Pratik Kumar

A Photoswitchable HaloTag for Spatiotemporal Control of Fluorescence in Living Cells Photoswitchable fluorophores are critical for advanced bioimaging. Here, we develop a photoswitchable self-labeling HaloTag that can reversibly modulate the emission of a bound fluorogenic dye via a ....

Our photoswitchable HaloTag is out in Angewandte Chemie @angewandtechemie.bsky.social ! We now also show that this system can be used to control emitter density in SMLM. Congrats to Franzi, Bego, and our amazing collaborators. Check it out: onlinelibrary.wiley.com/doi/full/10....

Congratulations Claire!

This work is now out @pnas.org. Result of fantastic collaborations with @so-lets-kilab70.bsky.social and Jason vevea @St Jude. Look out for two cool fluorescent ligands.

#AwardHighlight
Mousumi Baruah, post-doctoral researcher from Dr Pratik Kumar's lab, is the recipient of the National Post-doctoral Fellowship (N-PDF) by The Anusandhan National Research Foundation, India

Congratulations!🎉

@dyechemist.bsky.social

#CampusVisit
We recently welcomed 11th & 12th-grade students from DPS (N). They interacted with Dr Pratik Kumar & visited the labs of Prof Sanjay Sane & Dr Shashi Thutupalli.

The students learned how science is interdisciplinary and not done in silos.

@dyechemist.bsky.social @stpalli.bsky.social

#CampusVisit
Students of Bangalore International School visited NCBS last week.
They started the visit with an activity to learn critical thinking. @dyechemist.bsky.social spoke about life as a scientist & Aksha Chowdhary, wildlife master’s alum, shared her journey.
They also visited the Ear Lab

Come and do some chemistry for biology with us!

If making chemical tools for biology excites you, consider applying to the NCBS graduate program! My lab plans to hire 1–2 graduate students this cycle. More info on my lab @ dyecraftlab.com

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I think it's worth a try! But I don't have any data to support how they will behave in the yeast.

Alternate abstract image for our latest manuscript

Ow boy! Just when I thought I couldn't be impressed by a JQ1 containing compound anymore... it gets mashed with my favourite Janelia Fluor dye (JF635) and a halotag ligand. Exceptional work #chembio

Thanks Sam

We hope this idea will pave the way for the generation of many new cell-permeable chemical tools for biology. @rhodamine110.bsky.social @dyerfulchymist.bsky.social

Even Cooler: When BRD4 was translocated to constitutive heterochromatin, we observed increased transcriptional activity (histone H3.3 accumulation as a proxy). This shows that multifunctional fluorescent ligands can functionally alter chromatin in living cells!

There’s More! Using the same Si-rhodamine dye, we created JQ1-containing fluorescent ligands to manipulate the localization of BRD4. @so-lets-kilab70.bsky.social showed rapid translocation of BRD4 from euchromatin to HaloTag sites at the nucleolus.

These live-cell permeable biotins are great for affinity purification. Here, Jason Vevea figured out their in-cell labeling performance and purified mitochondria! This works so much better than the commercial biotin-HaloTag ligand (this doesn't work actually!)

We could use this to guess apriori cell-impermeable (yellow) and cell-permeable (red and magenta) biotin-containing rhodamine ligands! We used imaging to verify this for HaloTag fusions at the cell surface, mitochondria, ER, and nucleus.

We discovered that dyes with low lactone–zwitterion equilibrium constants and high distribution coefficients (logD) are great for making cell-permeable multifunctional ligands!

Self-labeling tags like HaloTag are great for labeling proteins with synthetic molecules. However, creating multifunctional ligands is tricky due to the competing demands of cell permeability vs. functionality.

🧵Prepint alert! Optimizing Multifunctional Fluorescent Ligands for Intracellular Labeling | tinyurl.com/3n55hvsc. With Jason Vevea, Ed Chapman, and @so-lets-kilab70.bsky.social, we combined dye chemistry, HaloTag, microscopy and cell biology to make protein purification and manipulation tools.

'Ubiquitin Lysine-Linkages' from the review 'Ubiquitin: a structural perspective' in Molecular Cell

New to #ubiquitin? Been with it for a while? Either way this review may be for you 🤩

Excited to share our review article in @molcell.bsky.social, diving deep into everything #ubiquitin
Read here 👉: kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...

@cellpress.bsky.social
@wehi-research.bsky.social

Me!

Me!

We made a photoswitchable HaloTag (psHaloTag), which can reversibly turn-on fluorogenic dyes upon illumination 💡. Congrats to Franzi, Bego and all co-authors, check out our preprint below 👇
www.biorxiv.org/content/10.1...

My aim is to integrate chemical tool building as an integral part of @NCBS, Bangalore Life Sciences Cluster and beyond. I am excited to return to India after a decade in the US. The lab will have lots of fun along with doing chemistry in an environment buzzing with excellent biologists!

I will hire at all levels (postdoc, graduate students, JRF, interns). We will train you in chemical synthesis, spectroscopy, biological labelling and fluorescence imaging, among other things. We will strongly emphasize developing soft skills and anything relevant to your career.

We have a few projects in mind with existing collaborators, but I am open to brainstorming. Feel free to email me to discuss ideas or to say hi 😀😀. For more details on what I do, please visit pratik-kumar.com

Super excited to start my lab @NCBS_Bangalore
in March 2025! The lab will primarily be powered by chemistry, and we will build chemical tools for biology with a strong focus on fluorescence imaging. We will collaborate widely and are open to any relevant areas of biology.