Single Molecule Biophysics Lab

Welcome to Single Molecule Biophysics Lab!! 

Here, the pupils along with Green-Lantern (our smFRET setup) are involved in exploring the dynamics of DNA to understand how  DNA repair pathways are regulated to maintain genome integrity, as well as monitoring how other environmental factors also affect the secondary structure of the DNAs.

At the Nucleo-Protein  Biophysics lab we study interesting biophysical problems involving DNA, RNA and Proteins. Additional to the Single Molecule Imaging System, We utilize a combination of techniques, such as Förster resonance energy transfer (FRET), Protein Induces Fluorescence Enhancement (PIFE), Fluorescence Correlation Spectroscopy (FCS), Circular Dichroism (CD), Time Correlated Single Photon Counting (TCSPC) and the conventional UV-vis and Fluorescence methods.

The interactions of the protein factors at the nanoscale plays a very important role in deciding the fate of cellular processes of an organism. Conventionally, images of cells are used to understand the relationship between molecules through their spatial organization. However, often the most important aspect of an interaction is the rate of binding, the dissociation constant, conformational change and other dynamics and dwell times. This information is especially useful for understanding the effect of inhibitors and small molecules or solution conditions on the behavior of a particular interaction, such as the activity of an enzyme induced by substrate binding. 

Single-molecule methods have matured into powerful and popular tools to probe the complex behaviour of biological molecules, due to their unique abilities to probe molecular structure, dynamics and function, unhindered by the averaging inherent in ensemble experiments. All classical structural and biochemistry/biophysics methods describe the behavior of enormous ensembles of molecules, averaging the measured parameters over the entire molecular population. How any one molecule may behave over time cannot be revealed by such studies; neither can the behavior of individual molecules having different conformations and properties. It is important to realize that seemingly homogenous populations of macromolecules that have no chemical differences do possess intermolecular variations. SM methods provide the only available way to study their functional differences, by recording the behavior of individual members of a certain population of molecules. In addition, SM approaches reveal fluctuations in the observable parameters of a single molecule over time, often with very high temporal resolution, usually on the order of milliseconds. 

Our research activity lies in understanding how variations in DNA structure can affect fundamental biological processes such as replication and transcription. To that end we are motivated by determining biomolecular mechanisms of action, with a long-term view to improved development of therapeutics. 

The interactions of the protein factors at the nanoscale plays a very important role in deciding the fate of cellular processes of an organism. Conventionally, images of cells are used to understand the relationship between molecules through their spatial organization. However, often the most important aspect of an interaction is the rate of binding, the dissociation constant, conformational change and other dynamics and dwell times. This information is especially useful for understanding the effect of inhibitors and small molecules or solution conditions on the behavior of a particular interaction, such as the activity of an enzyme induced by substrate binding. 

Single-molecule methods have matured into powerful and popular tools to probe the complex behaviour of biological molecules, due to their unique abilities to probe molecular structure, dynamics and function, unhindered by the averaging inherent in ensemble experiments. All classical structural and biochemistry/biophysics methods describe the behavior of enormous ensembles of molecules, averaging the measured parameters over the entire molecular population. How any one molecule may behave over time cannot be revealed by such studies; neither can the behavior of individual molecules having different conformations and properties. It is important to realize that seemingly homogenous populations of macromolecules that have no chemical differences do possess intermolecular variations. SM methods provide the only available way to study their functional differences, by recording the behavior of individual members of a certain population of molecules. In addition, SM approaches reveal fluctuations in the observable parameters of a single molecule over time, often with very high temporal resolution, usually on the order of milliseconds. 

Our research activity lies in understanding how variations in DNA structure can affect fundamental biological processes such as replication and transcription. To that end we are motivated by determining biomolecular mechanisms of action, with a long-term view to improved development of therapeutics.