Research

(1) Plasmonic Nanoassembly as an Optical Nanoantenna

One of our key research goals is to harness anisotropic plasmonic nanoassemblies as optical nanoantennas to control and manipulate light at the nanoscale. This approach aims to significantly enhance the signal-to-noise ratio in fluorescence-based detection technologies.

When individual metal nanoparticles are assembled into a well-defined plasmonic structure, the coupling of their localized surface plasmon resonances (LSPR) leads to an increase in the local density of optical states (LDOS) within the nanogap. This coupling creates intense electromagnetic hotspots, resulting in substantial enhancement of fluorescence and Raman signals from molecules located in these regions.

Anisotropic plasmonic nanostructures—such as rods, prisms, or bipyramids—are particularly attractive due to their sharp edges and tips that tightly confine light, producing highly intense hotspots. When assembled into dimers or higher-order structures, these nanoparticles exhibit hybrid plasmon modes, further amplifying the local electromagnetic fields.

Our lab focuses on the bottom-up chemical synthesis of plasmonic assemblies composed of anisotropic metal nanoparticles (Au, Ag, Al). We employ diverse chemical linkers to achieve precise control over the orientation, interparticle gap distance, and size of these nanoassemblies. We have also developed methods to halt the assembly at specific stages—such as dimer or trimer formation—to study their optical behavior.

Beyond synthesis, we are deeply interested in understanding the mechanism of nanoassembly formation, as this knowledge is essential for designing plasmonic architectures with tailored optical properties for next-generation sensing and photonic applications.

Selected Publications 

(1) S. Sharma, T. Minchella, S. Pradhan, D. Gérard, Q. Jiang, and S. Patra*, "pH controlled synthesis of end to end linked Au nanorod dimer in an aqueous solution for plasmon enhanced spectroscopic applications", Nanoscale, 16 (48), 22411-22422 (2024). IF 5.1

(2) Biomolecules inside a phase-separated condensate 

Cells contain membraneless compartments known as biomolecular condensates, which form through liquid–liquid phase separation (LLPS). These condensates help organize essential cellular processes such as transcription, replication, and stress response by concentrating specific proteins and nucleic acids into confined regions of space.

Inside these droplets, biomolecules exist in a crowded and confined environment that is very different from the dilute buffer conditions typically used in vitro, where the concentration of biomolecules is only a few micromolar. Such high local concentrations can significantly alter the structure, dynamics, and interactions of biomolecules. Yet, despite their biological importance, we still have a limited understanding of how the unique physical environment within condensates influences molecular behavior.

Our research aims to decode how LLPS environments affect biomolecular structure and interaction dynamics. To do this, we prepare model condensates that mimic cellular ones and apply advanced fluorescence spectroscopy and microscopy techniques to probe the thermodynamics and kinetics of biomolecular interactions inside these droplets.

Through this approach, we aim to gain a mechanistic understanding of how the condensate environment modulates biomolecular behavior. These insights will not only help us better understand the biophysical principles of cellular organization, but also provide clues to how changes in such environments could influence cellular function and disease mechanisms.

Selected Publications 

(1) S. Pradhan, M. Campanile, S. Sharma, R. Oliva*, and S. Patra*, "Mechanistic Insights into the c-MYC G-Quadruplex and Berberine Binding inside an Aqueous Two-Phase System Mimicking Biomolecular Condensates " J. Phys. Chem. Lett.,  15 (34), 8706-8714 (2024). IF 4.8

(3) Plasmonic Biosensing

Fast and reliable detection of disease biomarkers is essential for early diagnosis and public health monitoring. There is a growing need for molecular diagnostic tools that are:
• Fast – no need for amplification or extraction
• Simple – single-step, no washing, easy to operate
• Accurate – highly sensitive and specific to target biomarkers

Plasmonic biosensing offers all these advantages. The optical properties of metal nanoparticles, governed by localized surface plasmon resonance (LSPR), are extremely sensitive to their size, shape, and the surrounding chemical environment. This makes them ideal for ultrasensitive detection of disease biomarkers.

When light interacts with these nanoparticles, intense electromagnetic “hotspots” are formed, dramatically enhancing fluorescence and Raman signals. As a result, even trace amounts of biomarkers—down to the pico- or femtomolar range—can be detected, enabling early disease screening.

In our research group, we design and engineer plasmonic nanoparticles with tailored optical properties and surface functionalization strategies to position target analytes precisely within these hotspots. Our goal is to continuously push the detection limits of plasmonic biosensors, advancing early diagnostics and preventive healthcare.

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

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)