With all the GPS trackers and map apps out there, it’s almost impossible to get lost. But even though we know what a lot of small molecules are doing, we can lose track of exactly where those molecules are. That’s why Shankar Balasubramanian’s lab (University of Cambridge) developed Chem-map. Knowing this info could help researchers design even better drugs and imaging probes.
Sure, there are methods like Chem-Seq for chromatin binders, but small molecules can fall off during washing steps. Same goes for molecules that bind noncovalently to DNA itself. And the approaches often require lots of sample—not always an option. So, that means we still don’t have the coordinates of many approved drugs.
That’s where Balasubramanian’s team merged in. They wanted to develop an easy, general chemistry GPS to finally geolocate three types of small molecule interactions in situ: 1) with chromatin, 2) with DNA G-quadruplexes, and 3) intercalation in DNA. It’s kind of a riff on CUT&Tag, except here, the team has their eyes set on small molecules instead of proteins.
Want to navigate to your own favorite small molecule? Here’s your itinerary:
- Covalently attach an affinity tag to a small molecule
- Recruit Tn5 transposase to the binding site via a secondary antibody
- Activate Tn5 and let it do its thing, marking the site with transposition events
- Extract the fragments, amplify them, do a little sequencing and mapping, et voila!
The researchers used Chem-map to find where JQ1 bound in leukemia cells and got results similar to when they did CUT&Tag on BRD4, JQ1’s main target. And the raw data from the new method offered advantages over Click-Chem-seq data in those cells for JQ1. They also mapped two different molecules to G-quadruplex DNA, and showed where doxorubicin binds DNA.
With a few tweaks, Chem-map can adapt to many types of studies, even those with low sample amounts and rare sequences. And with all of this information, researchers could get a better understanding of exactly where small molecules bind, allowing them to develop advanced drugs to treat many types of diseases.
To find your own route, set a course for Nature Biotechnology, December 2022