Variance reducing and noise correction in protein quantification by measuring fluctuations in fluorescence due to photobleaching

Quantifying the absolute protein number using the ratio between the variance and the mean of the protein Fluorescence intensity is a straightforward method for microscopy imaging. Recently, this method has been expanded to fluorescence decaying processes due to photobleaching with binomial distribution. The article examines the method proposed and shows how it can be adapted to the case of variance in the initial number of proteins between the cells. The article shows that the method can be improved by the implementation of the information processing of each frame independently from other frames. By doing so, the variance in determining the protein number can be reduced. In addition, the article examines the management of unwanted noises in the measurement, offers a solution for the shot noise and background noise, examines the expected error caused by the decay constant inaccuracy, and analyzes the expected difficulties in conducting a practical experiment, which includes a non-exponential decay and variance in the photobleaching rate of the cells. The method can be applied to any superposition of n_0 discrete decaying processes. However, the evaluation of expected errors in quantification is essential for early planning of the experimental conditions and evaluation of the error.

Polarity-based fluorescence probes: properties and applications

Local polarity can affect the physical or chemical behaviors of surrounding molecules, especially in organisms. Cell polarity is the ultimate feedback of cellular status and regulation mechanisms. Hence, the abnormal alteration of polarity in organisms is closely linked with functional disorders and many diseases. It is incredibly significant to monitor and detect local polarity to explain the biological processes and diagnoses of some diseases. Because of their in vivo safe and real-time monitoring, several polarity-sensitive fluorophores and fluorescent probes have gradually emerged and been used in modern research. This review summarizes the fluorescence properties and applications of several representative polarity-sensitive fluorescent probes.

Design principles of spectroscopic probes for biological applications

Spectroscopic (chromogenic, fluorescent, or chemiluminescent) probes have been widely used in many fields due to their high sensitivity and unrivaled spatiotemporal resolution. This area is an old one but always full of activity, because the rapid development of science and technology requires not only new probes for specific purposes (e.g., subcellular imaging) but also the update of current probes with more satisfactory properties. Based on our experiences and including existing knowledge, in this mini-review we briefly discuss the design strategies, response modes, and bioapplications of small molecular spectroscopic probes, in particular their advantages and disadvantages as well as possible research trends, which may be helpful to those who are interested in this continually growing research area.

Macro-/micro-environment-sensitive chemosensing and biological imaging

We have summarized the research progress on fluorescent sensors responsive to environmental factors, including local viscosity, polarity, temperature, hypoxia and pH.

Single-molecule fluorescence quantification with a photobleached internal standard

In cellular and molecular biology, fluorophores are employed to aid in tracking and quantifying molecules involved in cellular function. We previously developed a sensitive single-molecule quantification technique to count the number of proteins and the variation of the protein number over the population of individual subcellular organelles. However, environmental effects on the fluorescent intensity of fluorophores can make it difficult to accurately quantify proteins using these sensitive techniques. In this letter, we demonstrate the use of photobleaching to extract an accurate single-molecule calibration intensity distribution from the sample directly to avoid any differences in environment that may alter the count. Using this technique, we were able to show that goat antimouse IgG antibody labeled with Alexa Fluor 488, an environmentally insensitive fluorophore, exhibited an average fluorescence equivalent to 4.6 single fluorophores. SynaptopHluorin vesicles, which contain the environmentally sensitive green fluorescent protein, exhibited an average of 4.4 single green fluorescent proteins per vesicle.

The visualized polarity-sensitive magnetic nanoparticles

Three polarity-sensitive organic molecules (DIAA, DIUA, and DISA) were designed and synthesized for functionalizing high-quality superparamagnetic Fe(3)O(4) nanoparticles (NPs) via the ligand exchange strategy to prepare polarity-sensitive Fe(3)O(4) NPs. The functional group is chosen to be the carboxyl group (one for DIAA and DIUA, two for DISA) that is a universal coordinating site for iron oxide NPs. The method for binding these functional molecules onto the surface of the NPs is simple and straightforward. Among the three molecules, the DISA molecules passivate the NPs' surface most efficiently owing to their particular structure with two carboxyl groups and a general good solubility. The DISA-functionalized Fe(3)O(4) NPs (DISA-Fe(3)O(4) NPs) display distinctly different fluorescence emissions in various solvents of different polarities with the magnetism well preserving. The prepared polarity-sensitive Fe(3)O(4) NPs that are dual functional can be used as a visualized polarity sensor and perform NPs' superparamagnetic properties simultaneously. It also provides a conceptual design for preparing the polarity-sensitive nanomaterials with multifunction.

Analysis of local polarity change around Cys34 in bovine serum albumin during N-->B transition by a polarity-sensitive fluorescence probe

The change trend of the local environment of Cys34 domain in bovine serum albumin has been studied as a function of pH value by using thiol-specific and polarity-sensitive fluorescent probe 3-(4-chloro-6-p-maleimidylphenoxyl-1,3,5-triazinylamino)-7-dimethylamino-2-methyl-phenazine. The local polarity of the Cys34 domain is found to rise with the increase of pH values, and the corresponding dielectric constant is raised from 12.8 at pH 6.0 to 23.3 at pH 9.1. The result shows that the environment of the Cys34 domain is rather hydrophobic in normal state at pH 6.0 and becomes a little hydrophilic in the course of N-->B transition, which may be attributed to the slight unfolding of the protein and thus the increasing of exposure of the previously relatively buried Cys34. In addition, the increased dielectric constant (23.3) is much lower than that (80.1) of water, suggesting that the unfolding of bovine serum albumin does not cause the full exposure of the Cys34 to the aqueous media during the transition.