ISSN print edition: 0366-6352 ISSN electronic edition: 1336-9075 Registr. No.: MK SR 9/7 Published monthly

NARall: a novel tool for reconstruction of the all-atom structure of nucleic acids from heavily coarse-grained model

Łukasz Golon and Adam K. Sieradzan

Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland

E-mail: adam.sieradzan@ug.edu.pl

Received: 19 August 2022  Accepted: 13 December 2022

Abstract:

Nucleic acids are one of the most important cellular components. These molecules have been studied both experimentally and theoretically. As all-atom simulations are still limited to short time scales, coarse-grain modeling allows to study of those molecules on a longer time scale. Nucleic-Acid united RESidue (NARES-2P) is a low-resolution coarse-grained model with two centers of interaction per repeating unit. It has been successfully applied to study DNA self-assembly and telomeric properties. This force field enables the study of nucleic acids Behavior on a long time scale but lacks atomistic details. In this article, we present new software to reconstruct atomistic details from the NARES-2P model. It has been applied to RNA pseudoknot, nucleic acid four-way junction, G-quadruplex and DNA duplex converted to NARES-2P model and back. Moreover, it was applied to DNA structure folded and self-assembled with NARES-2P.

Keywords: Nucleic acids; All-atom structure reconstruction; NARES-2P

Full paper is available at www.springerlink.com.

DOI: 10.1007/s11696-022-02634-x

Chemical Papers 77 (5) 2437–2445 (2023)