The wormlike chain model effectively captures the average, long-chain behavior of DNA. However, the mechanics and kinetics of short DNA molecules vary significantly depending on sequence and context. These variations may impact genomic processes within cells. In this talk, I will present two recent studies from my lab that explore such unusual properties of DNA.
The first study examines the melting kinetics of short DNA duplexes in different contexts. Using single-molecule FRET, we found that duplexes connected by a single-stranded gap (ssg) exhibit slower melting rates compared to separated duplexes. The stabilization factor is greater than that expected from a single-stranded overhang alone. We speculate that mutual duplex stabilization occurs through stacking interactions propagating through the ssg, consistent with all-atom MD simulation results.
The second study explores how anisotropic bendability of DNA base pair steps influences the conformation of DNA loops. DNA (~100 base pairs) ligated into a minicircle tends to adopt a specific poloidal (inside-out) orientation to minimize bending energy. To study this poloidal bias and its dependence on DNA sequence, we developed two experimental approaches: (1) a single-molecule fluorescence assay to measure protein binding affinities at various positions along the minicircle, and (2) protein localization relative to the minicircle using AFM. I will explain the underlying concepts behind these approaches and share our recent findings.