Liquid Crystalline Ordering of Banana-Shaped Gapped DNA Duplexes

In-phase adenine-tracts (A-tracts) introduce intrinsic bending to DNA resulting in banana-shaped macromolecules. We investigate how such sequence-dependent bending influences DNA-based liquid crystal (LC) phases formed by gapped DNA (GDNA) constructs. By incorporating three in-phase A-tracts into duplex arms, we created GDNA constructs with bent duplexes and examined their LC phases using temperature-resolved synchrotron small-angle X-ray scattering and polarizing optical microscopy. The bent constructs exhibit a transition from a bilayer smectic-B phase to a monolayer smectic-A phase, although at ∼30 °C lower temperatures compared to GDNA with straight duplexes. At 25 °C, we estimate a bending angle of ∼11° per A-tract, which decreases with increasing DNA concentration and temperature. Moreover, we demonstrate that the stability of the LC phases increases up to ∼30 mM Mg²⁺ but decreases at higher concentrations. The lower stability of the LC phases of bent duplexes implies a reduced propensity for DNA condensation and heterochromatin formation.