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Haimov E, Hedley JG, Kornyshev AA. Nonlocal structural effects of water on DNA homology recognition. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:40LT01. [PMID: 38936395 DOI: 10.1088/1361-648x/ad5cb7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/27/2024] [Indexed: 06/29/2024]
Abstract
The mechanism behind mutual recognition of homologous DNA sequences prior to genetic recombination is one of the remaining puzzles in molecular biology. Leading models of homology recognition, based on classical electrostatics, neglect the short-range nonlocal screening effects arising from structured water around DNA, and hence may only provide insight for relatively large separations between interacting DNAs. We elucidate the role of the effects of the nonlocal dielectric response of water on DNA-DNA interaction and show that these can dramatically enhance the driving force for recognition.
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Affiliation(s)
- Ehud Haimov
- Department of Chemistry, Faculty of Natural Sciences, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane W12 0BZ, United Kingdom
| | - Jonathan G Hedley
- Department of Chemistry, Faculty of Natural Sciences, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane W12 0BZ, United Kingdom
| | - Alexei A Kornyshev
- Department of Chemistry, Faculty of Natural Sciences, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane W12 0BZ, United Kingdom
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Templeton C, Hamilton I, Russell R, Elber R. Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations. J Phys Chem B 2023; 127:8796-8808. [PMID: 37815452 DOI: 10.1021/acs.jpcb.3c04354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Biological processes require DNA and RNA helices to pack together in specific interhelical orientations. While electrostatic repulsion between backbone charges is expected to be maximized when helices are in parallel alignment, such orientations are commonplace in nature. To better understand how the repulsion is overcome, we used experimental and computational approaches to investigate how the orientational preferences of DNA helices depend on the concentration and valence of mobile cations. We used Förster resonance energy transfer (FRET) to probe the relative orientations of two 24-bp helices held together via a freely rotating PEG linker. At low cation concentrations, the helices preferred more "cross"-like orientations over those closer to parallel, and this preference was reduced with increasing salt concentrations. The results were in good quantitative agreement with Poisson-Boltzmann (PB) calculations for monovalent salt (Na+). However, PB underestimated the ability of mixtures of monovalent and divalent ions (Mg2+) to reduce the conformational preference. As a complementary approach, we performed all-atom molecular dynamics (MD) simulations and found better agreement with the experimental results. While MD and PB predict similar electrostatic forces, MD predicts a greater accumulation of Mg2+ in the ion atmosphere surrounding the DNA. Mg2+ occupancy is predicted to be greater in conformations close to the parallel orientation than in conformations close to the crossed orientation, enabling a greater release of Na+ ions and providing an entropic gain (one bound ion for two released). MD predicts an entropy gain larger than that of PB because of the increased Mg2+ occupancy. The entropy changes have a negligible effect at low Mg2+ concentrations because the free energies are dominated by electrostatic repulsion. However, as the Mg2+ concentration increases, charge screening is more effective and the mixing entropy produces readily detectable changes in packing preferences. Our results underline the importance of mixing entropy of counterions in nucleic acid interactions and provide a new understanding on the impact of a mixed ion atmosphere on the packing of DNA helices.
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Affiliation(s)
- Clark Templeton
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
- Department of Physics, FU Berlin, 14195 Berlin, Germany
| | - Ian Hamilton
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ron Elber
- Institute for Computational Engineering and Science, Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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Alexiou TS, Likos CN. Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency. J Phys Chem B 2023; 127:6969-6981. [PMID: 37493448 PMCID: PMC10424236 DOI: 10.1021/acs.jpcb.3c02216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/12/2023] [Indexed: 07/27/2023]
Abstract
A computational investigation of the effects of molecular topology, namely, linear and circular, as well as counterion valency, on the ensuing pairwise effective interactions between DNA molecules in an unlinked state is presented. Umbrella sampling simulations have been performed through the introduction of bias potential along a reaction coordinate defined as the distance between the centers-of-mass of pairs of DNA molecules, and effective pair interaction potentials have been computed by employing the weighted histogram analysis method. An interesting comparison can be drawn between the different DNA topologies studied here, especially with regard to the contrasting effects of divalent counterions on the effective pair potentials: while DNA-DNA repulsion in short center-of-mass distances decreases significantly in the presence of divalent counterion-ions (as compared to monovalent ions) for linear DNA, the opposite effect occurs for the DNA minicircles. This can be attributed to the fact that linear DNA fragments can easily adopt relative orientations that minimize electrostatic and steric repulsions by rotating relative to one another and by exhibiting more pronounced bending due to the presence of free ends.
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Affiliation(s)
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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Winogradoff D, Li P, Joshi H, Quednau L, Maffeo C, Aksimentiev A. Chiral Systems Made from DNA. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003113. [PMID: 33717850 PMCID: PMC7927625 DOI: 10.1002/advs.202003113] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/13/2020] [Indexed: 05/05/2023]
Abstract
The very chemical structure of DNA that enables biological heredity and evolution has non-trivial implications for the self-organization of DNA molecules into larger assemblies and provides limitless opportunities for building functional nanostructures. This progress report discusses the natural organization of DNA into chiral structures and recent advances in creating synthetic chiral systems using DNA as a building material. How nucleic acid chirality naturally comes into play in a diverse array of situations is considered first, at length scales ranging from an individual nucleotide to entire chromosomes. Thereafter, chiral liquid crystal phases formed by dense DNA mixtures are discussed, including the ongoing efforts to understand their origins. The report then summarizes recent efforts directed toward building chiral structures, and other structures of complex topology, using the principle of DNA self-assembly. Discussed last are existing and proposed functional man-made nanostructures designed to either probe or harness DNA's chirality, from plasmonics and spintronics to biosensing.
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Affiliation(s)
- David Winogradoff
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Pin‐Yi Li
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Himanshu Joshi
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Lauren Quednau
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Christopher Maffeo
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Aleksei Aksimentiev
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
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Tortora MMC, Mishra G, Prešern D, Doye JPK. Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis. SCIENCE ADVANCES 2020; 6:eaaw8331. [PMID: 32789165 PMCID: PMC7399560 DOI: 10.1126/sciadv.aaw8331] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/16/2020] [Indexed: 05/20/2023]
Abstract
Lyotropic cholesteric liquid crystal phases are ubiquitously observed in biological and synthetic polymer solutions, characterized by a complex interplay between thermal fluctuations and entropic and enthalpic forces. The elucidation of the link between microscopic features and macroscopic chiral structure, and of the relative roles of these competing contributions on phase organization, remains a topical issue. Here, we provide theoretical evidence of a previously unidentified mechanism of chirality amplification in lyotropic liquid crystals, whereby phase chirality is governed by fluctuation-stabilized helical deformations in the conformations of their constituent molecules. Our results compare favorably to recent experimental studies of DNA origami assemblies and demonstrate the influence of intramolecular mechanics on chiral supramolecular order, with potential implications for a broad class of experimentally relevant colloidal systems.
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Affiliation(s)
- Maxime M. C. Tortora
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Garima Mishra
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Domen Prešern
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Jonathan P. K. Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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Wu L, Sun H. Manipulation of cholesteric liquid crystal phase behavior and molecular assembly by molecular chirality. Phys Rev E 2019; 100:022703. [PMID: 31574769 DOI: 10.1103/physreve.100.022703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 06/10/2023]
Abstract
Molecular simulation is used to study the effect of molecular chirality on liquid crystalline phase transition and molecular assembly behavior. Based on a flexible chain (FCh) model with helical arrangement of side beads, the phase behavior of FCh models with various molecular chiralities are studied as functions of pressure (or density). By modifying the molecular chirality of FCh, we can manipulate the relative stability of the nematic and cholesteric phases continuously; and we found that increasing molecular chirality may destabilize cholesteric order due to the effective reduction of chiral interactions. A semismectic phase is identified in the high-density region, in which the two-dimensional fluid layers overlap due to shift alignment formed by FCh particles. The global phase diagram of the FCh model is constructed and the potential energy surface is calculated to elucidate the formation of cholesteric phase in terms of two-body interactions.
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Affiliation(s)
- Liang Wu
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huai Sun
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China
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Tortora MMC, Doye JPK. Incorporating particle flexibility in a density functional description of nematics and cholesterics. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1464226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Maxime M. C. Tortora
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, United Kingdom
| | - Jonathan P. K. Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, United Kingdom
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