Single-molecule techniques have transformed biological research by enabling direct observation and manipulation of individual molecules. These methods overcome ensemble averaging inherent in bulk meas...

Amid enormous shifts, many scientists pushed back and risked dismissal from their jobs even as federal agencies fired thousands of employees

Nucleic acid structures are stabilized by both base pairing and base stacking. While energetics of base pairing interactions are relatively well established, our understanding of the energetic contributions of base stacking remain incomplete. Here, we use a combination of single-molecule and computational biophysics approaches to investigate the effect of strand polarity on base-stacking energetics. We designed pairs of DNA constructs with reversed stacking polarities at nick sites, along with corresponding no-stack controls to isolate stacking contributions. Performing single-molecule force-clamp assays with a Centrifuge Force Microscope (CFM), we observed polarity-dependent differences in stacking energetics. These differences were most pronounced in purine–purine and certain purine–pyrimidine interactions. Notably, a 5′ purine stacked on a 3′ pyrimidine was generally more stable than the reverse polarity. We employed molecular dynamics (MD) simulations to observe stacking interfaces in the DNA constructs. The simulations were qualitatively consistent with our experiments, and showed positional differences between opposite polarity stacking pairs, giving some insight into the origin of these polarity differences. Overall, these results demonstrate that base polarity can modulate stacking stability and should be considered when designing short duplex regions such as overhangs in molecular biology and biotechnology applications.

The Life Sciences Research Building, which is home to cutting-edge labs where researchers from the RNA Institute blend bench science with AI to help accelerate the development of RNA-based treatments ...

Proposal 1 would officially authorize that use while securing thousands of acres of new protected land in return.

Published in Expert Opinion on Drug Delivery (Ahead of Print, 2025)