Unveiling mysterious fluorescence and establishing structure-function relationship of carbon nanodots

Carbon nanodots are a new class of nanomaterials with sizes in the range of 3-5 nm, having interesting fluorescence properties like excitation-dependent emission. But the recent research, with major revelations from our group, suggests that in the bottom-up approach, the fluorescence associated with CNDs may originate significantly from molecular fluorophores and/or their aggregates, quasi CNDs (molecular fluorophores attached to the core of CNDs) or polymer dots. These are produced as by-products or even the sole product of CNDs synthesis. Our two chemical science publications discuss the origin of fluorescence in two different carbon dot systems in support of the above conclusions. The comment published in nature communication develops caution in the research community, by setting up purification and characterization protocols for getting carbon nanodots.

Specific labeling of cellular organelles with fluorescent nanodots for super-resolution microscopy 

The superresolution microscopy helped to overcome the diffraction limit and propelled the fluorescence-based light microscopy towards nanoscale level visualization, unveiling many biology-related problems. To achieve the same, it is important to develop probes that could specifically label cellular organelles with high precision. We showed for the first time phalloidin conjugated orange emissive carbon dot that could specifically stain actin filaments which were used to study muscle architecture in dbn-1(vit7)C. elegans.

Discovering and exploring bulk as well as the single-molecule fluorescence blinking behavior in fluorescent nanomaterials

The fluorescence behavior study of fluorescent nanoparticles has helped tremendously in shedding light on their fluorescence mechanism, which is typically more complicated than that of fluorophore molecules. But still, there are many fluorescent particle systems whose single-molecule properties are unexplored. One such system is that of nanoclusters made from metallic elements like gold, silver and copper. For the first time, we were able to show single-molecule blinking behavior in BSA protein-coated gold nanoclusters, which were used to obtain super-resolved images of lysosomes down to 60 nm in size. Further works in the same direction are in progress.

Developing probes for microscopic and spectroscopic visualization of biologically relevant events

Understanding many biological events through spectroscopic and microscopic methods would lend them great authenticity, which is usually lacking in many chemical-based indirect methods. In this direction, we used carbon dots to visualize the diameter of the protein corona formed around the nanoparticle under the Transmission Electron Microscope for the first time. And using another carbon dot the extent of hydrogen bonding inside cells was measured using Fluorescent lifetime imaging also.

Using fluorescence lifetime imaging (FLIM) and superresolution microscopy towards a better understanding of drug delivery systems

It is important to notice that, most often than not the clinical studies can only answer if a drug delivery nanocarrier could work or not, but fails to explain “How” and “why?”. Answers to such critical questions could be found with the help of advanced microscopy techniques like Transmission Electron microscopy, Fluorescence lifetime imaging and super-resolution microscopy. In this direction, we are using fluorescent probes to study the effect of drugs on different cellular organelles and their effects in bringing about the apoptosis process. By looking at organelles like nucleus, lysosome and mitochondria we can visualize the effect of drugs in first hand and compare their toxicity effects under varying environmental conditions.

COVID-19 causing SARS-CoV-2 virus’s spike protein investigation for

novel drug discovery and mutational impact analysis

Novel coronavirus (NCoV-19) also known as SARS CoV-2 is the emerging pathogen that reasoned for coronavirus disease 19 (COVID-19) associated causalities worldwide and continues doing so. Inhibition of the interaction of the receptor-binding domain (RBD) of the spike protein to the human angiotensin-converting enzyme (ACE 2) receptor is the most effective therapeutic formulation to restrict the contagious respiratory illness and multiple organ failure caused by SARS-CoV-2. Based on structure decoding of the RBD domain of spike protein using machine learning and deep learning-based tools, our group has generated a new set of small molecules, which have strong inhibiting properties on the binding of spike protein to ACE-2 receptors. The newly designed molecules showed better performance than several existing repurposing drugs. Conformational changes from closed to closed lock and open conformations of the SARS-CoV-2 binding to ACE 2 receptor were observed in presence of these small molecular inhibitors. Besides identifying the novel inhibitors against COVID-19, our group has recently investigated the high mutational potential of the interacting region of the SARS-CoV-2 virus with ACE2 receptor which is a growing concern among scientific communities and health professionals since it brings the effectiveness of repurposed drugs and vaccines for COVID-19 into question. In this latest work, we have identified 52 energetically favorable Spike mutations at the interface while binding to ACE2, of which only 36 significantly enhance the stabilization of the Spike-ACE2 complex. The stability order and molecular interactions of these mutations were also identified. The highest stabilizing mutation V503D confirmed in our study is also known for neutralization resistance.