Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 14, Issue 7, Pages 3603-3620Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.8b00291
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Funding
- Foundation for Polish Science
- Humboldt foundation fellowship
- National Science Centre, Poland [DEC-2016/20/T/NZ2/00576 Etiuda, DEC-2014/12/W/ST5/00589 Symfonia]
- Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw [G31-4, GA65-17]
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Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.
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