Bottom-Up Coarse-Grained Modeling of DNA

• Main Authors: Tiedong Sun, Vishal Minhas, Nikolay Korolev, Alexander Mirzoev, Alexander P. Lyubartsev, Lars Nordenskiöld
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2021-03-01
• Series: Frontiers in Molecular Biosciences
• Subjects: DNA condensation; coarse-grained model; molecular renormalization group; inverse Monte Carlo; multi-scale coarse-graining; force matching
• Online Access: https://www.frontiersin.org/articles/10.3389/fmolb.2021.645527/full

Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations. The so-called bottom-up coarse-graining practice separates fast and slow dynamic processes in molecular systems by averaging out fast degrees of freedom represented by the underlying fine-grained model. The resulting effective potential of interaction includes the contribution from fast degrees of freedom effectively in the form of potential of mean force. The pair-wise additive potential is usually adopted to construct the coarse-grained Hamiltonian for its efficiency in a computer simulation. In this review, we present a few well-developed bottom-up coarse-graining methods, discussing their application in modeling DNA properties such as DNA flexibility (persistence length), conformation, “melting,” and DNA condensation.