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Longatte G, Lisi F, Bakthavathsalam P, Böcking T, Gaus K, Tilley RD, Gooding JJ. Biomolecular Binding under Confinement: Statistical Predictions of Steric Influence in Absence of Long-Distance Interactions. Chemphyschem 2021; 23:e202100765. [PMID: 34856050 DOI: 10.1002/cphc.202100765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/24/2021] [Indexed: 11/08/2022]
Abstract
We propose a theoretical model for the influence of confinement on biomolecular binding at the single-molecule scale at equilibrium, based on the change of the number of microstates (localization and orientation) upon reaction. Three cases are discussed: DNA sequences shorter and longer than the single strain DNA Kuhn length and spherical proteins, confined into a spherical container (liposome, droplet, etc.). The influence of confinement is found to be highly dependent on the molecular structure and significant for large molecules (relative to container size).
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Affiliation(s)
- Guillaume Longatte
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Fabio Lisi
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Padmavathy Bakthavathsalam
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, ARC Centre of Excellence in Advanced Molecular Imaging, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, ARC Centre of Excellence in Advanced Molecular Imaging, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Richard D Tilley
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, NSW 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, NSW 2052, Australia
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