All Outputs (2)

Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences (2024)
Journal Article
Maity, H., Nguyen, H. T., Hori, N., & Thirumalai, D. (2024). Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences. Journal of Physical Chemistry Letters, 15(14), 3820–3827. https://doi.org/10.1021/acs.jpclett.3c03553

Repeat RNA sequences self-associate to form condensates. Simulations of a coarse-grained single-interaction site model for (CAG)n (n = 30 and 31) show that the salt-dependent free energy gap, ΔGS, between the ground (perfect hairpin) and the excited... Read More about Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences.

Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences (2024)
Journal Article
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

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