Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences

Mondal, Balaka; Chakraborty, Debayan; Hori, Naoto; Nguyen, Hung T.; Thirumalai, D.

Abstract

Interplay between divalent cations (Mg2+ and Ca2+) and single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), as well as stacking interactions, is important in nucleosome stability and phase separation in nucleic acids. Quantitative techniques accounting for ion–DNA interactions are needed to obtain insights into these and related problems. Toward this end, we created a sequence-dependent computational TIS-ION model that explicitly accounts for monovalent and divalent ions. Simulations of the rigid 24 base-pair (bp) dsDNA and flexible ssDNA sequences, dT30 and dA30, with varying amounts of the divalent cations show that the calculated excess number of ions around the dsDNA and ssDNA agree quantitatively with ion-counting experiments. Using an ensemble of all-atom structures generated from coarse-grained simulations, we calculated the small-angle X-ray scattering profiles, which are in excellent agreement with experiments. Although ion-counting experiments mask the differences between Mg2+ and Ca2+, we find that Mg2+ binds to the minor grooves and phosphate groups, whereas Ca2+ binds specifically to the minor groove. Both Mg2+ and Ca2+ exhibit a tendency to bind to the minor groove of DNA as opposed to the major groove. The dA30 conformations are dominated by stacking interactions, resulting in structures with considerable helical order. The near cancellation of the favorable stacking and unfavorable electrostatic interactions leads to dT30 populating an ensemble of heterogeneous conformations. The successful applications of the TIS-ION model are poised to confront many problems in DNA biophysics.

Citation

Mondal, B., Chakraborty, D., Hori, N., Nguyen, H. T., & Thirumalai, D. (2024). Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences. Journal of Chemical Theory and Computation, 20(7), 2934-2946. https://doi.org/10.1021/acs.jctc.3c01193

• Journal Article Type: Article
• Acceptance Date: Feb 22, 2024
• Online Publication Date: Mar 18, 2024
• Publication Date: Apr 9, 2024
• Deposit Date: Mar 18, 2024
• Publicly Available Date: Mar 19, 2025
• Journal: Journal of Chemical Theory and Computation
• Print ISSN: 1549-9618
• Electronic ISSN: 1549-9626
• Publisher: American Chemical Society
• Peer Reviewed: Peer Reviewed
• Volume: 20
• Issue: 7
• Pages: 2934-2946
• DOI: https://doi.org/10.1021/acs.jctc.3c01193
• Keywords: Cations, Conformation, Genetics, Ions, X-ray scattering
• Public URL: https://nottingham-repository.worktribe.com/output/31699869
• Publisher URL: https://pubs.acs.org/doi/10.1021/acs.jctc.3c01193
• Additional Information: This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Theory and Computation. To access the final edited and published work see https://pubs.acs.org/doi/10.1021/acs.jctc.3c01193