| Title: |
ANNaMo. Coarse-grained modeling for folding and assembly of RNA and DNA systems |
| Authors: |
Tosti Guerra, F.; Poppleton, E.; Šulc, P.; Rovigatti, L. |
| Contributors: |
Tosti Guerra, F.; Poppleton, E.; Šulc, P.; Rovigatti, L. |
| Publisher Information: |
American Institute of Physics; Melville, NY |
| Publication Year: |
2024 |
| Collection: |
Sapienza Università di Roma: CINECA IRIS |
| Subject Terms: |
folding dynamic; molecular dynamic; soft matter; thermodynamic; nanostructure; self assembly; nucleic acid; nucleotide; coarse-grain model; nanobiotechnology |
| Description: |
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales and system sizes involved. In this article, we present a new coarse-grained model for investigating the folding dynamics of nucleic acids. Our model represents three nucleotides with a patchy particle and is parameterized using well-established nearest-neighbor models. Thanks to the reduction of degrees of freedom and to a bond-swapping mechanism, our model allows for simulations at timescales and length scales that are currently inaccessible to more detailed models. To validate the performance of our model, we conducted extensive simulations of various systems: We examined the thermodynamics of DNA hairpins, capturing their stability and structural transitions, the folding of an MMTV pseudoknot, which is a complex RNA structure involved in viral replication, and also explored the folding of an RNA tile containing a k-type pseudoknot. Finally, we evaluated the performance of the new model in reproducing the melting temperatures of oligomers and the dependence on the toehold length of the displacement rate in toehold-mediated displacement processes, a key reaction used in molecular computing. All in all, the successful reproduction of experimental data and favorable comparisons with existing coarse-grained models validate the effectiveness of the new model. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
info:eu-repo/semantics/altIdentifier/pmid/38814009; info:eu-repo/semantics/altIdentifier/wos/WOS:001237985200005; volume:160; issue:20; firstpage:1; lastpage:14; numberofpages:14; journal:THE JOURNAL OF CHEMICAL PHYSICS; https://hdl.handle.net/11573/1711313 |
| DOI: |
10.1063/5.0202829 |
| Availability: |
https://hdl.handle.net/11573/1711313; https://doi.org/10.1063/5.0202829 |
| Rights: |
info:eu-repo/semantics/openAccess ; license:Tutti i diritti riservati (All rights reserved) ; license uri:iris.PRI00 |
| Accession Number: |
edsbas.D80163EF |
| Database: |
BASE |