Pratik Kumar, PhD

Pratik Kumar, PhD

HHMI Postdoctoral Associate

Janelia Research Campus

  I am an HHMI postdoc with Luke Lavis (Janelia). I use fluorescent dyes to make reagents for cell biology, neuroscience, pharmacology, and imaging.
  During my PhD with Scott Laughlin, I made light and enzyme-controlled cyclopropenes for bioorthogonal labeling/imaging in cellular systems. Before coming to the US, as an undergrad, I worked on bactericidal, cationic gemini surfactants with Jayanta Haldar.
  I strongly care about effective mentoring, diversity in academia, awareness about “alternative” career options, and communicating my science to public.


  • Fluorescent Tools
  • Bioorthogonal Reagents
  • Biological Imaging
  • Biomolecule Manipulation
  • Effective Mentoring
  • Diversity in Science
  • Scientific Awareness


  • PhD, Chemistry, 2019

    Stony Brook University, New York, US

  • MS and BS, Chemistry, 2013

    IISER-K, Kolkata, IN

  • Diploma, Chemistry, 2009-11

    JNCASR, Bangalore, IN

  • Scientists Teaching Science, 2020


  • OMIBS, 2018

    Marine Biological Laboratory, Woods Hole, US

Research Experience


HHMI Postdoctoral Associate w/ Luke Lavis

HHMI-Janelia Research Campus

Jul 2019 – Present Virginia, USA

Graduate Student w/ Scott Laughlin

Stony Brook University

Aug 2013 – May 2019 New York, USA

POCE Fellowship w/ Jayanta Haldar


Aug 2010 – May 2012 Bangalore, India

Research Summary


Caged Cyclopropenes

Using light or enzymes to control the bioorthogonal reactions of cyclopropenes

Bioorthogonal Neurotransmitters

Bringing bioorthogonal chemistry to the realm of neuroscience

Lipidated Spirocyclopropyls

Synthesis of spirocyclic systems, cyclic enamines, and their conjugation to lipids

Olfactory Circuit Labeling

Testing fluorescent boronic acid probes as tracers of neural circuitry

Bactericidal Gemini Surfactants

Biodegradable cationic surfactants that kill bacterial cells but not mammalian cells

Multiclick dyes

Far-red emitting dyes that fluoresce upon bioorthogonal activation

Multifunctional dyes

Visualizing and manipulating biomolecules

Single-molecule imaging dyes

Novel photoactivatable rhodamine dyes for single particle tracking

Yellow/Far-red photocages

Yellow or red-light removable photocages for spatiotemporal release of small molecules


Multifunctional fluorophores for live-cell imaging and affinity capture of proteins

Melding synthetic molecules and genetically encoded proteins to forge new tools for neuroscience

2,7-Diaminobenzopyrylium dyes are live-cell mitochondrial stains

Modular Enzyme- and Light-Based Activation of Cyclopropene-Tetrazine Ligation

Stable Cyclopropene-Containing Analogs of the Amino Acid Neurotransmitter Glutamate

Caged Cyclopropenes with Improved Tetrazine Ligation Kinetics

Modular Activatable Bioorthogonal Reagents

Lipidated Cyclopropenes via a Stable 3-N Spirocyclopropene Scaffold

Caged Cyclopropenes for Controlling Bioorthogonal Reactivity

Inexpensive Multigram-Scale Synthesis of Cyclic Enamines and 3-*N* Spirocyclopropyl Systems

A Photocaged, Cyclopropene-Containing Analog of the Amino Acid Neurotransmitter Glutamate

Cleavable Cationic Antibacterial Amphiphiles: Synthesis, Mechanism of Action, and Cytotoxicities

Aggregation Properties of Amide Bearing Cleavable Gemini Surfactants by Small Angle Neutron Scattering and Conductivity Studies