Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA

Fluorescent RNAs (FRs) provide an attractive approach to visualizing RNAs in live cells. Although the color palette of FRs has been greatly expanded recently, a green FR with high cellular brightness and photostability is still highly desired. Here we develop a fluorogenic RNA aptamer, termed Okra, that can bind and activate the fluorophore ligand ACE to emit bright green fluorescence. Okra has an order of magnitude enhanced cellular brightness than currently available green FRs, allowing the robust imaging of messenger RNA in both live bacterial and mammalian cells. We further demonstrate the usefulness of Okra for time-resolved measurements of ACTB mRNA trafficking to stress granules, as well as live-cell dual-color superresolution imaging of RNA in combination with Pepper620, revealing nonuniform and distinct distributions of different RNAs throughout the granules. The favorable properties of Okra make it a versatile tool for the study of RNA dynamics and subcellular localization.

Julolidine-based small molecular probes for fluorescence imaging of RNA in live cells

Intracellular RNA imaging with organic small molecular probes has been an intense topic, although the number of such reported dyes, particularly dyes with high quantum yields and long wavelength excitation/emission, is quite limited. The present work reports the design and synthesis of three cationic julolidine-azolium conjugates (OX-JLD, BTZ-JLD and SEZ-JLD) as turn-on fluorescent probes with appreciably high quantum yields and brightness upon interaction with RNA. A structure-efficiency relationship has been established for their potential for the interaction and imaging of intracellular RNA. Given their chemical structure, the free rotation between the donor and the acceptor gets restricted when the probes bind with RNA resulting in strong fluorescence emission towards a higher wavelength upon photoexcitation. A detailed investigation revealed that the photophysical properties and the optical responses of two probes, viz. BTZ-JLD and SEZ-JLD, towards RNA are very promising and qualify them to be suitable candidates for biological studies, particularly for cellular imaging applications. The probes allow imaging of intracellular RNA with prominent staining of nucleoli in live cells under a range of physiological conditions. The results of the cellular digest test established the appreciable RNA selectivity of BTZ-JLD and SEZ-JLD inside the cellular environment. Moreover, a comparison between the relative intensity profile of SEZ-JLD before and after the RNA-digestion test inside the cellular environment indicated that the interference of cellular viscosity in fluorescence enhancement is insignificant, and hence, SEZ-JLD can be used as a cell membrane permeable cationic molecular probe for deep-red imaging of intracellular RNA with a good degree of selectivity.

Biomimetic synthesis of maltodextrin-derived dendritic nanoparticle and its structural characterizations

The maltodextrin-derived dendritic nanoparticle was fabricated using microbial branching enzyme and its structural characterizations were investigated. During biomimetic synthesis, molecular weight distribution of maltodextrin substrate with 6.8 × 10⁴ g/mol shifted to the narrower and uniform distribution region with the larger molecular weight up to 6.3 × 10⁶ g/mol (MD12). The enzyme-catalyzed product had the larger size, higher molecular density as well as higher percentage of α-1,6 linkage, accompanying by more chain accumulations of DP 6-12 and disappearance of DP > 24, suggesting the biosynthesized glucan dendrimer had a compact tighter branched structure. The interaction of molecular rotor CCVJ and local structure of dendrimer was monitored, displaying there was a higher intensity related with the numerous nano-pockets at the branch points of MD12. The maltodextrin-derived dendrimers had the single spherical particulate shape with the size range of 10-90 nm. The mathematical models were also established to reveal the chain structuring during enzymatic reaction. The above results showed that the biomimetic strategy for novel dendritic nanoparticle with controllable structure arising from branching enzyme treated maltodextrin, which would help to enlarge the panel of available dendrimer.

Tetranitrile-anthracene as a probe for fluorescence detection of viscosity in fluid drinks via aggregation-induced emission

An AIE-based fluorescent probe was developed for monitoring the viscosity change during the spoilage process of fluid drinks.

Polymer-assisted drug sequestration from plasma protein by a surfactant with curtailed denaturing capacity

The capability of a surfactant to sequester a drug bound to plasma protein was investigated using steady-state and time-resolved spectroscopic techniques. Surfactants are known to denature protein, and hence are not suitable for the sequestration of a drug from protein. Herein, we show that the denaturing capacity of a surfactant is curtailed completely and its drug sequestration power is enhanced in the presence of biocompatible Pluronic micelles due to the formation of unique supramolecular assemblies. Further, our detailed studies indicate that the concentration of surfactant required for the sequestration of a drug is less than its critical micellar concentration (CMC). The extent of sequestration of drug by polymer-surfactant supramolecular assemblies can be tuned finely by controlling the concentration of surfactant. Detailed analysis showed that up to ∼85% sequestration of a drug from plasma protein could be achieved using a sub-CMC concentration of surfactant. Our results clearly show that controlled sequestration of a drug from plasma protein can be achieved with a reduction in the protein denaturing properties of surfactants.

Flow-dependent fluorescence of CCVJ

Background

The molecular rotor 9-(2-Carboxy-2-cyanovinyl)julolidine (CCVJ) is presumed to have a sensitivity towards velocity or shear which is supposed to result in a change in fluorescence quantum yield. Furthermore, a previously reported photoisomeric behavior may contribute to the measured fluorescence intensity changes. The goal of this research was to examine the hypothesized behavior theoretically and experimentally from the perspective of fluid dynamics.

Results

A correlation between stirring rate and intensity could not be established in the present experiments with a completely illuminated sample in contrast to previously reported experiments in spectrofluorometers. Experiments and theoretical models of a Poiseuille flow were in good agreement with the photoisomeric behavior but excluded the influence of shear. Further experiments in a flow chamber supported the photoisomery hypothesis as well.

Conclusion

No experimental evidence for the influence of velocity on the fluorescence intensity of CCVJ was found. The hypothesis of shear sensitivity was excluded as well. The results are consistent with the photoisomeric behavior of CCVJ.

Acridone in a biological nanocavity: detailed spectroscopic and docking analyses of probing both the tryptophan residues of bovine serum albumin

AD initially gets hooked to Trp 212 housed in domain IIA, inducing conformational changes in the protein and paving the way for the ligand to reach Trp 134 located in domain IB.

On the possibility to accelerate the thermal isomerizations of overcrowded alkene-based rotary molecular motors with electron-donating or electron-withdrawing substituents

We employ computational methods to investigate the possibility of using electron-donating or electron-withdrawing substituents to reduce the free-energy barriers of the thermal isomerizations that limit the rotational frequencies achievable by synthetic overcrowded alkene-based molecular motors. Choosing as reference systems one of the fastest motors known to date and two variants thereof, we consider six new motors obtained by introducing electron-donating methoxy and dimethylamino or electron-withdrawing nitro and cyano substituents in conjugation with the central olefinic bond connecting the two (stator and rotator) motor halves. Performing density functional theory calculations, we then show that electron-donating (but not electron-withdrawing) groups at the stator are able to reduce the already small barriers of the reference motors by up to 18 kJ mol(-1). This result outlines a possible strategy for improving the rotational frequencies of motors of this kind. Furthermore, exploring the origin of the catalytic effect, it is found that electron-donating groups exert a favorable steric influence on the thermal isomerizations, which is not manifested by electron-withdrawing groups. This finding suggests a new mechanism for controlling the critical steric interactions of these motors. Graphical Abstract The introduction of electron-donating groups in one of the fastest rotary molecular motors known to date is found to reduce the free-energy barriers of the thermal steps that limit the rotational frequencies by up to 18 kJ mol(-1).