End-to-end base stacking drives liquid crystalline phase formation in "gapped" DNA constructs

Small-angle/wide-angle x-ray scattering (SAXS/WAXS) and polarizing optical microscopy (POM) are used to study the liquid crystalline phases of “gapped” DNA (GDNA) constructs in an aqueous solution. In our previous studies, smectic liquid crystalline (LC) phases, which depend on temperature, DNA concentration (C_DNA), and the number of single thymine bases constituting the “gap” between the DNA duplexes, were observed [1,2]. At sufficiently high C_DNA, we observe a smectic-B phase wherein spontaneous end-to-end stacking of the DNA duplexes is accompanied by their in-plane ordering. By performing SAXS/WAXS measurements for temperatures in the range of 5 to 65°C, we determined the thermal melting temperature (T_m) of the end-to-end and side-by-side interactions that stabilize the positional order for DNA constructs, which differ in their terminal base pairs (AT-AT, AT-GC, or GC-GC) but are otherwise identical. We report remarkable variations in thermal stability (up to 25 °C shift in T_m) of these interactions, and the accompanying smectic order, due to these single base-pair alterations. Analysis of the melting data enables a comparison of relative enthalpic and entropic contributions to the interaction of free energy in each case.