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Maffeo C, Chou HY, Aksimentiev A. Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations. ADVANCED THEORY AND SIMULATIONS 2019; 2:1800191. [PMID: 31728433 PMCID: PMC6855400 DOI: 10.1002/adts.201800191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/15/2022]
Abstract
Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein-nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics and the advent of single-molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. In this review, we describe recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. We highlight the use of diverse computational methods to address specific problems of the fields and discuss unexplored possibilities that lie ahead for the computational approaches in these areas.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Han-Yi Chou
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
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Beltrán-Leiva MJ, Fuenzalida-Valdivia I, Cantero-López P, Bulhões-Figueira A, Alzate-Morales J, Páez-Hernández D, Arratia-Pérez R. Classical and Quantum Mechanical Calculations of the Stacking Interaction of NdIII Complexes with Regular and Mismatched DNA Sequences. J Phys Chem B 2019; 123:3219-3231. [DOI: 10.1021/acs.jpcb.9b00703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- María J. Beltrán-Leiva
- Relativistic Molecular Physics Group, Universidad Andres Bello, República 275, Santiago 8370146, Chile
| | - Isabel Fuenzalida-Valdivia
- Facultad de Ciencias Biológicas, Centro de Biotecnología Vegetal, Universidad Andres Bello, Santiago 8370146, Chile
| | - Plinio Cantero-López
- Relativistic Molecular Physics Group, Universidad Andres Bello, República 275, Santiago 8370146, Chile
- Center for Applied Nanosciences (CANS), Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 275, Santiago, 8370146, Chile
| | - Ana Bulhões-Figueira
- Centro Universitário Estácio de Ribeirão Preto, Rua Abrahão Issa Halach 980, Ribeirãnia, Ribeirão Preto, Sao Paulo 14096-160, Brazil
| | - Jans Alzate-Morales
- Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente 1141, Talca, Chile
| | - Dayán Páez-Hernández
- Relativistic Molecular Physics Group, Universidad Andres Bello, República 275, Santiago 8370146, Chile
- Center for Applied Nanosciences (CANS), Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 275, Santiago, 8370146, Chile
| | - Ramiro Arratia-Pérez
- Relativistic Molecular Physics Group, Universidad Andres Bello, República 275, Santiago 8370146, Chile
- Center for Applied Nanosciences (CANS), Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 275, Santiago, 8370146, Chile
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