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Bošković F, Maffeo C, Patiño-Guillén G, Tivony R, Aksimentiev A, Keyser UF. Nanopore Translocation Reveals Electrophoretic Force on Noncanonical RNA:DNA Double Helix. ACS NANO 2024; 18:15013-15024. [PMID: 38822455 PMCID: PMC11171748 DOI: 10.1021/acsnano.4c01466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/03/2024]
Abstract
Electrophoretic transport plays a pivotal role in advancing sensing technologies. So far, systematic studies have focused on the translocation of canonical B-form or A-form nucleic acids, while direct RNA analysis is emerging as the new frontier for nanopore sensing and sequencing. Here, we compare the less-explored dynamics of noncanonical RNA:DNA hybrids in electrophoretic transport to the well-researched transport of B-form DNA. Using DNA/RNA nanotechnology and solid-state nanopores, the translocation of RNA:DNA (RD) and DNA:DNA (DD) duplexes was examined. Notably, RD duplexes were found to translocate through nanopores faster than DD duplexes, despite containing the same number of base pairs. Our experiments reveal that RD duplexes present a noncanonical helix, with distinct transport properties from B-form DD molecules. We find that RD and DD molecules, with the same contour length, move with comparable velocity through nanopores. We examined the physical characteristics of both duplex forms using atomic force microscopy, atomistic molecular dynamics simulations, agarose gel electrophoresis, and dynamic light scattering measurements. With the help of coarse-grained and molecular dynamics simulations, we find the effective force per unit length applied by the electric field to a fragment of RD or DD duplex in nanopores with various geometries or shapes to be approximately the same. Our results shed light on the significance of helical form in nucleic acid translocation, with implications for RNA sensing, sequencing, and the molecular understanding of electrophoretic transport.
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Affiliation(s)
- Filip Bošković
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Christopher Maffeo
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | | | - Ran Tivony
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Aleksei Aksimentiev
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.
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Bošković F, Maffeo C, Patiño-Guillén G, Tivony R, Aksimentiev A, Keyser UF. Nanopore translocation reveals electrophoretic force on non-canonical RNA:DNA double helix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.12.557357. [PMID: 37745457 PMCID: PMC10515835 DOI: 10.1101/2023.09.12.557357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Electrophoretic transport plays a pivotal role in advancing sensing technologies. So far, systematic studies have focused on translocation of canonical B-form or A-form nucleic acids, while direct RNA analysis is emerging as the new frontier for nanopore sensing and sequencing. Here, we compare the less-explored dynamics of non-canonical RNA:DNA hybrids in electrophoretic transport with the well-researched transport of B-form DNA. Using DNA/RNA nanotechnology and solid-state nanopores, the translocation of RNA:DNA (RD) and DNA:DNA (DD) duplexes was examined. Notably, RD duplexes were found to translocate through nanopores faster than DD duplexes, despite containing the same number of base pairs. Our experiments reveal that RD duplexes present a non-canonical helix with distinct transport properties from B-form DD molecules. We find RD and DD molecules with the same contour length move with comparable velocity through nanopores. We examined the physical characteristics of both duplex forms using atomic force microscopy, atomistic molecular dynamics simulations, agarose gel electrophoresis, and dynamic light scattering measurements. With the help of coarse-grained and molecular dynamics simulations, we find the effective force per unit length applied by the electric field to a fragment of RD or DD duplex in nanopores with various geometries or shapes to be approximately the same within experimental errors. Our results shed light on the significance of helical form in nucleic acid translocation, with implications for RNA sensing, sequencing, and molecular understanding of electrophoretic transport.
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Roldán-Piñero C, Luengo-Márquez J, Assenza S, Pérez R. Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA. J Chem Theory Comput 2024; 20:2261-2272. [PMID: 38411091 PMCID: PMC10938644 DOI: 10.1021/acs.jctc.3c01089] [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] [Received: 10/02/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
The response of double-stranded DNA to external mechanical stress plays a central role in its interactions with the protein machinery in the cell. Modern atomistic force fields have been shown to provide highly accurate predictions for the fine structural features of the duplex. In contrast, and despite their pivotal function, less attention has been devoted to the accuracy of the prediction of the elastic parameters. Several reports have addressed the flexibility of double-stranded DNA via all-atom molecular dynamics, yet the collected information is insufficient to have a clear understanding of the relative performance of the various force fields. In this work, we fill this gap by performing a systematic study in which several systems, characterized by different sequence contexts, are simulated with the most popular force fields within the AMBER family, bcs1 and OL15, as well as with CHARMM36. Analysis of our results, together with their comparison with previous work focused on bsc0, allows us to unveil the differences in the predicted rigidity between the newest force fields and suggests a roadmap to test their performance against experiments. In the case of the stretch modulus, we reconcile these differences, showing that a single mapping between sequence-dependent conformation and elasticity via the crookedness parameter captures simultaneously the results of all force fields, supporting the key role of crookedness in the mechanical response of double-stranded DNA.
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Affiliation(s)
- Carlos Roldán-Piñero
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Juan Luengo-Márquez
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Instituto
Nicolás Cabrera, Universidad Autónoma
de Madrid, E-28049 Madrid, Spain
| | - Salvatore Assenza
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Instituto
Nicolás Cabrera, Universidad Autónoma
de Madrid, E-28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
| | - Rubén Pérez
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
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Shi X, Pumm AK, Maffeo C, Kohler F, Feigl E, Zhao W, Verschueren D, Golestanian R, Aksimentiev A, Dietz H, Dekker C. A DNA turbine powered by a transmembrane potential across a nanopore. NATURE NANOTECHNOLOGY 2024; 19:338-344. [PMID: 37884658 PMCID: PMC10950783 DOI: 10.1038/s41565-023-01527-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023]
Abstract
Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines at many scales, developing functional synthetic turbines at the nanoscale has remained challenging. Here, we experimentally demonstrate rationally designed nanoscale DNA origami turbines with three chiral blades. These DNA nanoturbines are 24-27 nm in height and diameter and can utilize transmembrane electrochemical potentials across nanopores to drive DNA bundles into sustained unidirectional rotations of up to 10 revolutions s-1. The rotation direction is set by the designed chirality of the turbine. All-atom molecular dynamics simulations show how hydrodynamic flows drive this turbine. At high salt concentrations, the rotation direction of turbines with the same chirality is reversed, which is explained by a change in the anisotropy of the electrophoretic mobility. Our artificial turbines operate autonomously in physiological conditions, converting energy from naturally abundant electrochemical potentials into mechanical work. The results open new possibilities for engineering active robotics at the nanoscale.
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Affiliation(s)
- Xin Shi
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
- Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Anna-Katharina Pumm
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching, Germany
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Fabian Kohler
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Elija Feigl
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Wenxuan Zhao
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Daniel Verschueren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
- The SW7 Group, London, UK
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, UK
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Hendrik Dietz
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
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Nanoturbine driven by flow across a nanopore. NATURE NANOTECHNOLOGY 2024; 19:279-280. [PMID: 37903893 DOI: 10.1038/s41565-023-01532-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
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Duraes ADS, Gezelter JD. A theory of pitch for the hydrodynamic properties of molecules, helices, and achiral swimmers at low Reynolds number. J Chem Phys 2023; 159:134105. [PMID: 37787128 DOI: 10.1063/5.0152546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023] Open
Abstract
We present a theory for pitch, a matrix property that is linked to the coupling of rotational and translational motion of rigid bodies at low Reynolds numbers. The pitch matrix is a geometric property of objects in contact with a surrounding fluid, and it can be decomposed into three principal axes of pitch and their associated moments of pitch. The moments of pitch predict the translational motion in a direction parallel to each pitch axis when the object is rotated around that axis and can be used to explain translational drift, particularly for rotating helices. We also provide a symmetrized boundary element model for blocks of the resistance tensor, allowing calculation of the pitch matrix for arbitrary rigid bodies. We analyze a range of chiral objects, including chiral molecules and helices. Chiral objects with a Cn symmetry axis with n > 2 show additional symmetries in their pitch matrices. We also show that some achiral objects have non-vanishing pitch matrices, and we use this result to explain recent observations of achiral microswimmers. We also discuss the small but non-zero pitch of Lord Kelvin's isotropic helicoid.
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Affiliation(s)
- Anderson D S Duraes
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
| | - J Daniel Gezelter
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
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Chinappi M, Morozzo Della Rocca B. Nanopores enable electrohydrodynamical DNA motor. NATURE NANOTECHNOLOGY 2023; 18:225-226. [PMID: 36526856 DOI: 10.1038/s41565-022-01288-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Rome, Italy.
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