1
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Todisco M, Radakovic A, Szostak JW. RNA Complexes with Nicks and Gaps: Thermodynamic and Kinetic Effects of Coaxial Stacking and Dangling Ends. J Am Chem Soc 2024; 146:18083-18094. [PMID: 38904115 PMCID: PMC11229006 DOI: 10.1021/jacs.4c05115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024]
Abstract
Multiple RNA strands can interact in solution and assume a large variety of configurations dictated by their potential for base pairing. Although duplex formation from two complementary oligonucleotides has been studied in detail, we still lack a systematic characterization of the behavior of higher order complexes. Here, we focus on the thermodynamic and kinetic effects of an upstream oligonucleotide on the binding of a downstream oligonucleotide to a common template, as we vary the sequence and structure of the contact interface. We show that coaxial stacking in RNA is well correlated with but much more stabilizing than helix propagation over an analogous intact double helix step (median ΔΔG°37 °C ≈ 1.7 kcal/mol). Consequently, approximating coaxial stacking in RNA with the helix propagation term leads to large discrepancies between predictions and our experimentally determined melting temperatures, with an offset of ≈10 °C. Our kinetic study reveals that the hybridization of the downstream probe oligonucleotide is impaired (lower kon) by the presence of the upstream oligonucleotide, with the thermodynamic stabilization coming entirely from an extended lifetime (lower koff) of the bound downstream oligonucleotide, which can increase from seconds to months. Surprisingly, we show that the effect of nicks is dependent on the length of the stacking oligonucleotides, and we discuss the binding of ultrashort (1-4 nt) oligonucleotides that are relevant in the context of the origin of life. The thermodynamic and kinetic data obtained in this work allow for the prediction of the formation and stability of higher-order multistranded complexes.
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Affiliation(s)
- Marco Todisco
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Aleksandar Radakovic
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Harvard Medical School,Department of Genetics, Boston, Massachusetts 02115, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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2
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van Galen M, Bok A, Peshkovsky T, van der Gucht J, Albada B, Sprakel J. De novo DNA-based catch bonds. Nat Chem 2024:10.1038/s41557-024-01571-4. [PMID: 38914727 DOI: 10.1038/s41557-024-01571-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 06/06/2024] [Indexed: 06/26/2024]
Abstract
All primary chemical interactions weaken under mechanical stress, which imposes fundamental mechanical limits on the materials constructed from them. Biological materials combine plasticity with strength, for which nature has evolved a unique solution-catch bonds, supramolecular interactions that strengthen under tension. Biological catch bonds use force-gated conformational switches to convert weak bonds into strong ones. So far, catch bonds remain exclusive to nature, leaving their potential as mechanoadaptive elements in synthetic systems untapped. Here we report the design and realization of artificial catch bonds. Starting from a minimal set of thermodynamic design requirements, we created a molecular motif capable of catch bonding. It consists of a DNA duplex featuring a cryptic domain that unfolds under tension to strengthen the interaction. We show that these catch bonds recreate force-enhanced rolling adhesion, a hallmark feature of biological catch bonds in bacteria and leukocytes. This Article introduces catch bonds into the synthetic domain, and could lead to the creation of artificial catch-bonded materials.
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Affiliation(s)
- Martijn van Galen
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen, Netherlands
| | - Annemarie Bok
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
| | - Taieesa Peshkovsky
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen, Netherlands
| | - Jasper van der Gucht
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen, Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, Netherlands.
| | - Joris Sprakel
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands.
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3
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Bauer MS, Gruber S, Hausch A, Melo MCR, Gomes PSFC, Nicolaus T, Milles LF, Gaub HE, Bernardi RC, Lipfert J. Single-molecule force stability of the SARS-CoV-2-ACE2 interface in variants-of-concern. NATURE NANOTECHNOLOGY 2024; 19:399-405. [PMID: 38012274 DOI: 10.1038/s41565-023-01536-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 09/26/2023] [Indexed: 11/29/2023]
Abstract
Mutations in SARS-CoV-2 have shown effective evasion of population immunity and increased affinity to the cellular receptor angiotensin-converting enzyme 2 (ACE2). However, in the dynamic environment of the respiratory tract, forces act on the binding partners, which raises the question of whether not only affinity but also force stability of the SARS-CoV-2-ACE2 interaction might be a selection factor for mutations. Using magnetic tweezers, we investigate the impact of amino acid substitutions in variants of concern (Alpha, Beta, Gamma and Delta) and on force-stability and bond kinetic of the receptor-binding domain-ACE2 interface at a single-molecule resolution. We find a higher affinity for all of the variants of concern (>fivefold) compared with the wild type. In contrast, Alpha is the only variant of concern that shows higher force stability (by 17%) compared with the wild type. Using molecular dynamics simulations, we rationalize the mechanistic molecular origins of this increase in force stability. Our study emphasizes the diversity of contributions to the transmissibility of variants and establishes force stability as one of the several factors for fitness. Understanding fitness advantages opens the possibility for the prediction of probable mutations, allowing a rapid adjustment of therapeutics, vaccines and intervention measures.
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Affiliation(s)
- Magnus S Bauer
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sophia Gruber
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | - Adina Hausch
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
- Center for Protein Assemblies, TUM School of Natural Sciences, Technical University of Munich, Munich, Germany
| | | | | | - Thomas Nicolaus
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | - Lukas F Milles
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hermann E Gaub
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | | | - Jan Lipfert
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany.
- Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
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4
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Stransky F, Kostrz D, Follenfant M, Pomplun S, Meyners C, Strick T, Hausch F, Gosse C. Use of DNA forceps to measure receptor-ligand dissociation equilibrium constants in a single-molecule competition assay. Methods Enzymol 2024; 694:51-82. [PMID: 38492958 DOI: 10.1016/bs.mie.2024.01.010] [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] [Indexed: 03/18/2024]
Abstract
The ability of biophysicists to decipher the behavior of individual biomolecules has steadily improved over the past thirty years. However, it still remains unclear how an ensemble of data acquired at the single-molecule level compares with the data acquired on an ensemble of the same molecules. We here propose an assay to tackle this question in the context of dissociation equilibrium constant measurements. A sensor is built by engrafting a receptor and a ligand onto a flexible dsDNA scaffold and mounting this assembly on magnetic tweezers. This way, looking at the position of the magnetic bead enables one to determine in real-time if the two molecular partners are associated or not. Next, to quantify the affinity of the scrutinized single-receptor for a given competitor, various amounts of the latter molecule are introduced in solution and the equilibrium response of the sensor is monitored throughout the titration protocol. Proofs of concept are established for the binding of three rapamycin analogs to the FKBP12 cis-trans prolyl isomerase. For each of these drugs the mean affinity constant obtained on a ten of individual receptors agrees with the one previously determined in a bulk assay. Furthermore, experimental contingencies are sufficient to explain the dispersion observed over the single-molecule values.
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Affiliation(s)
- François Stransky
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Dorota Kostrz
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Maryne Follenfant
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Sebastian Pomplun
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Christian Meyners
- Department of Chemistry and Biochemistry, Technical University Darmstadt, Darmstadt, Germany
| | - Terence Strick
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Felix Hausch
- Department of Chemistry and Biochemistry, Technical University Darmstadt, Darmstadt, Germany; Centre for Synthetic Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Charlie Gosse
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France.
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5
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Robbins A, Hildebolt H, Neuhoff M, Beshay P, Winter JO, Castro CE, Bundschuh R, Poirier MG. Cooperative control of a DNA origami force sensor. Sci Rep 2024; 14:4132. [PMID: 38374280 PMCID: PMC10876929 DOI: 10.1038/s41598-024-53841-3] [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: 06/26/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Biomolecular systems are dependent on a complex interplay of forces. Modern force spectroscopy techniques provide means of interrogating these forces, but they are not optimized for studies in constrained environments as they require attachment to micron-scale probes such as beads or cantilevers. Nanomechanical devices are a promising alternative, but this requires versatile designs that can be tuned to respond to a wide range of forces. We investigate the properties of a nanoscale force sensitive DNA origami device which is highly customizable in geometry, functionalization, and mechanical properties. The device, referred to as the NanoDyn, has a binary (open or closed) response to an applied force by undergoing a reversible structural transition. The transition force is tuned with minor alterations of 1 to 3 DNA oligonucleotides and spans tens of picoNewtons (pN). The DNA oligonucleotide design parameters also strongly influence the efficiency of resetting the initial state, with higher stability devices (≳10 pN) resetting more reliably during repeated force-loading cycles. Finally, we show the opening force is tunable in real time by adding a single DNA oligonucleotide. These results establish the potential of the NanoDyn as a versatile force sensor and provide fundamental insights into how design parameters modulate mechanical and dynamic properties.
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Affiliation(s)
- Ariel Robbins
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Hazen Hildebolt
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael Neuhoff
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Peter Beshay
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Jessica O Winter
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos E Castro
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Ralf Bundschuh
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.
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6
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Wei WS, Trubiano A, Sigl C, Paquay S, Dietz H, Hagan MF, Fraden S. Hierarchical assembly is more robust than egalitarian assembly in synthetic capsids. Proc Natl Acad Sci U S A 2024; 121:e2312775121. [PMID: 38324570 PMCID: PMC10873614 DOI: 10.1073/pnas.2312775121] [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: 07/25/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024] Open
Abstract
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and concentrations of subunits. By contrast, we introduce an assembly paradigm that allows large error-tolerance in the subunit affinity and helps avoid kinetic traps. Our combined experimental and computational approach uses a model system of triangular subunits programmed to assemble into T = 3 icosahedral capsids comprising 60 units. The experimental platform uses DNA origami to create monodisperse colloids whose three-dimensional geometry is controlled to nanometer precision, with two distinct bonds whose affinities are controlled to kBT precision, quantified in situ by static light scattering. The computational model uses a coarse-grained representation of subunits, short-ranged potentials, and Langevin dynamics. Experimental observations and modeling reveal that when the bond affinities are unequal, two distinct hierarchical assembly pathways occur, in which the subunits first form dimers in one case and pentamers in another. These hierarchical pathways produce complete capsids faster and are more robust against affinity variation than egalitarian pathways, in which all binding sites have equal strengths. This finding suggests that hierarchical assembly may be a general engineering principle for optimizing self-assembly of complex target structures.
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Affiliation(s)
- Wei-Shao Wei
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Anthony Trubiano
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Christian Sigl
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Stefan Paquay
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Hendrik Dietz
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Seth Fraden
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
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7
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Kodikara S, Gyawali P, Gleeson JT, Jákli A, Sprunt S, Balci H. Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation. Biomacromolecules 2024; 25:1009-1017. [PMID: 38166360 PMCID: PMC10866144 DOI: 10.1021/acs.biomac.3c01086] [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: 10/10/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/04/2024]
Abstract
The layered liquid crystalline phases formed by DNA molecules, which include rigid and flexible segments ("gapped DNA"), enable the study of both end-to-end stacking and side-to-side (helix-to-helix) lateral interactions, forming a model system to study such interactions at physiologically relevant DNA and ion concentrations. The observed layer structure exhibits long-range interlayer and in-layer positional correlations. In particular, the in-layer order has implications for DNA condensation, as it reflects whether these normally repulsive interactions become attractive under certain ionic conditions. Using synchrotron small-angle X-ray scattering measurements, we investigate the impact of divalent Mg2+ cations (in addition to a constant 150 mM Na+) on the stability of the inter- and in-layer DNA ordering as a function of temperature between 5 and 65 °C. DNA constructs with different terminal base pairings were created to mediate the strength of the attractive end-to-end stacking interactions between the blunt ends of the gapped DNA constructs. We demonstrate that the stabilities at a fixed DNA concentration of both interlayer and in-layer order are significantly enhanced even at a few mM Mg2+ concentration. The stabilities are even higher at 30 mM Mg2+; however, a marked decrease is observed at 100 mM Mg2+, suggesting a change in the nature of side-by-side interactions within this Mg2+ concentration range. We discuss the implications of these results in terms of counterion-mediated DNA-DNA attraction and DNA condensation.
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Affiliation(s)
- Sineth
G. Kodikara
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Prabesh Gyawali
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - James T. Gleeson
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Antal Jákli
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
- Advanced
Materials and Liquid Crystal Institute, Kent State University, Kent, Ohio 44242, United States
| | - Samuel Sprunt
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
- Advanced
Materials and Liquid Crystal Institute, Kent State University, Kent, Ohio 44242, United States
| | - Hamza Balci
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
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8
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Vogt M, List J, Langecker M, Santiago I, Simmel FC, Kopperger E. Electrokinetic Torque Generation by DNA Nanorobotic Arms Studied via Single-Molecule Fluctuation Analysis. J Phys Chem B 2023; 127:10710-10722. [PMID: 38060372 DOI: 10.1021/acs.jpcb.3c05959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
DNA nanotechnology has enabled the creation of supramolecular machines, whose shape and function are inspired from traditional mechanical engineering as well as from biological examples. As DNA inherently is a highly charged biopolymer, the external application of electric fields provides a versatile, computer-programmable way to control the movement of DNA-based machines. However, the details of the electrohydrodynamic interactions underlying the electrical manipulation of these machines are complex, as the influence of their intrinsic charge, the surrounding cloud of counterions, and the effect of electrokinetic fluid flow have to be taken into account. In this work, we identify the relevant effects involved in this actuation mechanism by determining the electric response of an established DNA-based nanorobotic arm to varying design and operation parameters. Borrowing an approach from single-molecule biophysics, we determined the electrical torque exerted on the nanorobotic arms by analyzing their thermal fluctuations when oriented in an electric field. We analyze the influence of various experimental and design parameters on the "actuatability" of the nanostructures and optimize the generated torque according to these parameters. Our findings give insight into the physical processes involved in the actuation mechanism and provide general guidelines that aid in designing and efficiently operating electrically driven nanorobotic devices made from DNA.
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Affiliation(s)
- Matthias Vogt
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Jonathan List
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Martin Langecker
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Ibon Santiago
- CIC nanoGUNE BRTA, Donostia-San Sebastián 20018, Spain
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Enzo Kopperger
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
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9
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Banerjee A, Anand M, Kalita S, Ganji M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. NATURE NANOTECHNOLOGY 2023; 18:1474-1482. [PMID: 37591937 PMCID: PMC10716042 DOI: 10.1038/s41565-023-01485-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
Abstract
The DNA double helix structure is stabilized by base-pairing and base-stacking interactions. However, a comprehensive understanding of dinucleotide base-stacking energetics is lacking. Here we combined multiplexed DNA-based point accumulation in nanoscale topography (DNA-PAINT) imaging with designer DNA nanostructures and measured the free energy of dinucleotide base stacking at the single-molecule level. Multiplexed imaging enabled us to extract the binding kinetics of an imager strand with and without additional dinucleotide stacking interactions. The DNA-PAINT data showed that a single additional dinucleotide base stacking results in up to 250-fold stabilization for the DNA duplex nanostructure. We found that the dinucleotide base-stacking energies vary from -0.95 ± 0.12 kcal mol-1 to -3.22 ± 0.04 kcal mol-1 for C|T and A|C base-stackings, respectively. We demonstrate the application of base-stacking energetics in designing DNA-PAINT probes for multiplexed super-resolution imaging, and efficient assembly of higher-order DNA nanostructures. Our results will aid in designing functional DNA nanostructures, and DNA and RNA aptamers, and facilitate better predictions of the local DNA structure.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Simanta Kalita
- New Chemistry Unit and Chemistry and Physics of Materials Unit, The Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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10
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Lee JY, Koh H, Kim DN. A computational model for structural dynamics and reconfiguration of DNA assemblies. Nat Commun 2023; 14:7079. [PMID: 37925463 PMCID: PMC10625641 DOI: 10.1038/s41467-023-42873-4] [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: 06/18/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023] Open
Abstract
Recent advances in constructing a structured DNA assembly whose configuration can be dynamically changed in response to external stimuli have demanded the development of an efficient computational modeling approach to expedite its design process. Here, we present a computational framework capable of analyzing both equilibrium and non-equilibrium dynamics of structured DNA assemblies at the molecular level. The framework employs Langevin dynamics with structural and hydrodynamic finite element models that describe mechanical, electrostatic, base stacking, and hydrodynamic interactions. Equilibrium dynamic analysis for various problems confirms the solution accuracy at a near-atomic resolution, comparable to molecular dynamics simulations and experimental measurements. Furthermore, our model successfully simulates a long-time-scale close-to-open-to-close dynamic reconfiguration of the switch structure in response to changes in ion concentration. We expect that the proposed model will offer a versatile way of designing responsive and reconfigurable DNA machines.
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Affiliation(s)
- Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Heeyuen Koh
- Soft Foundry Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Soft Foundry Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
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11
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Hao H, Cai H, Yang B, Lou S, Guo Z, Lu W, Tian Z. Versatile DNA Balances via Adjacent Base Stacking for Homogeneous Assay of Energy Parameters, Small Molecules, And Ribonuclease. Anal Chem 2023; 95:14643-14650. [PMID: 37733486 DOI: 10.1021/acs.analchem.3c02431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Homogeneous assays often obviate any separation and washing steps, thus minimizing the risks of contamination and false positive. DNA toehold exchange is a homogeneous, reversible process whose thermodynamic properties can be finely tuned for various assay applications. However, the developed probes often rely on direct interactions of analytes with DNA strands involved in toehold exchange, limiting the versatility of probe design. Here, the coaxial adjacent stacking between one auxiliary strand and another invading strand offers a favorable ΔG to shift one DNA balance, while the auxiliary strand is independent of the DNA balance itself. Therefore, such a DNA balance allowed fine tuning of the equilibrium via adjustment of the auxiliary strand alone. The energy contribution of base stacking can be quantified in a homogeneous solution based on the difference in the equilibrium constant. Besides, the proof of concept for DNA balance allows effective assay of a small molecule or ribonuclease in a homogeneous solution. This novel DNA balance via adjacent base stacking provides an interesting alternative to homogeneously assay various analytes.
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Affiliation(s)
- Huimin Hao
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Hanfen Cai
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Bin Yang
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Shuyan Lou
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Zihua Guo
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Weiyi Lu
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Zhen Tian
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
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12
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Fedorova L, Crossley ER, Mulyar OA, Qiu S, Freeman R, Fedorov A. Profound Non-Randomness in Dinucleotide Arrangements within Ultra-Conserved Non-Coding Elements and the Human Genome. BIOLOGY 2023; 12:1125. [PMID: 37627009 PMCID: PMC10452674 DOI: 10.3390/biology12081125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
Long human ultra-conserved non-coding elements (UCNEs) do not have any sequence similarity to each other or other characteristics that make them unalterable during vertebrate evolution. We hypothesized that UCNEs have unique dinucleotide (DN) composition and arrangements compared to the rest of the genome. A total of 4272 human UCNE sequences were analyzed computationally and compared with the whole genomes of human, chicken, zebrafish, and fly. Statistical analysis was performed to assess the non-randomness in DN spacing arrangements within the entire human genome and within UCNEs. Significant non-randomness in DN spacing arrangements was observed in the entire human genome. Additionally, UCNEs exhibited distinct patterns in DN arrangements compared to the rest of the genome. Approximately 83% of all DN pairs within UCNEs showed significant (>10%) non-random genomic arrangements at short distances (2-6 nucleotides) relative to each other. At the extremes, non-randomness in DN spacing distances deviated up to 40% from expected values and were frequently associated with GpC, CpG, ApT, and GpG/CpC dinucleotides. The described peculiarities in DN arrangements have persisted for hundreds of millions of years in vertebrates. These distinctive patterns may suggest that UCNEs have specific DNA conformations.
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Affiliation(s)
- Larisa Fedorova
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Emily R. Crossley
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA;
| | - Oleh A. Mulyar
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Shuhao Qiu
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA;
| | - Ryan Freeman
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Alexei Fedorov
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA;
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA;
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13
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Robbins A, Hildebolt H, Neuhoff M, Beshay P, Winter JO, Castro CE, Bundschuh R, Poirier MG. Cooperative control of a DNA origami force sensor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546608. [PMID: 37425797 PMCID: PMC10327127 DOI: 10.1101/2023.06.26.546608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Most biomolecular systems are dependent on a complex interplay of forces. Modern force spectroscopy techniques provide means of interrogating these forces. These techniques, however, are not optimized for studies in constrained or crowded environments as they typically require micron-scale beads in the case of magnetic or optical tweezers, or direct attachment to a cantilever in the case of atomic force microscopy. We implement a nanoscale force-sensing device using a DNA origami which is highly customizable in geometry, functionalization, and mechanical properties. The device, referred to as the NanoDyn, functions as a binary (open or closed) force sensor that undergoes a structural transition under an external force. The transition force is tuned with minor alterations of 1 to 3 DNA oligonucleotides and spans tens of picoNewtons (pN). This actuation of the NanoDyn is reversible and the design parameters strongly influence the efficiency of resetting the initial state, with higher stability devices (≳10 pN) resetting more reliably during repeated force-loading cycles. Finally, we show that the opening force can be adjusted in real time by the addition of a single DNA oligonucleotide. These results establish the NanoDyn as a versatile force sensor and provide fundamental insights into how design parameters modulate mechanical and dynamic properties.
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Affiliation(s)
- Ariel Robbins
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Hazen Hildebolt
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Michael Neuhoff
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Peter Beshay
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Jessica O. Winter
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Carlos E. Castro
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G. Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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14
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Wang YJ, Valotteau C, Aimard A, Villanueva L, Kostrz D, Follenfant M, Strick T, Chames P, Rico F, Gosse C, Limozin L. Combining DNA scaffolds and acoustic force spectroscopy to characterize individual protein bonds. Biophys J 2023; 122:2518-2530. [PMID: 37290437 PMCID: PMC10323022 DOI: 10.1016/j.bpj.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 12/13/2022] [Accepted: 05/03/2023] [Indexed: 06/10/2023] Open
Abstract
Single-molecule data are of great significance in biology, chemistry, and medicine. However, new experimental tools to characterize, in a multiplexed manner, protein bond rupture under force are still needed. Acoustic force spectroscopy is an emerging manipulation technique which generates acoustic waves to apply force in parallel on multiple microbeads tethered to a surface. We here exploit this configuration in combination with the recently developed modular junctured-DNA scaffold that has been designed to study protein-protein interactions at the single-molecule level. By applying repetitive constant force steps on the FKBP12-rapamycin-FRB complex, we measure its unbinding kinetics under force at the single-bond level. Special efforts are made in analyzing the data to identify potential pitfalls. We propose a calibration method allowing in situ force determination during the course of the unbinding measurement. We compare our results with well-established techniques, such as magnetic tweezers, to ensure their accuracy. We also apply our strategy to study the force-dependent rupture of a single-domain antibody with its antigen. Overall, we get a good agreement with the published parameters that have been obtained at zero force and population level. Thus, our technique offers single-molecule precision for multiplexed measurements of interactions of biotechnological and medical interest.
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Affiliation(s)
- Yong Jian Wang
- Aix-Marseille Université, CNRS, INSERM, Laboratoire Adhesion et Inflammation, Turing Centre for Living systems, Marseille, France.
| | - Claire Valotteau
- Aix-Marseille Université, CNRS, INSERM, Laboratoire Adhesion et Inflammation, Turing Centre for Living systems, Marseille, France
| | - Adrien Aimard
- Aix-Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, Centre de Recherche en Cancerologie de Marseille, Marseille, France
| | - Lorenzo Villanueva
- Aix-Marseille Université, CNRS, INSERM, Laboratoire Adhesion et Inflammation, Turing Centre for Living systems, Marseille, France
| | - Dorota Kostrz
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Maryne Follenfant
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Terence Strick
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
| | - Patrick Chames
- Aix-Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, Centre de Recherche en Cancerologie de Marseille, Marseille, France
| | - Felix Rico
- Aix-Marseille Université, CNRS, INSERM, Laboratoire Adhesion et Inflammation, Turing Centre for Living systems, Marseille, France
| | - Charlie Gosse
- Institut de Biologie de l'Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France.
| | - Laurent Limozin
- Aix-Marseille Université, CNRS, INSERM, Laboratoire Adhesion et Inflammation, Turing Centre for Living systems, Marseille, France.
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15
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Tang Y, Liu H, Wang Q, Qi X, Yu L, Šulc P, Zhang F, Yan H, Jiang S. DNA Origami Tessellations. J Am Chem Soc 2023. [PMID: 37329284 DOI: 10.1021/jacs.3c03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Molecular tessellation research aims to elucidate the underlying principles that govern intricate patterns in nature and to leverage these principles to create precise and ordered structures across multiple scales, thereby facilitating the emergence of novel functionalities. DNA origami nanostructures are excellent building blocks for constructing tessellation patterns. However, the size and complexity of DNA origami tessellation systems are currently limited by several unexplored factors relevant to the accuracy of essential design parameters, the applicability of design strategies, and the compatibility between different tiles. Here, we present a general method for creating DNA origami tiles that grow into tessellation patterns with micrometer-scale order and nanometer-scale precision. Interhelical distance (D) was identified as a critical design parameter determining tile conformation and tessellation outcome. Finely tuned D facilitated the accurate geometric design of monomer tiles with minimized curvature and improved tessellation capability, enabling the formation of single-crystalline lattices ranging from tens to hundreds of square micrometers. The general applicability of the design method was demonstrated by 9 tile geometries, 15 unique tile designs, and 12 tessellation patterns covering Platonic, Laves, and Archimedean tilings. Particularly, we took two strategies to increase the complexity of DNA origami tessellation, including reducing the symmetry of monomer tiles and coassembling tiles of different geometries. Both yielded various tiling patterns that rivaled Platonic tilings in size and quality, indicating the robustness of the optimized tessellation system. This study will promote DNA-templated, programmable molecular and material patterning and open up new opportunities for applications in metamaterial engineering, nanoelectronics, and nanolithography.
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Affiliation(s)
- Yue Tang
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Hao Liu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Qi Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaodong Qi
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Lu Yu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Fei Zhang
- Department of Chemistry, School of Arts & Sciences-Newark, Rutgers University, Newark, New Jersey 07102, United States
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Shuoxing Jiang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
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16
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Luengo-Márquez J, Zalvide-Pombo J, Pérez R, Assenza S. Force-dependent elasticity of nucleic acids. NANOSCALE 2023; 15:6738-6744. [PMID: 36942727 DOI: 10.1039/d2nr06324g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The perturbation of the elasticity of NAs arising from these deformations is not properly considered by most theoretical frameworks. In this work, we introduce a novel method to assess the impact of mechanical stress on the elastic response of dsDNA and dsRNA through the analysis of the fluctuations of the double helix. Application of this approach to atomistic simulations reveals qualitative differences in the force dependence of the mechanical properties of dsDNA with respect to those of dsRNA, which we relate to structural features of these molecules by means of physically-sound minimalistic models.
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Affiliation(s)
- Juan Luengo-Márquez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
- Instituto Nicolás Cabrera, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan Zalvide-Pombo
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Salvatore Assenza
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
- Instituto Nicolás Cabrera, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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17
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Kodikara S, Gyawali P, Gleeson JT, Jakli A, Sprunt S, Balci H. Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4838-4846. [PMID: 36952670 PMCID: PMC10078606 DOI: 10.1021/acs.langmuir.3c00318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Positionally ordered bilayer liquid crystalline nanostructures formed by gapped DNA (GDNA) constructs provide a practical window into DNA-DNA interactions at physiologically relevant DNA concentrations; concentrations several orders of magnitude greater than those in commonly used biophysical assays. The bilayer structure of these states of matter is stabilized by end-to-end base stacking interactions; moreover, such interactions also promote in-plane positional ordering of duplexes that are separated from each other by less than twice the duplex diameter. The end-to-end stacked as well as in-plane ordered duplexes exhibit distinct signatures when studied via small-angle X-ray scattering (SAXS). This enables analysis of the thermal stability of both the end-to-end and side-by-side interactions. We performed synchrotron SAXS experiments over a temperature range of 5-65 °C on GDNA constructs that differ only by the terminal base-pairs at the blunt duplex ends, resulting in identical side-by-side interactions, while end-to-end base stacking interactions are varied. Our key finding is that bilayers formed by constructs with GC termination transition into the monolayer state at temperatures as much as 30 °C higher than for those with AT termination, while mixed (AT/GC) terminations have intermediate stability. By modeling the bilayer melting in terms of a temperature-dependent reduction in the average fraction of end-to-end paired duplexes, we estimate the stacking free energies in DNA solutions of physiologically relevant concentrations. The free-energies thereby determined are generally smaller than those reported in single-molecule studies, which might reflect the elevated DNA concentrations in our studies.
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Affiliation(s)
- Sineth
G. Kodikara
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Prabesh Gyawali
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - James T. Gleeson
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Antal Jakli
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
- Advanced
Materials and Liquid Crystals Institute, Kent State University, Kent, Ohio 44242, United States
| | - Samuel Sprunt
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
- Advanced
Materials and Liquid Crystals Institute, Kent State University, Kent, Ohio 44242, United States
| | - Hamza Balci
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
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18
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Liebl K, Zacharias M. Toward Force Fields with Improved Base Stacking Descriptions. J Chem Theory Comput 2023; 19:1529-1536. [PMID: 36795949 DOI: 10.1021/acs.jctc.2c01121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Recent DNA force fields indicate good performance in describing flexibility and structural stability of double-stranded B-DNA. However, it is not clear how accurately base stacking interactions are represented that are critical for simulating structure formation processes and conformational changes. Based on the equilibrium nucleoside association and base pair nicking, we find that the recent Tumuc1 force field improves the description of base stacking compared to previous state-of-the-art force fields. Nevertheless, base pair stacking is still overstabilized compared to experiment. We propose a rapid method to reweight calculated free energies of stacking upon force field modifications in order to generate improved parameters. A decrease of the Lennard-Jones attraction between nucleo-bases alone appears insufficient; however, adjustments in the partial charge distribution on base atoms could help to further improve the force field description of base stacking.
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Affiliation(s)
- Korbinian Liebl
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Martin Zacharias
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching 85748, Germany
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19
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Abraham Punnoose J, Thomas KJ, Chandrasekaran AR, Vilcapoma J, Hayden A, Kilpatrick K, Vangaveti S, Chen A, Banco T, Halvorsen K. High-throughput single-molecule quantification of individual base stacking energies in nucleic acids. Nat Commun 2023; 14:631. [PMID: 36746949 PMCID: PMC9902561 DOI: 10.1038/s41467-023-36373-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Base stacking interactions between adjacent bases in DNA and RNA are important for many biological processes and in biotechnology applications. Previous work has estimated stacking energies between pairs of bases, but contributions of individual bases has remained unknown. Here, we use a Centrifuge Force Microscope for high-throughput single molecule experiments to measure stacking energies between adjacent bases. We found stacking energies strongest between purines (G|A at -2.3 ± 0.2 kcal/mol) and weakest between pyrimidines (C|T at -0.5 ± 0.1 kcal/mol). Hybrid stacking with phosphorylated, methylated, and RNA nucleotides had no measurable effect, but a fluorophore modification reduced stacking energy. We experimentally show that base stacking can influence stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and assess accuracy of force fields in molecular dynamics simulations. Our results provide insights into fundamental DNA interactions that are critical in biology and can inform design in biotechnology applications.
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Affiliation(s)
- Jibin Abraham Punnoose
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kevin J Thomas
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | | | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kacey Kilpatrick
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Alan Chen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Thomas Banco
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
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20
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Hall DM, Stevens MJ, Grason GM. Building blocks of non-Euclidean ribbons: size-controlled self-assembly via discrete frustrated particles. SOFT MATTER 2023; 19:858-881. [PMID: 36636841 DOI: 10.1039/d2sm01371a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Geometric frustration offers a pathway to soft matter self-assembly with controllable finite sizes. While the understanding of frustration in soft matter assembly derives almost exclusively from continuum elastic descriptions, a current challenge is to understand the connection between microscopic physical properties of misfitting "building blocks" and emergent assembly behavior at the mesoscale. We present and analyze a particle-based description of what is arguably the best studied example for frustrated soft matter assembly, negative-curvature ribbon assembly, observed in both assemblies of chiral surfactants and shape-frustrated nanoparticles. Based on our particle model, known as saddle wedge monomers, we numerically test the connection between microscopic shape and interactions of the misfitting subunits and the emergent behavior at the supra-particle scale, specifically focussing on the propagation and relaxation of inter-particle strains, the emergent role of extrinsic shape on frustrated ribbons and the equilibrium regime of finite width selection. Beyond the intuitive role of shape misfit, we show that self-limitation is critically dependent on the finite range of cohesive interactions, with larger size finite assemblies requiring increasing short-range interparticle forces. Additionally, we demonstrate that non-linearities arising from discrete particle interactions alter self-limiting behavior due to both strain-softening in shape-flattened assembly and partial yielding of highly strained bonds, which in turn may give rise to states of hierarchical, multidomain assembly. Tracing the regimes of frustration-limited assembly to the specific microscopic features of misfitting particle shapes and interactions provides necessary guidance for translating the theory of size-programmable assembly into design of intentionally-frustrated colloidal particles.
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Affiliation(s)
- Douglas M Hall
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA.
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA.
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21
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Luo Y, Chang J, Yang D, Bryan JS, MacIsaac M, Pressé S, Wong WP. Resolving Molecular Heterogeneity with Single-Molecule Centrifugation. J Am Chem Soc 2023; 145:3276-3282. [PMID: 36716175 PMCID: PMC9936575 DOI: 10.1021/jacs.2c11450] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
For many classes of biomolecules, population-level heterogeneity is an essential aspect of biological function─from antibodies produced by the immune system to post-translationally modified proteins that regulate cellular processes. However, heterogeneity is difficult to fully characterize for multiple reasons: (i) single-molecule approaches are needed to avoid information lost by ensemble-level averaging, (ii) sufficient statistics must be gathered on both a per-molecule and per-population level, and (iii) a suitable analysis framework is required to make sense of a potentially limited number of intrinsically noisy measurements. Here, we introduce an approach that overcomes these difficulties by combining three techniques: a DNA nanoswitch construct to repeatedly interrogate the same molecule, a benchtop centrifuge force microscope (CFM) to obtain thousands of statistics in a highly parallel manner, and a Bayesian nonparametric (BNP) inference method to resolve separate subpopulations with distinct kinetics. We apply this approach to characterize commercially available antibodies and find that polyclonal antibody from rabbit serum is well-modeled by a mixture of three subpopulations. Our results show how combining a spatially and temporally multiplexed nanoswitch-CFM assay with BNP analysis can help resolve complex biomolecular interactions in heterogeneous samples.
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Affiliation(s)
- Yi Luo
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States,Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States,Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jeffrey Chang
- Department
of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Darren Yang
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States,Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States,Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - J. Shepard Bryan
- Department
of Physics, Arizona State University, Tempe, Arizona 85287, United States,Center
for
Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Molly MacIsaac
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States,Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States,Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steve Pressé
- Department
of Physics, Arizona State University, Tempe, Arizona 85287, United States,Center
for
Biological Physics, Arizona State University, Tempe, Arizona 85287, United States,School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Wesley P. Wong
- Program
in Cellular and Molecular Medicine, Boston
Children’s Hospital, Boston, Massachusetts 02115, United States,Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States,Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States,
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22
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Lee J, Lee S. Non-Invasive, Reliable, and Fast Quantification of DNA Loading on Gold Nanoparticles by a One-Step Optical Measurement. Anal Chem 2023; 95:1856-1866. [PMID: 36633590 DOI: 10.1021/acs.analchem.2c03378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
An exquisite, versatile, and reproducible quantification of DNA loading on gold nanoparticles (Au NPs) has long been pursued because this loading influences the analytical, therapeutic, and self-assembly behaviors of DNA-Au NPs. Nevertheless, the existing methods used thus far rely solely on the invasive detachment and subsequent spectroscopic quantification of DNA, which are error-prone and highly dependent on trained personnel. Here, we present a non-invasive optical framework that can determine the number of DNA strands on Au NPs by versatile one-step measurement of the visible absorption spectra of DNA-Au NP solutions without any invasive modifications or downstream processes. Using effective medium theory in conjunction with electromagnetic numerical calculation, the change in DNA loading density, resulting from varying the ion concentration, Au NP size, DNA strand length, and surrounding temperature, can be tracked in situ merely by the one-step measurement of visible absorption spectra, which is otherwise impossible to achieve. Moreover, the simplicity and robustness of this method promote reproducible DNA loading quantification regardless of experimental adeptness, which is in stark contrast with existing invasive and multistep methods. Overall, the optical framework outlined in this work can contribute to democratizing research on DNA-Au NPs and facilitating their rapid adoption in transformative applications.
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Affiliation(s)
- Jaewon Lee
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Seungwoo Lee
- KU-KIST Graduate School of Converging Science and Technology, Department of Integrative Energy Engineering, Department of Biomicrosystem Technology, and KU Photonics Center, Korea University, Seoul 02841, Republic of Korea
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23
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Dreher Y, Fichtler J, Karfusehr C, Jahnke K, Xin Y, Keller A, Göpfrich K. Genotype-phenotype mapping with polyominos made from DNA origami tiles. Biophys J 2022; 121:4840-4848. [PMID: 36088535 PMCID: PMC9811662 DOI: 10.1016/j.bpj.2022.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/18/2022] [Accepted: 09/06/2022] [Indexed: 01/07/2023] Open
Abstract
The correlation between genetic information and characteristics of a living cell-its genotype and its phenotype-constitutes the basis of genetics. Here, we experimentally realize a primitive form of genotype-phenotype mapping with DNA origami. The DNA origami can polymerize into two-dimensional lattices (phenotype) via blunt-end stacking facilitated by edge staples at the seam of the planar DNA origami. There are 80 binding positions for edge staples, which allow us to translate an 80-bit long binary code (genotype) onto the DNA origami. The presence of an edge staple thus corresponds to a "1" and its absence to a "0." The interactions of our DNA-based system can be reproduced by a polyomino model. Polyomino growth simulations qualitatively reproduce our experimental results. We show that not only the absolute number of base stacks but also their sequence position determine the cluster size and correlation length of the orientation of single DNA origami within the cluster. Importantly, the mutation of a few bits can result in major morphology changes of the DNA origami cluster, while more often, major sequence changes have no impact. Our experimental realization of a correlation between binary information ("genotype") and cluster morphology ("phenotype") thus reproduces key properties of genotype-phenotype maps known from living systems.
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Affiliation(s)
- Yannik Dreher
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Julius Fichtler
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany
| | - Christoph Karfusehr
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Max Planck School Matter to Life, Heidelberg University, Heidelberg, Germany
| | - Kevin Jahnke
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Yang Xin
- Paderborn University, Technical and Macromolecular Chemistry, Paderborn, Germany
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Paderborn, Germany
| | - Kerstin Göpfrich
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany.
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24
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Zhou C, Yang D, Sensale S, Sharma P, Wang D, Yu L, Arya G, Ke Y, Wang P. A bistable and reconfigurable molecular system with encodable bonds. SCIENCE ADVANCES 2022; 8:eade3003. [PMID: 36399380 PMCID: PMC9674029 DOI: 10.1126/sciadv.ade3003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Molecular systems with ability to controllably transform between different conformations play pivotal roles in regulating biochemical functions. Here, we report the design of a bistable DNA origami four-way junction (DOJ) molecular system that adopts two distinct stable conformations with controllable reconfigurability by using conformation-controlled base stacking. Exquisite control over DOJ's conformation and transformation is realized by programming the stacking bonds (quasi-blunt-ends) within the junction to induce prescribed coaxial stacking of neighboring junction arms. A specific DOJ conformation may be achieved by encoding the stacking bonds with binary stacking sequences based on thermodynamic calculations. Dynamic transformations of DOJ between various conformations are achieved by using specific environmental and molecular stimulations to reprogram the stacking codes. This work provides a useful platform for constructing self-assembled DNA nanostructures and nanomachines and insights for future design of artificial molecular systems with increasing complexity and reconfigurability.
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Affiliation(s)
- Chunyang Zhou
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
- College of Life Sciences and Technology, Changchun University of Science and Technology, Changchun 130013, Jilin, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Sebastian Sensale
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Pranav Sharma
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Dongfang Wang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Lei Yu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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25
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Fedorova L, Mulyar OA, Lim J, Fedorov A. Nucleotide Composition of Ultra-Conserved Elements Shows Excess of GpC and Depletion of GG and CC Dinucleotides. Genes (Basel) 2022; 13:2053. [PMID: 36360290 PMCID: PMC9690913 DOI: 10.3390/genes13112053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 08/27/2023] Open
Abstract
The public UCNEbase database, comprising 4273 human ultra-conserved noncoding elements (UCNEs), was thoroughly investigated with the aim to find any nucleotide signals or motifs that have made these DNA sequences practically unchanged over three hundred million years of evolution. Each UCNE comprises over 200 nucleotides and has at least 95% identity between humans and chickens. A total of 31,046 SNPs were found within the UCNE database. We demonstrated that every human has over 300 mutations within 4273 UCNEs. No association of UCNEs with non-coding RNAs, nor preference of a particular meiotic recombination rate within them were found. No sequence motifs associated with UCNEs nor their flanking regions have been found. However, we demonstrated that UCNEs have strong nucleotide and dinucleotide sequence abnormalities compared to genome averages. Specifically, UCNEs are depleted for CC and GG dinucleotides, while GC dinucleotides are in excess of 28%. Importantly, GC dinucleotides have extraordinarily strong stacking free-energy inside the DNA helix and unique resistance to dissociation. Based on the adjacent nucleotide stacking abnormalities within UCNEs, we conjecture that peculiarities in dinucleotide distribution within UCNEs may create unique 3D conformation and specificity to bind proteins. We also discuss the strange dynamics of multiple SNPs inside UCNEs and reasons why these sequences are extraordinarily conserved.
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Affiliation(s)
| | | | - Jan Lim
- CRI Genetics LLC, Santa Monica, CA 90404, USA
| | - Alexei Fedorov
- CRI Genetics LLC, Santa Monica, CA 90404, USA
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA
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26
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Geometrically programmed self-limited assembly of tubules using DNA origami colloids. Proc Natl Acad Sci U S A 2022; 119:e2207902119. [PMID: 36252043 PMCID: PMC9618141 DOI: 10.1073/pnas.2207902119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nature is replete with self-assembled materials that have one or more self-limited dimensions, including shells, tubules, and fibers. Despite significant advances in making nanometer- and micrometer-scale subunits, the programmable assembly of similar self-limiting architectures from synthetic components has remained largely out of reach. In this article, we create geometrically programmed subunits using DNA origami and study their assembly into tubules with a self-limited width. We show that the average self-limited dimension can be tuned by changing the local curvature encoded in a single subunit. Exploiting the programmability of our system, we further test the tradeoffs between fidelity and complexity embodied by two paradigms for self-limited assembly: self-closure through programmed curvature and addressable assembly through programmed specific interactions. Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are needed. To address this challenge, we explore the tradeoffs between addressable assembly and self-closing assembly of a specific class of self-limiting structures: cylindrical tubules. We make triangular subunits using DNA origami that have specific, valence-limited interactions and designed binding angles, and we study their assembly into tubules that have a self-limited width that is much larger than the size of an individual subunit. In the simplest case, the tubules are assembled from a single component by geometrically programming the dihedral angles between neighboring subunits. We show that the tubules can reach many micrometers in length and that their average width can be prescribed through the dihedral angles. We find that there is a distribution in the width and the chirality of the tubules, which we rationalize by developing a model that considers the finite bending rigidity of the assembled structure as well as the mechanism of self-closure. Finally, we demonstrate that the distributions of tubules can be further sculpted by increasing the number of subunit species, thereby increasing the assembly complexity, and demonstrate that using two subunit species successfully reduces the number of available end states by half. These results help to shed light on the roles of assembly complexity and geometry in self-limited assembly and could be extended to other self-limiting architectures, such as shells, toroids, or triply periodic frameworks.
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27
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A modular spring-loaded actuator for mechanical activation of membrane proteins. Nat Commun 2022; 13:3182. [PMID: 35902570 PMCID: PMC9334261 DOI: 10.1038/s41467-022-30745-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
How cells respond to mechanical forces by converting them into biological signals underlie crucial cellular processes. Our understanding of mechanotransduction has been hindered by technical barriers, including limitations in our ability to effectively apply low range piconewton forces to specific mechanoreceptors on cell membranes without laborious and repetitive trials. To overcome these challenges we introduce the Nano-winch, a robust, easily assembled, programmable DNA origami-based molecular actuator. The Nano-winch is designed to manipulate multiple mechanoreceptors in parallel by exerting fine-tuned, low- piconewton forces in autonomous and remotely activated modes via adjustable single- and double-stranded DNA linkages, respectively. Nano-winches in autonomous mode can land and operate on the cell surface. Targeting the device to integrin stimulated detectable downstream phosphorylation of focal adhesion kinase, an indication that Nano-winches can be applied to study cellular mechanical processes. Remote activation mode allowed finer extension control and greater force exertion. We united remotely activated Nano-winches with single-channel bilayer experiments to directly observe the opening of a channel by mechanical force in the force responsive gated channel protein, BtuB. This customizable origami provides an instrument-free approach that can be applied to control and explore a diversity of mechanotransduction circuits on living cells. Studies on mechanotransduction are limited by our ability to apply low range forces to specific mechanoreceptors on cell membranes. Here the authors report the Nano-winch, a programmable DNA origami-based molecular actuator, to manipulate multiple mechanoreceptors in parallel by exerting piconewton forces.
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28
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Feng A, Zhou Y, Al-Shebami MAY, Chen L, Pan Z, Xu W, Zhao S, Zeng B, Xiao Z, Yang Y, Hong W. σ-σ Stacked supramolecular junctions. Nat Chem 2022; 14:1158-1164. [PMID: 35902741 DOI: 10.1038/s41557-022-01003-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
Intermolecular charge transport plays an essential role in organic electronic materials and biological systems. To date, experimental investigations of intermolecular charge transport in molecular materials and electronic devices have been restricted to conjugated systems in which π-π stacking interactions are involved. Herein we demonstrate that the σ-σ stacking interactions between neighbouring non-conjugated molecules offer an efficient pathway for charge transport through supramolecular junctions. The conductance of σ-σ stacked molecular junctions formed between two non-conjugated cyclohexanethiol or single-anchored adamantane molecules is comparable to that of π-π stacked molecular junctions formed between π-conjugated benzene rings. The current-voltage characteristics and flicker noise analysis demonstrate the existence of stacked molecular junctions formed between the electrode pairs and exhibit the characteristics of through-space charge transport. Density functional theory calculations combined with the non-equilibrium Green's function method reveal that efficient charge transport occurs between two molecules configured with σ-σ stacking interactions.
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Affiliation(s)
- Anni Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Yu Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Mohammed A Y Al-Shebami
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Lichuan Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Zhichao Pan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Wei Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Shiqiang Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Biaofeng Zeng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Zongyuan Xiao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China.
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China.
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29
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Fontana F, Bellini T, Todisco M. Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesco Fontana
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, via Vanvitelli 32, 20129 Milano, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, via Vanvitelli 32, 20129 Milano, Italy
| | - Marco Todisco
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, via Vanvitelli 32, 20129 Milano, Italy
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30
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Abstract
To impart directionality to the motions of a molecular mechanism, one must overcome the random thermal forces that are ubiquitous on such small scales and in liquid solution at ambient temperature. In equilibrium without energy supply, directional motion cannot be sustained without violating the laws of thermodynamics. Under conditions away from thermodynamic equilibrium, directional motion may be achieved within the framework of Brownian ratchets, which are diffusive mechanisms that have broken inversion symmetry1-5. Ratcheting is thought to underpin the function of many natural biological motors, such as the F1F0-ATPase6-8, and it has been demonstrated experimentally in synthetic microscale systems (for example, to our knowledge, first in ref. 3) and also in artificial molecular motors created by organic chemical synthesis9-12. DNA nanotechnology13 has yielded a variety of nanoscale mechanisms, including pivots, hinges, crank sliders and rotary systems14-17, which can adopt different configurations, for example, triggered by strand-displacement reactions18,19 or by changing environmental parameters such as pH, ionic strength, temperature, external fields and by coupling their motions to those of natural motor proteins20-26. This previous work and considering low-Reynolds-number dynamics and inherent stochasticity27,28 led us to develop a nanoscale rotary motor built from DNA origami that is driven by ratcheting and whose mechanical capabilities approach those of biological motors such as F1F0-ATPase.
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31
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Romero-Sanchez IC, Castellano LE, Laurati M. Tuning the Effective Interactions between Spherical Double-Stranded DNA Brushes. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ivany C. Romero-Sanchez
- División de Ciencias e Ingenierías, Universidad de Guanajuato, 47150 León, Mexico
- Dipartimento di Chimica & CSGI, Università di Firenze, 50019 Sesto Fiorentino, Italy
| | - Laura E. Castellano
- División de Ciencias e Ingenierías, Universidad de Guanajuato, 47150 León, Mexico
| | - Marco Laurati
- Dipartimento di Chimica & CSGI, Università di Firenze, 50019 Sesto Fiorentino, Italy
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32
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Abstract
Cellular processes and functions can be regulated by mechanical forces. Nanodevices that can measure and manipulate these forces are critical tools in chemical and cellular biology. Synthetic DNA oligonucleotides have been used to develop a wide range of powerful nanodevices due to their programmable nature and precise and predictable self-assembly. In recent years, various types of DNA-based mechanical nanodevices have been engineered for studying molecular-level forces. With the help of these nanodevices, our understanding of cellular responses to physical forces has been significantly advanced. In this article, we have reviewed some recent developments in DNA-based mechanical sensors and regulators for application in the characterization of cellular biomechanics and the manipulation of cellular morphology, motion and other functions. The design principles discussed in this article can be further used to inspire other types of powerful DNA-based mechanical nanodevices.
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Affiliation(s)
- Qian Tian
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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33
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Abstract
In the dynamic environment of the airways, where SARS-CoV-2 infections are initiated by binding to human host receptor ACE2, mechanical stability of the viral attachment is a crucial fitness advantage. Using single-molecule force spectroscopy techniques, we mimic the effect of coughing and sneezing, thereby testing the force stability of SARS-CoV-2 RBD:ACE2 interaction under physiological conditions. Our results reveal a higher force stability of SARS-CoV-2 binding to ACE2 compared to SARS-CoV-1, causing a possible fitness advantage. Our assay is sensitive to blocking agents preventing RBD:ACE2 bond formation. It will thus provide a powerful approach to investigate the modes of action of neutralizing antibodies and other agents designed to block RBD binding to ACE2 that are currently developed as potential COVID-19 therapeutics. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are initiated by attachment of the receptor-binding domain (RBD) on the viral Spike protein to angiotensin-converting enzyme-2 (ACE2) on human host cells. This critical first step occurs in dynamic environments, where external forces act on the binding partners and avidity effects play an important role, creating an urgent need for assays that can quantitate SARS-CoV-2 interactions with ACE2 under mechanical load. Here, we introduce a tethered ligand assay that comprises the RBD and the ACE2 ectodomain joined by a flexible peptide linker. Using magnetic tweezers and atomic force spectroscopy as highly complementary single-molecule force spectroscopy techniques, we investigate the RBD:ACE2 interaction over the whole physiologically relevant force range. We combine the experimental results with steered molecular dynamics simulations and observe and assign fully consistent unbinding and unfolding events across the three techniques, enabling us to establish ACE2 unfolding as a molecular fingerprint. Measuring at forces of 2 to 5 pN, we quantify the force dependence and kinetics of the RBD:ACE2 bond in equilibrium. We show that the SARS-CoV-2 RBD:ACE2 interaction has higher mechanical stability, larger binding free energy, and a lower dissociation rate compared to SARS-CoV-1, which helps to rationalize the different infection patterns of the two viruses. By studying how free ACE2 outcompetes tethered ACE2, we show that our assay is sensitive to prevention of bond formation by external binders. We expect our results to provide a way to investigate the roles of viral mutations and blocking agents for targeted pharmaceutical intervention.
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34
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Lallemang M, Yu L, Cai W, Rischka K, Hartwig A, Haag R, Hugel T, Balzer BN. Multivalent non-covalent interactions lead to strongest polymer adhesion. NANOSCALE 2022; 14:3768-3776. [PMID: 35171194 DOI: 10.1039/d1nr08338d] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multivalent interactions play a leading role in biological processes such as the inhibition of inflammation or virus internalization. The multivalent interactions show enhanced strength and better selectivity compared to monovalent interactions, but they are much less understood due to their complexity. Here, we detect molecular interactions in the range of a few piconewtons to several nanonewtons and correlate them with the formation and subsequent breaking of one or several bonds and assign these bonds. This becomes possible by performing atomic force microcopy (AFM)-based single molecule force spectroscopy of a multifunctional polymer covalently attached to an AFM cantilever tip on a substrate bound polymer layer of the multifunctional polymer. Varying the pH value and the crosslinking state of the polymer layer, we find that bonds of intermediate strength (non-covalent), like coordination bonds, give the highest multivalent bond strength, even outperforming strong (covalent) bonds. At the same time, covalent bonds enhance the polymer layer density, increasing in particular the number of non-covalent bonds. In summary, we can show that the key for the design of stable and durable polymer coatings is to provide a variety of multivalent interactions and to keep the number of non-covalent interactions at a high level.
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Affiliation(s)
- Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Leixiao Yu
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takusstraße 3, 14195 Berlin, Germany
| | - Wanhao Cai
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
| | - Klaus Rischka
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Straße 12, 28359 Bremen, Germany
| | - Andreas Hartwig
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Straße 12, 28359 Bremen, Germany
- University of Bremen, Department 2 Biology/Chemistry, Leobener Straße 3, 28359 Bremen, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takusstraße 3, 14195 Berlin, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
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35
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Romero-Sanchez I, Pihlajamaa I, Adžić N, Castellano LE, Stiakakis E, Likos CN, Laurati M. Blunt-End Driven Re-entrant Ordering in Quasi Two-Dimensional Dispersions of Spherical DNA Brushes. ACS NANO 2022; 16:2133-2146. [PMID: 35130432 PMCID: PMC8867906 DOI: 10.1021/acsnano.1c07799] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We investigate the effects of crowding on the conformations and assembly of confined, highly charged, and thick polyelectrolyte brushes in the osmotic regime. Particle tracking experiments on increasingly dense suspensions of colloids coated with ultralong double-stranded DNA (dsDNA) fragments reveal nonmonotonic particle shrinking, aggregation, and re-entrant ordering. Theory and simulations show that aggregation and re-entrant ordering arise from the combined effect of shrinking, which is induced by the osmotic pressure exerted by the counterions absorbed in neighbor brushes and of a short-range attractive interaction competing with electrostatic repulsion. An unconventional mechanism gives origin to the short-range attraction: blunt-end interactions between stretched dsDNA fragments of neighboring brushes, which become sufficiently intense for dense and packed brushes. The attraction can be tuned by inducing free-end backfolding through the addition of monovalent salt. Our results show that base stacking is a mode parallel to hybridization to steer colloidal assembly in which attractions can be fine-tuned through salinity and, potentially, grafting density and temperature.
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Affiliation(s)
- Ivany Romero-Sanchez
- Dipartimento
di Chimica & CSGI, Università
di Firenze, 50019 Sesto Fiorentino, Italy
- División
de Ciencias e Ingenierías, Universidad
de Guanajuato, 37150 León, Mexico
| | - Ilian Pihlajamaa
- Faculty
of Physics, University of Vienna, Bolzmanngasse 5, A-1090 Vienna, Austria
- Eindhoven
University of Technology, Department of
Applied Physics, Soft Matter and Biological Physics, Postbus 513, NL-5600 MB Eindhoven, The Netherlands
| | - Natasa Adžić
- Faculty
of Physics, University of Vienna, Bolzmanngasse 5, A-1090 Vienna, Austria
| | - Laura E. Castellano
- División
de Ciencias e Ingenierías, Universidad
de Guanajuato, 37150 León, Mexico
| | - Emmanuel Stiakakis
- Biomacromolecular
Systems and Processes, Institute of Biological Information Processing
(IBI-4), 4 Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Christos N. Likos
- Faculty
of Physics, University of Vienna, Bolzmanngasse 5, A-1090 Vienna, Austria
| | - Marco Laurati
- Dipartimento
di Chimica & CSGI, Università
di Firenze, 50019 Sesto Fiorentino, Italy
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36
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Fan Q, He Z, Xiong J, Chao J. Smart Drug Delivery Systems Based on DNA Nanotechnology. Chempluschem 2022; 87:e202100548. [PMID: 35233992 DOI: 10.1002/cplu.202100548] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/13/2022] [Indexed: 11/12/2022]
Abstract
The development of DNA nanotechnology has attracted tremendous attention in biotechnological and biomedical fields involving biosensing, bioimaging and disease therapy. In particular, precise control over size and shape, easy modification, excellent programmability and inherent homology make the sophisticated DNA nanostructures vital for constructing intelligent drug carriers. Recent advances in the design of multifunctional DNA-based drug delivery systems (DDSs) have demonstrated the effectiveness and advantages of DNA nanostructures, showing the unique benefits and great potential in enhancing the delivery of pharmaceutical compounds and reducing systemic toxicity. This Review aims to overview the latest researches on DNA nanotechnology-enabled nanomedicine and give a perspective on their future opportunities.
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Affiliation(s)
- Qin Fan
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, 210000, P. R. China
| | - Zhimei He
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing, 210000, P. R. China
| | - Jinxin Xiong
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, 210000, P. R. China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, 210000, P. R. China
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing, 210000, P. R. China
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Mickolajczyk KJ, Olinares PDB, Chait BT, Liu S, Kapoor TM. The MIDAS domain of AAA mechanoenzyme Mdn1 forms catch bonds with two different substrates. eLife 2022; 11:73534. [PMID: 35147499 PMCID: PMC8837202 DOI: 10.7554/elife.73534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Catch bonds are a form of mechanoregulation wherein protein-ligand interactions are strengthened by the application of dissociative tension. Currently, the best-characterized examples of catch bonds are between single protein-ligand pairs. The essential AAA (ATPase associated with diverse cellular activities) mechanoenzyme Mdn1 drives at least two separate steps in ribosome biogenesis, using its MIDAS domain to extract the ubiquitin-like (UBL) domain-containing proteins Rsa4 and Ytm1 from ribosomal precursors. However, it must subsequently release these assembly factors to reinitiate the enzymatic cycle. The mechanism underlying the switching of the MIDAS-UBL interaction between strongly and weakly bound states is unknown. Here, we use optical tweezers to investigate the force dependence of MIDAS-UBL binding. Parallel experiments with Rsa4 and Ytm1 show that forces up to ~4 pN, matching the magnitude of force produced by AAA proteins similar to Mdn1, enhance the MIDAS domain binding lifetime up to 10-fold, and higher forces accelerate dissociation. Together, our studies indicate that Mdn1's MIDAS domain can form catch bonds with more than one UBL substrate, and provide insights into how mechanoregulation may contribute to the Mdn1 enzymatic cycle during ribosome biogenesis.
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Affiliation(s)
- Keith J Mickolajczyk
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, United States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, United States
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, United States
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Gvozden K, Novak Ratajczak S, Orellana AG, Kentzinger E, Rücker U, Dhont JKG, De Michele C, Stiakakis E. Self-Assembly of All-DNA Rods with Controlled Patchiness. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104510. [PMID: 34837474 DOI: 10.1002/smll.202104510] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/15/2021] [Indexed: 05/23/2023]
Abstract
Double-stranded DNA (dsDNA) fragments exhibit noncovalent attractive interactions between their tips. It is still unclear how DNA liquid crystal self-assembly is affected by such blunt-end attractions. It is demonstrated that stiff dsDNA fragments with moderate aspect ratio can specifically self-assemble in concentrated aqueous solutions into different types of smectic mesophases on the basis of selectively screening of blunt-end DNA stacking interactions. To this end, this type of attractions are engineered at the molecular level by constructing DNA duplexes where the attractions between one or both ends are screened by short hairpin caps. All-DNA bilayer and monolayer smectic-A type of phases, as well as a columnar phase, can be stabilized by controlling attractions strength. The results imply that the so far elusive smectic-A in DNA rod-like liquid crystals is a thermodynamically stable phase. The existence of the bilayer smectic phase is confirmed by Monte-Carlo simulations of hard cylinders decorated with one attractive terminal site. This work demonstrates that DNA blunt-ends behave as well-defined monovalent attractive patches whose strength and position can be potentially precisely tuned, highlighting unique opportunities concerning the stabilization of nonconventional DNA-based lyotropic liquid crystal phases assembled by all-DNA patchy particles with arbitrary geometry and composition.
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Affiliation(s)
- Katarina Gvozden
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing (IBI-4), Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Sanja Novak Ratajczak
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing (IBI-4), Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Alberto G Orellana
- Dipartimento di Fisica, Sapienza Universita di Roma, Piazzale A. Moro 5, Roma, 00185, Italy
| | - Emmanuel Kentzinger
- Jülich Centre for Neutron Science JCNS and Peter Grünberg Institut PGI, JARA-FIT, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Ulrich Rücker
- Jülich Centre for Neutron Science JCNS and Peter Grünberg Institut PGI, JARA-FIT, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jan K G Dhont
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing (IBI-4), Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Cristiano De Michele
- Dipartimento di Fisica, Sapienza Universita di Roma, Piazzale A. Moro 5, Roma, 00185, Italy
| | - Emmanuel Stiakakis
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing (IBI-4), Forschungszentrum Jülich, D-52425, Jülich, Germany
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Ha T, Kaiser C, Myong S, Wu B, Xiao J. Next generation single-molecule techniques: Imaging, labeling, and manipulation in vitro and in cellulo. Mol Cell 2022; 82:304-314. [PMID: 35063098 DOI: 10.1016/j.molcel.2021.12.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022]
Abstract
Owing to their unique abilities to manipulate, label, and image individual molecules in vitro and in cellulo, single-molecule techniques provide previously unattainable access to elementary biological processes. In imaging, single-molecule fluorescence resonance energy transfer (smFRET) and protein-induced fluorescence enhancement in vitro can report on conformational changes and molecular interactions, single-molecule pull-down (SiMPull) can capture and analyze the composition and function of native protein complexes, and single-molecule tracking (SMT) in live cells reveals cellular structures and dynamics. In labeling, the abilities to specifically label genomic loci, mRNA, and nascent polypeptides in cells have uncovered chromosome organization and dynamics, transcription and translation dynamics, and gene expression regulation. In manipulation, optical tweezers, integration of single-molecule fluorescence with force measurements, and single-molecule force probes in live cells have transformed our mechanistic understanding of diverse biological processes, ranging from protein folding, nucleic acids-protein interactions to cell surface receptor function.
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Affiliation(s)
- Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
| | - Christian Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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40
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Tych K, Rief M. Using Single-Molecule Optical Tweezers to Study the Conformational Cycle of the Hsp90 Molecular Chaperone. Methods Mol Biol 2022; 2478:401-425. [PMID: 36063329 DOI: 10.1007/978-1-0716-2229-2_15] [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] [Indexed: 06/15/2023]
Abstract
The heat shock protein 90 (Hsp90) family of chaperones are well-known, highly important components of the cellular systems which regulate protein homeostasis. Essential in eukaryotes, Hsp90s is also found in prokaryotes, including archaea. Hsp90 is a dimeric protein, with each monomer consisting of three separate structural domains, and undergoes large conformational changes as part of its functional cycle. This cycle is driven by interactions with nucleotides, cochaperone proteins, client proteins and allosteric effects enacted by these and by posttranslational modifications. All of these influence the rate and degree of the opening and closing of the dimer as well as the relative domain orientations and its overall rigidity. Optical tweezers, which can access many of these functionally important conformational changes, therefore provide a unique tool for the study of this large and complex molecular chaperone. Here, we provide protocols for the design and implementation of different Hsp90 constructs and optical tweezers experiments for addressing the many open questions about the function of this important molecular chaperone.
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Affiliation(s)
- Katarzyna Tych
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.
| | - Matthias Rief
- Department of Physics, Technical University of Munich, Garching-bei-München, Germany.
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41
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Borodina T, Smirnov V, Serykh V, Rozentsveig I. π-Stacking interactions in new arylsulphonylamine-substituted derivatives of imidazo[2,1-b]thiazol. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Grupa U, Liebl K, Zacharias M. Orientation Dependence of DNA Blunt-End Stacking Studied by Free-Energy Simulations. J Phys Chem B 2021; 125:13850-13857. [PMID: 34928161 DOI: 10.1021/acs.jpcb.1c07829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA blunt ends can associate mediated by stacking interactions between the terminal base pairs that form blunt ends. The blunt end association plays a role in DNA repair and recombination processes and can also be of importance for the design of DNA-based nano-materials. Its function depends on the sequence and on the geometric arrangement that leads to stable interaction. For a stacked state, the relative orientation (twisting) of the base pairs is important. Molecular dynamics and advanced sampling simulations were used to calculate free energy change associated with twist changes of the stacked blunt-end base pairs. The calculations reproduce blunt stacking arrangements found in crystal structures of DNA oligonucleotides as free energy minima. To elucidate the physical origin of the stabilization of certain angular arrangements, the interactions between backbone atoms in the blunt-end stack were switched off in additional free energy calculations. It allows us to decipher the contributions to stacking stabilization due to the nucleobases and the backbone and to analyze the sequence dependence of the angular stacking preferences. Good qualitative agreement was also found for the comparison with quantum mechanical calculations. The results may help in the design of novel DNA-based materials.
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Affiliation(s)
- Ulrich Grupa
- Center of Functional Protein Assemblies and Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Korbinian Liebl
- Center of Functional Protein Assemblies and Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Martin Zacharias
- Center of Functional Protein Assemblies and Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
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43
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Shrestha P, Yang D, Tomov TE, MacDonald JI, Ward A, Bergal HT, Krieg E, Cabi S, Luo Y, Nathwani B, Johnson-Buck A, Shih WM, Wong WP. Single-molecule mechanical fingerprinting with DNA nanoswitch calipers. NATURE NANOTECHNOLOGY 2021; 16:1362-1370. [PMID: 34675411 PMCID: PMC8678201 DOI: 10.1038/s41565-021-00979-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/16/2021] [Indexed: 05/31/2023]
Abstract
Decoding the identity of biomolecules from trace samples is a longstanding goal in the field of biotechnology. Advances in DNA analysis have substantially affected clinical practice and basic research, but corresponding developments for proteins face challenges due to their relative complexity and our inability to amplify them. Despite progress in methods such as mass spectrometry and mass cytometry, single-molecule protein identification remains a highly challenging objective. Towards this end, we combine DNA nanotechnology with single-molecule force spectroscopy to create a mechanically reconfigurable DNA nanoswitch caliper capable of measuring multiple coordinates on single biomolecules with atomic resolution. Using optical tweezers, we demonstrate absolute distance measurements with ångström-level precision for both DNA and peptides, and using multiplexed magnetic tweezers, we demonstrate quantification of relative abundance in mixed samples. Measuring distances between DNA-labelled residues, we perform single-molecule fingerprinting of synthetic and natural peptides, and show discrimination, within a heterogeneous population, between different posttranslational modifications. DNA nanoswitch calipers are a powerful and accessible tool for characterizing distances within nanoscale complexes that will enable new applications in fields such as single-molecule proteomics.
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Affiliation(s)
- Prakash Shrestha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Toma E Tomov
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - James I MacDonald
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Andrew Ward
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Hans T Bergal
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Biophysics Program, Harvard University, Cambridge, MA, USA
| | - Elisha Krieg
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Serkan Cabi
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yi Luo
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Bhavik Nathwani
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander Johnson-Buck
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Biophysics Program, Harvard University, Cambridge, MA, USA
| | - William M Shih
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Wesley P Wong
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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Abstract
Invention of DNA origami has transformed the fabrication and application of biological nanomaterials. In this review, we discuss DNA origami nanoassemblies according to their four fundamental mechanical properties in response to external forces: elasticity, pliability, plasticity and stability. While elasticity and pliability refer to reversible changes in structures and associated properties, plasticity shows irreversible variation in topologies. The irreversible property is also inherent in the disintegration of DNA nanoassemblies, which is manifested by its mechanical stability. Disparate DNA origami devices in the past decade have exploited the mechanical regimes of pliability, elasticity, and plasticity, among which plasticity has shown its dominating potential in biomechanical and physiochemical applications. On the other hand, the mechanical stability of the DNA origami has been used to understand the mechanics of the assembly and disassembly of DNA nano-devices. At the end of this review, we discuss the challenges and future development of DNA origami nanoassemblies, again, from these fundamental mechanical perspectives.
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Affiliation(s)
- Jiahao Ji
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
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45
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Yang S, Liu W, Zhang Y, Wang R. Bottom-Up Fabrication of Large-Scale Gold Nanorod Arrays by Surface Diffusion-Mediated DNA Origami Assembly. ACS APPLIED MATERIALS & INTERFACES 2021; 13:50516-50523. [PMID: 34637259 DOI: 10.1021/acsami.1c13173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Self-assembly of anisotropic metal nanoparticles serves as an effective bottom-up route for the nanofabrication of novel artifacts. However, there still are many challenges to rationally manipulate anisotropic particles due to the size and geometric restrictions. To avoid the aggregation and mishybridization from DNA sticky-end-guided assembly in buffer solution, in this work, we utilized a cation-controlled surface diffusion strategy to the spatial arrangement of gold nanorods (AuNRs) into 1D and 2D arrays by using DNA origami tiles as binding frames on the solid-liquid interface through π-π stacking interactions. To facilitate the further manipulation of those patterns, a novel pattern transfer method was introduced to transfer the arrays of AuNRs from a liquid to a dry ambient environment with high yield and minor structural damage. The results demonstrated a successful strategy of DNA origami-assisted, large-scale assembly of AuNRs for constructing complex superstructures with potential applications in the nanofabrication of plasmonic and electronic devices.
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Affiliation(s)
- Shuo Yang
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Wenyan Liu
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
- Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Yuwei Zhang
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Risheng Wang
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
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46
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Altun A, Garcia-Ratés M, Neese F, Bistoni G. Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex. Chem Sci 2021; 12:12785-12793. [PMID: 34703565 PMCID: PMC8494058 DOI: 10.1039/d1sc03868k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/26/2021] [Indexed: 01/21/2023] Open
Abstract
Herein, we provide new insights into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of a large portion of human B-DNA by using advanced quantum mechanical methods. Our results indicate that (i) the effect of non-neighboring bases on the inter-strand interaction is negligibly small, (ii) London dispersion effects are essential for the stability of the duplex structure, (iii) the largest contribution to the stability of the duplex structure is the Watson-Crick base pairing - consistent with previous computational investigations, (iv) the effect of stacking between adjacent bases is relatively small but still essential for the duplex structure stability and (v) there are no cooperativity effects between intra-strand stacking and inter-strand base pairing interactions. These results are consistent with atomic force microscope measurements and provide the first theoretical validation of nearest neighbor approaches for predicting thermodynamic data of arbitrary DNA sequences.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Miquel Garcia-Ratés
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
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47
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Dohnalová H, Lankaš F. Deciphering the mechanical properties of
B‐DNA
duplex. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
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48
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Beltrán SM, Slepian MJ, Taylor RE. Extending the Capabilities of Molecular Force Sensors via DNA Nanotechnology. Crit Rev Biomed Eng 2021; 48:1-16. [PMID: 32749116 DOI: 10.1615/critrevbiomedeng.2020033450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
At the nanoscale, pushing, pulling, and shearing forces drive biochemical processes in development and remodeling as well as in wound healing and disease progression. Research in the field of mechanobiology investigates not only how these loads affect biochemical signaling pathways but also how signaling pathways respond to local loading by triggering mechanical changes such as regional stiffening of a tissue. This feedback between mechanical and biochemical signaling is increasingly recognized as fundamental in embryonic development, tissue morphogenesis, cell signaling, and disease pathogenesis. Historically, the interdisciplinary field of mechanobiology has been driven by the development of technologies for measuring and manipulating cellular and molecular forces, with each new tool enabling vast new lines of inquiry. In this review, we discuss recent advances in the manufacturing and capabilities of molecular-scale force and strain sensors. We also demonstrate how DNA nanotechnology has been critical to the enhancement of existing techniques and to the development of unique capabilities for future mechanosensor assembly. DNA is a responsive and programmable building material for sensor fabrication. It enables the systematic interrogation of molecular biomechanics with forces at the 1- to 200-pN scale that are needed to elucidate the fundamental means by which cells and proteins transduce mechanical signals.
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Affiliation(s)
- Susana M Beltrán
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Marvin J Slepian
- Department of Medicine and Sarver Heart Center, University of Arizona, Tucson; Department of Biomedical Engineering, University of Arizona, Tucson; Department of Materials Science and Engineering, University of Arizona, Tucson
| | - Rebecca E Taylor
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
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49
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Symphony of the DNA flexibility and sequence environment orchestrates p53 binding to its responsive elements. Gene 2021; 803:145892. [PMID: 34375633 DOI: 10.1016/j.gene.2021.145892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 08/05/2021] [Indexed: 11/23/2022]
Abstract
The p53 tumor suppressor protein maintains the genome fidelity and integrity by modulating several cellular activities. It regulates these events by interacting with a heterogeneous set of response elements (REs) of regulatory genes in the background of chromatin configuration. At the p53-RE interface, both the base readout and torsional-flexibility of DNA account for high-affinity binding. However, DNA structure is an entanglement of a multitude of physicochemical features, both local and global structure should be considered for dealing with DNA-protein interactions. The goal of current research work is to conceptualize and abstract basic principles of p53-RE binding affinity as a function of structural alterations in DNA such as bending, twisting, and stretching flexibility and shape. For this purpose, we have exploited high throughput in-vitro relative affinity information of responsive elements and genome binding events of p53 from HT-Selex and ChIP-Seq experiments respectively. Our results confirm the role of torsional flexibility in p53 binding, and further, we reveal that DNA axial bending, stretching stiffness, propeller twist, and wedge angles are intimately linked to p53 binding affinity when compared to homeodomain, bZIP, and bHLH proteins. Besides, a similar DNA structural environment is observed in the distal sequences encompassing the actual binding sites of p53 cistrome genes. Additionally, we revealed that p53 cistrome target genes have unique promoter architecture, and the DNA flexibility of genomic sequences around REs in cancer and normal cell types display major differences. Altogether, our work provides a keynote on DNA structural features of REs that shape up the in-vitro and in-vivo high-affinity binding of the p53 transcription factor.
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50
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Abstract
DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general 'rules' that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.
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