Probing the anisotropic bendability of double-stranded DNA

The structure of double-stranded DNA (dsDNA) features a crooked helical axis and grooves of different widths. This intrinsic structural asymmetry suggests the presence of anisotropic bendability at the level of single base pair steps. However, measuring this local anisotropic bendability through experimental means remains a challenge. In this study, we utilize a single-molecule DNA looping assay to probe the local asymmetric bendability of DNA, both with and without a base pair mismatch. Our experimental approach is to compare the looping rates of two short DNA molecules (~100 bp), each containing two identical tri-nucleotides positioned just one helical turn (10 bp) apart in either the same (cis) or opposing (trans) orientation. The difference in looping rates serves as a proxy for the anisotropic bendability of the tri-nucleotides. The majority of the tri-nucleotides we examined exhibit a faster looping rate in the cis configuration than in trans, indicative of their inherent bending anisotropy. Notably, the presence of a base pair mismatch tends to diminish this anisotropy. To validate our findings, we compare our experimental data with the projected looping probabilities of DNA based on a model generated through all-atom molecular dynamics simulations. This work provides new insights into the mechanics of DNA at the short-length scale.