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Ken Halvorsen

@halvorsenlab.bsky.social
243 followers 168 following 89 posts

Mostly posting science from our lab at RNA Institute, UAlbany.

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Ken Halvorsen @halvorsenlab.bsky.social · 19/05/2026
If it helps at all, here's an example I used for my MIRA renewal progress report vs. the abridged version in my biosketch.
Abraham Punnoose, J., Cole, D., Melfi, T., Morya, V., Madhanagopal, B.R., Chen, A.A., Vangaveti, S., Chandrasekaran, A.R., & Halvorsen, K. (2025). Tuning the Stability of DNA Tetrahedra with Base Stacking Interactions. Nano Letters 25, 3605-3612. PMCID: PMC11887421. [R35GM124720 for JAP, DC, VM, and KH (sole support for Halvorsen lab – concept, design, execution, analysis of tetrahedron experiments); other authors: R35GM133469 for TM, SV, and AA (MD simulations); R35GM150672 for BRM and ARC (DLS and AFM experiments)]nanotechnology. This project (PMC11887421) was supported by MIRA R35GM124720 for our lab & two other MIRA R35GM133469, R35GM150672 for collaborating labs. These studies advance DNA nanotechnology by addressing issues of
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Ken Halvorsen @halvorsenlab.bsky.social · 06/05/2026
Excited to share our new preprint (www.biorxiv.org/content/10.6...), integrating aptamer based sensing into our DNA nanoswitch platform for protein detection. The project almost died about 4 times, and it's nice to see 10 yrs of back burner simmering coming out fully baked. @arunrichard.bsky.social
Design of a dual detecting DNA nanoswitch where aptamer binding of a protein target causes a loop of a specific size to form.  When read on gel electrophoresis, two proteins can be detected simultaneously, in this case VEGF producing a large loop and thrombin producing a smaller loop.
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Ken Halvorsen @halvorsenlab.bsky.social · 27/01/2026
I'm very excited about this new preprint on our work (www.biorxiv.org/content/10.6...). We re-engineered gel electrophoresis for our DNA-base biosensors and came up with a 3D printed mini-gel, complete with electrodes. short thread...
images of a conventional gel box and 3D printed mini boxes with resulting gel band images
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Ken Halvorsen @halvorsenlab.bsky.social · 05/12/2025
Christmas came early! New science toy from @lumicks.bsky.social for @thernainstitute.bsky.social - very excited to get this all set up and operational.
large crates packed with science equipment
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Ken Halvorsen @halvorsenlab.bsky.social · 26/09/2025
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...
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Ken Halvorsen @halvorsenlab.bsky.social · 23/08/2025
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.
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Ken Halvorsen @halvorsenlab.bsky.social · 20/06/2025
this one actually made me LOL though
A terrible AI image of an interdisciplinary triangle that is actually a circle
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Ken Halvorsen @halvorsenlab.bsky.social · 12/03/2025
Was great to catch up and talk science and life with @jesssfisher.bsky.social yesterday at her visit to UAlbany!
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Ken Halvorsen @halvorsenlab.bsky.social · 24/02/2025
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.
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Ken Halvorsen @halvorsenlab.bsky.social · 24/02/2025
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.
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Ken Halvorsen @halvorsenlab.bsky.social · 24/02/2025
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.
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Ken Halvorsen @halvorsenlab.bsky.social · 24/02/2025
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.
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Ken Halvorsen @halvorsenlab.bsky.social · 24/02/2025
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.
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Ken Halvorsen @halvorsenlab.bsky.social · 30/12/2024
You too can make it to step 90 (my favorite), which amazingly made it through peer review, editorial review, and copy editing :)
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Ken Halvorsen @halvorsenlab.bsky.social · 30/12/2024
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.
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Ken Halvorsen @halvorsenlab.bsky.social · 30/12/2024
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).
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Ken Halvorsen @halvorsenlab.bsky.social · 18/12/2024
Fun to get together for pre-holiday lab lunch today. Managed to get almost all of us (missing 3).
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Ken Halvorsen @halvorsenlab.bsky.social · 27/11/2024
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!
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Ken Halvorsen @halvorsenlab.bsky.social · 21/11/2024
Great to see people from the lab enthusiastically presenting their work! @thernainstitute.bsky.social
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Ken Halvorsen @halvorsenlab.bsky.social · 21/11/2024
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
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