Liquid Crystalline Ordering of Banana-Shaped Gapped DNA Duplexes

In-phase adenine-tracts (A-tracts) introduce intrinsic bending to double stranded DNA resulting in banana-shaped macromolecules. In this study, we investigate how such sequence-dependent bending influences DNA-based liquid crystalline (LC) phases formed by gapped DNA (GDNA) constructs. By incorporating three in-phase A-tracts into each duplex arm, we created a GDNA construct with bent duplexes and examined the LC phases they form using temperature-resolved synchrotron small-angle X-ray scattering and polarizing optical microscopy. Like the analogous constructs containing straight (rod-like) duplexes, the bent constructs exhibit a transition from bi-layer smectic-B phase to a monolayer smectic-A phase, although at ~30 °C lower temperatures. By comparing the monolayer spacing between the bent and straight constructs, we estimate a bending angle of ~11° per A-tract at room temperature and at physiologically relevant salt and c _DNA . The bending angle decreases with increasing DNA concentration and temperature. Moreover, we demonstrate that divalent cations enhance the stability of the smectic-B phase up to ~30 mM Mg ²⁺ but reduce it beyond that. The reduced thermal stabilities of the bilayer and in-layer ordering of bent duplexes imply reduced propensity for DNA condensation and heterochromatin formation under physiological conditions.