edu.ucar.opensky::articles:24013 UCAR/NCAR - Library OpenSky Support PO Box 3000 Boulder CO 80307-3000 opensky@ucar.edu http://opensky.ucar.edu/ homepage pointOfContact 2025-12-25T06:43:56.423377 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) https://n2t.org/ark:/85065/d7r49v3f Understanding DNA interactions in crowded environments with a coarse-grained model 2020-10-12T00:00:00Z publication https://n2t.org/ark:/85065/d7r49v3f https://doi.org/10.1093/nar/gkaa854 Hong, F. author Schreck, John S. author Å ulc, P. author UCAR/NCAR - Library publisher Nucleic acid interactions under crowded environments are of great importance for biological processes and nanotechnology. However, the kinetics and thermodynamics of nucleic acid interactions in a crowded environment remain poorly understood. We use a coarse-grained model of DNA to study the kinetics and thermodynamics of DNA duplex and hairpin formation in crowded environments. We find that crowders can increase the melting temperature of both an 8-mer DNA duplex and a hairpin with a stem of 6-nt depending on the excluded volume fraction of crowders in solution and the crowder size. The crowding induced stability originates from the entropic effect caused by the crowding particles in the system. Additionally, we study the hybridization kinetics of DNA duplex formation and the formation of hairpin stems, finding that the reaction rate k(on) is increased by the crowding effect, while k(on) is changed only moderately. The increase in k(on) mostly comes from increasing the probability of reaching a transition state with one base pair formed. A DNA strand displacement reaction in a crowded environment is also studied with the model and we find that rate of toehold association is increased, with possible applications to speeding up strand displacement cascades in nucleic acid nanotechnology. UCAR/NCAR - Library OpenSky Support PO Box 3000 Boulder CO 80307-3000 opensky@ucar.edu http://opensky.ucar.edu/ homepage pointOfContact PDF Text theme Resource Type 2016-01-01T00:00:00Z publication Copyright author(s). This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. None eng geoscientificInformation