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Walker-Gibbons R, Zhu X, Behjatian A, Bennett TJD, Krishnan M. Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations. Sci Rep 2024; 14:20582. [PMID: 39232063 PMCID: PMC11375218 DOI: 10.1038/s41598-024-70641-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 08/20/2024] [Indexed: 09/06/2024] Open
Abstract
Inferring the 3D structure and conformation of disordered biomolecules, e.g., single stranded nucleic acids (ssNAs), remains challenging due to their conformational heterogeneity in solution. Here, we use escape-time electrometry (ETe) to measure with sub elementary-charge precision the effective electrical charge in solution of short to medium chain length ssNAs in the range of 5-60 bases. We compare measurements of molecular effective charge with theoretically calculated values for simulated molecular conformations obtained from Molecular Dynamics simulations using a variety of forcefield descriptions. We demonstrate that the measured effective charge captures subtle differences in molecular structure in various nucleic acid homopolymers of identical length, and also that the experimental measurements can find agreement with computed values derived from coarse-grained molecular structure descriptions such as oxDNA, as well next generation ssNA force fields. We further show that comparing the measured effective charge with calculations for a rigid, charged rod-the simplest model of a nucleic acid-yields estimates of molecular structural dimensions such as linear charge spacings that capture molecular structural trends observed using high resolution structural analysis methods such as X-ray scattering. By sensitively probing the effective charge of a molecule, electrometry provides a powerful dimension supporting inferences of molecular structural and conformational properties, as well as the validation of biomolecular structural models. The overall approach holds promise for a high throughput, microscopy-based biomolecular analytical approach offering rapid screening and inference of molecular 3D conformation, and operating at the single molecule level in solution.
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Affiliation(s)
- Rowan Walker-Gibbons
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Xin Zhu
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Ali Behjatian
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Timothy J D Bennett
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Madhavi Krishnan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
- The Kavli Institute for Nanoscience Discovery, Sherrington Road, Oxford, OX1 3QU, UK.
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2
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Mathur N, Singh A, Singh N. Force-induced unzipping of DNA in the presence of solvent molecules. Biophys Chem 2024; 307:107175. [PMID: 38244296 DOI: 10.1016/j.bpc.2024.107175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024]
Abstract
The melting of double-stranded DNA (dsDNA) in the presence of solvent molecules is a fundamental process with significant implications for understanding the thermal and mechanical behavior of DNA and its interactions with the surrounding environment. The solvents play an essential role in the structural transformation of DNA subjected to a pulling force. In this study, we simulate the thermal and force induced denaturation of dsDNA and elucidate the solvent dependent melting behavior, identifying key factors that influence the stability of DNA melting in presence of solvent molecules. Using a statistical model, we first find the melting profile of short heterogeneous DNA molecules in the presence of solvent molecules in Force ensemble. We also investigate the effect of solvent's strengths on the melting profile of DNA. In the force ensemble, we consider two homogeneous DNA chains and apply the force on different locations along the chain in the presence of solvent molecules. Different pathways manifest the melting of the molecule in both ensembles, and we found several interesting features of melting DNA in a constant force ensemble, such as lower critical force when the chain is pulled from the base pair close to a solvent molecule. The results provide new insights into the force-induced unzipping of DNA and could be used to develop new methods for controlling the unzipping process. By providing a better understanding of melting and unzipping of dsDNA in the presence of solvent molecules, this study provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA nanostructures.
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Affiliation(s)
- Neha Mathur
- Birla Institute of Technology & Science, Pilani 333031, India
| | - Amar Singh
- Birla Institute of Technology & Science, Pilani 333031, India.
| | - Navin Singh
- Birla Institute of Technology & Science, Pilani 333031, India
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Mahanta S, Vallejo-Ramirez P, Karedla N, Puczkarski P, Krishnan M. Wide-field optical imaging of electrical charge and chemical reactions at the solid-liquid interface. Proc Natl Acad Sci U S A 2022; 119:e2209955119. [PMID: 36459653 PMCID: PMC9894211 DOI: 10.1073/pnas.2209955119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/26/2022] [Indexed: 12/04/2022] Open
Abstract
From molecules and particles to macroscopic surfaces immersed in fluids, chemical reactions often endow interfaces with electrical charge which in turn governs surface interactions and interfacial phenomena. The ability to measure the electrical properties of a material immersed in any solvent, as well as to monitor the spatial heterogeneity and temporal variation thereof, has been a long-standing challenge. Here, we describe an optical microscopy-based approach to probe the surface charge distribution of a range of materials, including inorganic oxide, polymer, and polyelectrolyte films, in contact with a fluid. The method relies on optical visualization of the electrical repulsion between diffusing charged probe molecules and the unknown surface to be characterized. Rapid image-based measurements enable us to further determine isoelectric points of the material as well as properties of its ionizable chemical groups. We further demonstrate the ability to optically monitor chemically triggered surface charge changes with millisecond time resolution. Finally, we present a scanning-surface probe technique capable of diffraction-limited imaging of spatial heterogeneities in chemical composition and charge over large areas. This technique will enable facile characterization of the solid-liquid interface with wide-ranging relevance across application areas from biology to engineering.
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Affiliation(s)
- Sushanta Mahanta
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OxfordOX1 3QZ, United Kingdom
| | - Pedro Vallejo-Ramirez
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OxfordOX1 3QZ, United Kingdom
| | - Narain Karedla
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OxfordOX1 3QZ, United Kingdom
| | - Paweł Puczkarski
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OxfordOX1 3QZ, United Kingdom
| | - Madhavi Krishnan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OxfordOX1 3QZ, United Kingdom
- The Kavli Institute for Nanoscience Discovery, OxfordOX1 3QU, United Kingdom
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4
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Bespalova M, Öz R, Westerlund F, Krishnan M. Single-Molecule Trapping and Measurement in a Nanostructured Lipid Bilayer System. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13923-13934. [PMID: 36326814 PMCID: PMC9671048 DOI: 10.1021/acs.langmuir.2c02203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/15/2022] [Indexed: 06/16/2023]
Abstract
The repulsive electrostatic force between a biomolecule and a like-charged surface can be geometrically tailored to create spatial traps for charged molecules in solution. Using a parallel-plate system composed of silicon dioxide surfaces, we recently demonstrated single-molecule trapping and high precision molecular charge measurements in a nanostructured free energy landscape. Here we show that surfaces coated with charged lipid bilayers provide a system with tunable surface properties for molecular electrometry experiments. Working with molecular species whose effective charge and geometry are well-defined, we demonstrate the ability to quantitatively probe the electrical charge density of a supported lipid bilayer. Our findings indicate that the fraction of charged lipids in nanoslit lipid bilayers can be significantly different from that in the precursor lipid mixtures used to generate them. We also explore the temporal stability of bilayer properties in nanofluidic systems. Beyond their relevance in molecular measurement, such experimental systems offer the opportunity to examine lipid bilayer formation and wetting dynamics on nanostructured surfaces.
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Affiliation(s)
- Maria Bespalova
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OxfordOX1 3QZ, United Kingdom
| | - Robin Öz
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96Gothenburg, Sweden
| | - Fredrik Westerlund
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96Gothenburg, Sweden
| | - Madhavi Krishnan
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OxfordOX1 3QZ, United Kingdom
- The
Kavli Institute for Nanoscience Discovery, Sherrington Road, OxfordOX1 3QU, United Kingdom
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5
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Kloes G, Bennett TJD, Chapet-Batlle A, Behjatian A, Turberfield AJ, Krishnan M. Far-Field Electrostatic Signatures of Macromolecular 3D Conformation. NANO LETTERS 2022; 22:7834-7840. [PMID: 36125326 PMCID: PMC9562458 DOI: 10.1021/acs.nanolett.2c02485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In solution as in vacuum, the electrostatic field distribution in the vicinity of a charged object carries information on its three-dimensional geometry. We report on an experimental study exploring the effect of molecular shape on long-range electrostatic interactions in solution. Working with DNA nanostructures carrying approximately equal amounts of total charge but each in a different three-dimensional conformation, we demonstrate that the geometry of the distribution of charge in a molecule has substantial impact on its electrical interactions. For instance, a tetrahedral structure, which is the most compact distribution of charge we tested, can create a far-field effect that is effectively identical to that of a rod-shaped molecule carrying half the amount of total structural charge. Our experiments demonstrate that escape-time electrometry (ETe) furnishes a rapid and facile method to screen and identify 3D conformations of charged biomolecules or molecular complexes in solution.
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Affiliation(s)
- Gunnar Kloes
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Timothy J. D. Bennett
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Alma Chapet-Batlle
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Ali Behjatian
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Andrew J. Turberfield
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
- The Kavli
Institute for Nanoscience Discovery, Sherrington Road, Oxford OX1 3QU, United Kingdom
| | - Madhavi Krishnan
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
- The Kavli
Institute for Nanoscience Discovery, Sherrington Road, Oxford OX1 3QU, United Kingdom
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