RESEARCH PROJECTS
RESEARCH PROJECTS
Embedded Files
A. Investigating Biomolecular Condensate Formation by Oncogenic Fusion Transcription Factors, and its Role in Aberrant Transcription Regulation.
~17% of all cancer types are associated with different fusion proteins that primarily belong to two classes, such as transcription factor (TF) and kinase. Fusion TFs bind to a promoter region and aberrantly regulate the expression of target genes, causing a pathogenic situation. Few recent reports suggest that fusion TFs could form biomolecular condensates through the multivalent interaction among low complexity domains (LCDs). However, the underlying mechanism is not yet clearly understood. In our lab, we study biomolecular condensate formation by in vitro as well as in-cell experiments using fluorescence spectroscopy and advanced microscopy imaging [Confocal microscopy, Total Internal Fluorescence (TIRF) microscopy, Super-resolution microscopy (STORM, PALM, and PAINT), and single particle tracking (SPT)]. Additionally, we employ diverse biochemical assays to elucidate the cause-and-function relationship of condensate formation.
B. Developing Super-resolution Microscopy Methods Based on Peptide-PAINT.
Point accumulation for imaging in nanoscale topography (PAINT) is a single-molecule methodology for super-resolution microscopy, which achieves a localization precision of approximately 5–25 nm. Moreover, Peptide-PAINT using transfected docker simplifies imaging procedures in comparison to other commonly employed methods such as Stochastic Optical Reconstruction Microscopy (STORM) and Photo-activated Localization Microscopy (PALM), and DNA-PAINT. [Ref.: Maity et al., Small Methods, 2023]
We are interested in advancing nanoscopic imaging techniques based on Peptide-PAINT by leveraging knowledge in chemistry, machine learning-based computation biophysics, and protein biophysics. We employ this advancement in elucidating nanoscale structural features of endogenous proteins in mammalian cells and deciphering the link between structure and both pathological and physiological functions.
C. Designing Highly Specific Protein Binders.
In case of single molecule imaging-based super-resolution microscopy, notably STORM, PALM, and conventional PAINT, a fluorophore/docker strand is selectively conjugated to a protein of interest (POI) via a primary antibody, subsequently followed by a secondary antibody, which is considerably bigger than the POI. Consequently, it introduces an approximate linkage error of 20-30 nm, larger than the localization precision of single molecule imaging. Moreover, numerous essential proteins lack accessible primary antibodies. In our lab, we design specific protein binders, significantly smaller than primary and secondary antibodies, against key functional proteins. We employ machine learning-based computational tools to design binders, and subsequently, validate by experiments.
Page updated
Google Sites
Report abuse