oligonucleotide probe labelled with specific dyes. Since the fine details of the topological information and control mechanisms of G-quadruplex forming sequences are very much essential for targeting and tuning several important biological processes relevant to cancer proliferation and developing stimuli responsive sensors, it is sure that many more contributions in this field will emerge in the coming years.     

Micropolarity and microviscosity of Pluronics L62 and L64 core–shell aggregates in water at various concentrations and additives examined by absorption and fluorescence probes

The microstructure of aggregates formed in aqueous solutions of the triblock copolymers poly(ethylene oxide) (PEO)–poly(propylene oxide)–PEO, Pluronics L62 and L64, and the effect of additives (n-butanol, n-hexanol, and o-xylene) on the local polarity and viscosity were investigated using several absorption and fluorescence probes with different hydrophilic/hydrophobic trade-offs. The absorption probe was 2,2,6,6-tetramethylpiperidine-1-oxyl and the fluorescence probes pyrene (P), 1-anilinonaphthalene-8-sulfonic acid (ANS), 1,10-bis(1-pyrene) decane (PD), and N-[5-(dimethylamino)naphthalene-1-sulfonyl]hexadecylamine (Dansyl). The specific absorption and fluorescence parameters, sensitive to changes in micropolarity and microviscosity, were related to the hydration calibration curves carried out in homogeneous tetraethylene glycol/water mixtures. Thus, the effective local hydration of the molecular probe solubilized in the guest aggregate was quantified, and at the same time, the probe location is established with respect of the corona and core aggregate. The ANS and PD probes evidence differences in microviscosity and track the effect of the block copolymer structure and additive concentration on microviscosity.     

Recent Development of DNA-modified AIEgen Probes for Biomedical Application

A variety of DNA-based probes are utilized for the detections of multiple analytes and DNA nanotechnology has been thriving for recent decades and achieving numerous nanostructures,mainly focusing on DNA morphology modulation and multifunctional systems engineered into to the complicated works.Among the numerous detections,fluorescence method is a non-invasive,highly selective and sensitive means for varieties of applications,but their emissions are often compromised by the aggregation-caused quenching(ACQ)effect,which weakens their applications.The aggregation induced emission luminogens(AIEgens)are created with non emissive or weakly emissive in a low concentration but emit strong fluorescence in a high concentration with aggregated states.Herein,numerous functionalized AIEgens have been emerged and used for detection and imaging and DNA-modified AIEgen probes are introduced.In this vein,here we report the progress on DNA-modified AIEgen probes in recent years and highlight their conjugation strategies including covalent bonding,electrostatic interaction and their applications of biosensing.Moreover,multiple DNA strands are needed to introduce into the DNA-modified AIEgen probes for more purposes.At the end,some challenges are mentioned to discuss the new trend of DNA-modified AIEgen probes.     

A new surfactant-fluorescence probe for detecting shape transitions in self-assembled systems

A new kind of fluorescence probe, a fluorophore-labeled anionic surfactant, sodium 12-(N-dansyl)amino-dodecanate (12-DAN-ADA), was designed and synthesized. The applications of 12-DAN-ADA as a fluorescence probe in molecular assemblies, especially in the transitions between micelles and vesicles, were investigated systematically. It was found that 12-DAN-ADA can efficiently differentiate the two different aggregate types (shapes) in mixed cationic and anionic surfactant systems and double-chain cationic surfactant systems. Experimental results showed that the fluorescence anisotropy of 12-DAN-ADA increased sharply, the emission maxima became blue-shifted, and the fluorescence lifetime rose notably when the aggregates transformed from micelles to vesicles in mixed cationic and anionic surfactant systems. The fluorescence anisotropy can also distinguish different aggregate types in single-component double-chain cationic surfactant systems. Further studies demonstrated that 12-DAN-ADA is a more useful probe of transitions between micelles and vesicles than commonly used fluorescence probes, such as pyrene and 1,6-diphenyl-1,3,5-hexatriene (DPH).     

Ester-Derivatized Indoles as Fluorescent and Infrared Probes for Hydration Environments?

Tryptophan derivatives have long been used as site-specific biological probes. 4-Cyanotryptophan emits in the visible region and is the smallest blue fluorescent amino acid probe for biological applications. Other indole or tryptophan analogs may emit at even longer wavelengths than 4-cyanotryptophan. We performed FTIR, UV-Vis, and steady-state and time-resolved fluorescence spectroscopy on six ester-derivatized indoles in different solvents. Methyl indole-4-carboxylate emits at 450 nm with a long fluorescence lifetime, and is a promising candidate for a fluorescent probe. The ester-derivatized indoles could be used as spectroscopic probes to study local protein environments. Our measurements provide a guide for choosing esterderivatized indoles to use in practice and data for computational modeling of the effect of substitution on the electronic transitions of indole.     

Redesign of a Fluorogenic Labeling System To Improve Surface Charge,Brightness, and Binding Kinetics for Imaging the Functional Localization of Bromodomains

Protein labeling with fluorogenic probes is a powerful method for the imaging of cellular proteins. The labeling time and fluorescence contrast of the fluorogenic probes are critical factors for the precise spatiotemporal imaging of protein dynamics in living cells. To address these issues, we took mutational and chemical approaches to increase the labeling kinetics and fluorescence intensity of fluorogenic PYP‐tag probes. Because of charge‐reversal mutations in PYP‐tag and probe redesign, the labeling reaction was accelerated by a factor of 18 in vitro, and intracellular proteins were detected with an incubation period of only 1 min. The brightness of the probe both in vitro and in living cells was enhanced by the mutant tag. Furthermore, we applied this system to the imaging analysis of bromodomains. The labeled mutant tag successfully detected the localization of bromodomains to acetylhistone and the disruption of the bromodomain–acetylhistone interaction by a bromodomain inhibitor.     

Redesign of a Fluorogenic Labeling System To Improve Surface Charge,Brightness, and Binding Kinetics for Imaging the Functional Localization of Bromodomains

Protein labeling with fluorogenic probes is a powerful method for the imaging of cellular proteins. The labeling time and fluorescence contrast of the fluorogenic probes are critical factors for the precise spatiotemporal imaging of protein dynamics in living cells. To address these issues, we took mutational and chemical approaches to increase the labeling kinetics and fluorescence intensity of fluorogenic PYP‐tag probes. Because of charge‐reversal mutations in PYP‐tag and probe redesign, the labeling reaction was accelerated by a factor of 18 in vitro, and intracellular proteins were detected with an incubation period of only 1 min. The brightness of the probe both in vitro and in living cells was enhanced by the mutant tag. Furthermore, we applied this system to the imaging analysis of bromodomains. The labeled mutant tag successfully detected the localization of bromodomains to acetylhistone and the disruption of the bromodomain–acetylhistone interaction by a bromodomain inhibitor.