Research

(1) Breaching the diffraction limit in single molecule detection using nanoplasmonics: 

Next stage development of single molecule fluorescence tools for real life practical applications requires to fulfil two most important criteria

(i) first, to ensure good signal to noise ratio in the single molecule fluorescence measurement,

(ii) second, the ability to perform these measurements at elevated concentrations e.g. μM concentration where most of the biological interactions occur.

However, diffraction of light in a classical confocal optics posed a serious challenge for the efficient detection of a single molecule. The large size mismatch between a single molecule (<~5 nm) and the diffraction limited focal spot (~250 nm) leads to an inefficient light-matter interaction resulting large statistical noise and poor temporal resolution in the single molecule measurements. Furthermore, to isolate a single molecule in confocal volume requires an extremely dilute sample in the nonphysiological concentration range typically nM to pM.  Therefore, an alternative strategy is needed to expand the scope of single molecule fluorescence spectroscopy for successful commercial applications such as DNA sequencing, drug screening and biomedical applications etc.

In our research group, we introduce the concept of nanoplasmonics to breach the diffraction limit in single molecule fluorescence detection. We utilize the localized surface plasmons of the metallic nanostructures to manipulate and control light matter interaction in the nanoscale. The localized surface plasmons of the metallic nanostructures breach the diffraction limit by converting the freely propagating incident electromagnetic field to a localized electromagnetic field in a tiny nanometer space at the vicinity of the metallic nanostructures. Such a concentrated electromagnetic field enhances the light-matter interaction in the nanoscale and improves the net detected signal from the single molecule. The smaller observation volume offer by the localization of the electromagentic field also enables us to perform the single molecule measurement at biologically relevant μM concentration.  

Our research team designed and fabricate metallic nanostructures of different shape and geometry to optimize the enhancement factor in single molecule fluorescence detection. Using these nanostructure, we are continuously pushing the limit of single molecule detection to expand its capabilities in widespread applications.

Selected Publications 

(2) Understanding the Structure and Interaction Dynamics of the Biomolecules using Single Molecule Fluorescence Tools

One of our major research interest is to find out the structure function relationship of the biomolecules e.g. proteins, DNA and RNA etc. Biomolecules are not static and are actually dynamic and this structural dynamics is intimately related to their function. As for example a protein change its shape to accommodate a ligand to its binding site, an enzyme undergoes rearrangement in the active site to catalyze a reaction. Furthermore, these biomolecules interact with each other in a high fidelity manner to perform their function in an extremely specific manner. To understand this the best option is to look at one molecule at a time when the molecule is performing its function to resolve the static and dynamic heterogeneity which is averaged out in an ensemble measurement.

In our study, we are using single molecule Förster resonance energy transfer (smFRET) tool to decipher the structure and interaction dynamics of the biomolecules. FRET is very sensitive to distance change in the nanometric scale and is a molecular ruler. Hence, FRET is ideally suited to probe the structural dynamics of the biomolecules. The biomolecule of interest is labelled with donor and acceptor fluorophore at specific location and therefore any changes in the biomolecules structure can be probed from the change in FRET efficiency. Using smFRET, we are currently investigating a wide variety of functionally important DNA, RNA and protein molecules. Our main interest here is to study the DNA-protein interactions which have potential applications to anticancer and antiviral therapy.  

Selected Publications

(1) S. Patra, V. Schuabb, I. Kiesel, J. M. Knop, R. Oliva, R. Winter, Exploring the effects of cosolutes and crowding on the volumetric and kinetic profile of the conformational dynamics of a poly dA loop DNA hairpin: a single-molecule FRET study, Nulceic Acids Res. 47, 981-996 (2019). (IF : 16.971) 

(2) S. Patra, C. Anders, N. Erwin, R. Winter, Osmolyte effects on the conformational dynamics of a DNA hairpin at ambient and extreme environmental conditions, Angew. Chem. Int. Ed., 129, 5127-5131 (2017). (IF : 15.336)