Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions

• Published in: Langmuir 2023-04, Vol.39 (13), p.4838-4846
• Main Authors: Kodikara, Sineth G., Gyawali, Prabesh, Gleeson, James T., Jakli, Antal, Sprunt, Samuel, Balci, Hamza
• Format: Article
• Language: English
• Subjects: Base Pairing; Chemistry; DNA - chemistry; Materials Science; Nucleic Acid Conformation; Scattering, Small Angle; Temperature; Thermodynamics; X-Ray Diffraction
• ISSN: 0743-7463; 1520-5827; 1520-5827
• DOI: 10.1021/acs.langmuir.3c00318

Positionally ordered bilayer liquid crystalline nanostructures formed by gapped DNA (GDNA) constructs provide a practical window into DNA–DNA interactions at physiologically relevant DNA concentrations; concentrations several orders of magnitude greater than those in commonly used biophysical assays. The bilayer structure of these states of matter is stabilized by end-to-end base stacking interactions; moreover, such interactions also promote in-plane positional ordering of duplexes that are separated from each other by less than twice the duplex diameter. The end-to-end stacked as well as in-plane ordered duplexes exhibit distinct signatures when studied via small-angle X-ray scattering (SAXS). This enables analysis of the thermal stability of both the end-to-end and side-by-side interactions. We performed synchrotron SAXS experiments over a temperature range of 5–65 °C on GDNA constructs that differ only by the terminal base-pairs at the blunt duplex ends, resulting in identical side-by-side interactions, while end-to-end base stacking interactions are varied. Our key finding is that bilayers formed by constructs with GC termination transition into the monolayer state at temperatures as much as 30 °C higher than for those with AT termination, while mixed (AT/GC) terminations have intermediate stability. By modeling the bilayer melting in terms of a temperature-dependent reduction in the average fraction of end-to-end paired duplexes, we estimate the stacking free energies in DNA solutions of physiologically relevant concentrations. The free-energies thereby determined are generally smaller than those reported in single-molecule studies, which might reflect the elevated DNA concentrations in our studies.