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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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Bos I, Terenzi C, Sprakel J. Chemical Feedback in Templated Reaction-Assembly Networks. Macromolecules 2020; 53:10675-10685. [PMID: 33328693 PMCID: PMC7726899 DOI: 10.1021/acs.macromol.0c01915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/02/2020] [Indexed: 02/06/2023]
Abstract
Chemical feedback between building block synthesis and their subsequent supramolecular self-assembly into nanostructures has profound effects on assembly pathways. Nature harnesses feedback in reaction-assembly networks in a variety of scenarios including virion formation and protein folding. Also in nanomaterial synthesis, reaction-assembly networks have emerged as a promising control strategy to regulate assembly processes. Yet, how chemical feedback affects the fundamental pathways of structure formation remains unclear. Here, we unravel the pathways of a templated reaction-assembly network that couples a covalent polymerization to an electrostatic coassembly process. We show how the supramolecular staging of building blocks at a macromolecular template can accelerate the polymerization reaction and prevent the formation of kinetically trapped structures inherent to the process in the absence of feedback. Finally, we establish a predictive kinetic reaction model that quantitatively describes the pathways underlying these reaction-assembly networks. Our results shed light on the fundamental mechanisms by which chemical feedback can steer self-assembly reactions and can be used to rationally design new nanostructures.
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Affiliation(s)
- Inge Bos
- Physical Chemistry
and Soft Matter, Wageningen University &
Research, Stippeneng
4, 6708 WE Wageningen, The Netherlands
| | - Camilla Terenzi
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, 6708
WE Wageningen, The Netherlands
| | - Joris Sprakel
- Physical Chemistry
and Soft Matter, Wageningen University &
Research, Stippeneng
4, 6708 WE Wageningen, The Netherlands
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Fejer SN. Minimalistic coarse-grained modeling of viral capsid assembly. COMPUTATIONAL APPROACHES FOR UNDERSTANDING DYNAMICAL SYSTEMS: PROTEIN FOLDING AND ASSEMBLY 2020; 170:405-434. [DOI: 10.1016/bs.pmbts.2019.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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