Christmas came early! New science toy from @lumicks.bsky.social for @thernainstitute.bsky.social - very excited to get this all set up and operational.

Well, it's been a minute but we have a new preprint to share! Final project in our lab by @jibinpunnoose.bsky.social, investigating strand polarity in base stacking. We measured experimentally with centrifuge force microscope and computationally with MD.

www.biorxiv.org/content/10.1...

Yesterday we bid farewell to Jibin, who has been in the lab for 7 years and is starting as Assistant professor of chemistry at SUNY New Paltz. Congrats and best wishes - we were so fortunate to have you in the lab.

this one actually made me LOL though

Was great to catch up and talk science and life with @jesssfisher.bsky.social yesterday at her visit to UAlbany!

To conclude, we designed a few tetrahedra to illustrate how design choices affect stability. Tetrahedra with a 4bp sticky end & weak terminal stacking didn't stably form at RT. Strengthening the terminal stacks resulted in very stable tetrahedra, similar to some 6bp tetrahedra.

For this second point, we turned to computational collaborators in the Chen and Vengaveti labs to help make sense of this. They did MD simulations and found qualitatively similar results, supporting a polarity effect.

To measure overall stability, we subjected the tetrahedra to different temperatures for an hour and measured how much remained intact. Dadrian performed experimental triplicates on all of these and we analyzed the "melting" temperatures.

This design allowed us to maintain the base pairing interactions in the sticky ends while altering the base stacking interactions. Our super dedicated team member Dadrian built all of these and confirmed formation.

Here, we wanted to design tetrahedra that would allow us to test all 16 possible base stacking interactions one at a time. We chose a 6 bp sticky end and designed strands so that only one side had a terminal stacking interaction.

You too can make it to step 90 (my favorite), which amazingly made it through peer review, editorial review, and copy editing :)

We hope this encourages others to build CFM - really it can be done by anyone in the lab. The assembly is shown step by step in supplemental video tutorials, including my terrible soldering skills on display.

By redesigning our 3D printed housing and carefully selecting commercially available parts, we enabled a roughly 24 hour build time (90% of which is 3D printing time) and a ~$1000 cost (excluding centrifuge and PC).

Fun to get together for pre-holiday lab lunch today. Managed to get almost all of us (missing 3).

Some of the fun of science is chipped away (inadvertently or not) by reviewers, editors and copy editors - so I am thrilled and surprised that my favorite fun/cheesy step survived the gauntlet and will be in our final protocol paper for CFM (centrifuge force microscope). Coming soon!

Great to see people from the lab enthusiastically presenting their work! @thernainstitute.bsky.social

After much planning, today we are excited to put on the 15th life science research symposium! Great turnout with 160+ attendees, 65 posters, 12 trainee talks, 3 keynotes. @ualbany.bsky.social @thernainstitute.bsky.social