Sustained unidirectional rotation of a self-organized DNA rotor on a nanopore

Shi, Xin; Pumm, Anna-Katharina; Isensee, Jonas; Zhao, Wenxuan; Verschueren, Daniel; Martín-González, Alejandro; Golestanian, Ramin; Dietz, Hendrik; Dekker, Cees

doi:10.1038/s41567-022-01683-z

Cited by 38 publications

(38 citation statements)

References 32 publications

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“…Recently reported nanostructures utilize an electro‐chemical gradient to power unidirectional rotation. [ 79,80 ] And a recent motor design developed by Pumm et al. consists of a rotor arm component constrained sterically to uniaxial rotations around the pivot point within the plane of a triangular platform.…”

Section: Dna Origami Nanoactuatorsmentioning

confidence: 99%

“…Recently reported nanostructures utilize an electro-chemical gradient to power unidirectional rotation. [79,80] And a recent motor design developed by Pumm et al consists of a rotor arm component constrained sterically to uniaxial rotations around the pivot point within the plane of a triangular platform. The motor is powered by a simple external energy modulation that does not need any feedback or information supplied by the user to direct the motors.…”

Section: Dna Origami Nanoactuatorsmentioning

confidence: 99%

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Mechanical DNA Origami to Investigate Biological Systems

et al. 2022

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ciently flexible to be packaged into nuclei around chromosomes and be subjected to various processes, such as replication and transcription, while also behaving as an entropic spring. [1,2] Today, DNA is increasingly being used as a building material to construct nano-objects with defined shape and size. The principle of Watson-Crick complementarity permits the design and production of self-assembling macromolecular objects with custom 3D shape. Of particular importance, these nanodevices can serve as molecular machines inspired by nature that can perform complex tasks dynamically and reliably using different design approaches. Creating these DNA nano-objects with specified shapes was first conceptualized more than 40 years ago by Seeman [3] and experimentally achieved 10 years later. [4] A significant breakthrough in the construction of nanometer-sized DNA objects occurred in 2006 with the introduction of the 2D DNA origami method by Rothemund, [5] and 3D DNA origami method introduced by Shih et al. in 2009. [6] Since these developments, DNA origami method has been thoroughly tested and applied to become, progressively, the gold standard method to build DNA nanostructures. [7] Self-assembled DNA origami are made from a scaffold strand of single-stranded DNA (ssDNA), typically M13 phage genomic DNA, which is folded by a complementary set of short oligonucleotide staple strands. [5,6,8] Initial DNA origami structures were static objects, albeit able to incorporate functionalized chemistries and biomolecules in a site-specific manner with well-defined spatial arrangement. [5,9,10] The well-characterized DNA-base pairing provides an easy means to control DNA interactions. This has allowed sequence programmability to rationalize the design into precisely defined geometries with increasingly complexity, including 2D, [11] 3D lattice, [12] and wireframe structures [13,14] with defined functions and operations, with micrometer, [15] and gigadalton scale multicomponent assemblies. [16,17] DNA origami objects have now graduated to dynamic movements with mechanical articulation or actuation programmed to respond to specific stimuli, including devices that open [18][19][20][21] or close [22] in response to target molecules (Figure 1). There are DNA origami devices that undergo multistage movement by strand-displacement reactions. [23,24] It is now possible for DNA origami devices to respond to electric fields [25,26] and light. [27,28] The ability to both program stimuli responsiveness and to create a multicomponent object able to communicate between the different components, to propagate information, andThe ability to self-assemble DNA nanodevices with programmed structural dynamics that can sense and respond to the local environment can enable transformative applications in fields including mechanobiology and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. In this review, the current s...

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Section: Dna Origami Nanoactuatorsmentioning

confidence: 99%

Section: Dna Origami Nanoactuatorsmentioning

confidence: 99%

Mechanical DNA Origami to Investigate Biological Systems

et al. 2022

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“…9,12 In addition to enabling nucleic acid and peptide sequencing and label-free biomolecule detection, nanopore technology provides a platform to build devices with sustained directional rotary motions, forming essential building blocks for more advanced nanomachines or synthetic cells. 13,14 Realizing the full potential of nanopore technology relies on the ability to precisely control the nanopore's physical and biochemical characteristics, including channel diameter and depth, mechanical stiffness, and surface chemistry. 7,8 As an information-rich molecule for building self-assembled nano-structures with programmable geometry, mechanics, and chemical modifications, DNA has emerged as a promising material for nanopore engineering.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Nearly all of today’s nanopore implementations can be categorized into two types: synthetic and biological. , The bulk of synthetic nanopores are solid-state nanopores, typically made by beam milling on silicon chips to achieve pores with controllable geometry . Biological pores, , exemplified by transmembrane protein channels fabricated through molecular biology methods, allow for site-specific and atomically precise modifications. , In addition to enabling nucleic acid and peptide sequencing and label-free biomolecule detection, nanopore technology provides a platform to build devices with sustained directional rotary motions, forming essential building blocks for more advanced nanomachines or synthetic cells. , …”

Section: Introductionmentioning

confidence: 99%

Functionalized DNA-Origami-Protein Nanopores Generate Large Transmembrane Channels with Programmable Size-Selectivity

et al. 2022

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The DNA-origami technique has enabled the engineering of transmembrane nanopores with programmable size and functionality, showing promise in building biosensors and synthetic cells. However, it remains challenging to build large (>10 nm), functionalizable nanopores that spontaneously perforate lipid membranes. Here, we take advantage of pneumolysin (PLY), a bacterial toxin that potently forms wide ring-like channels on cell membranes, to construct hybrid DNA−protein nanopores. This PLY-DNA-origami complex, in which a DNA-origami ring corrals up to 48 copies of PLY, targets the cholesterol-rich membranes of liposomes and red blood cells, readily forming uniformly sized pores with an average inner diameter of ∼22 nm. Such hybrid nanopores facilitate the exchange of macromolecules between perforated liposomes and their environment, with the exchange rate negatively correlating with the macromolecule size (diameters of gyration: 8−22 nm). Additionally, the DNA ring can be decorated with intrinsically disordered nucleoporins to further restrict the diffusion of traversing molecules, highlighting the programmability of the hybrid nanopores. PLY-DNA pores provide an enabling biophysical tool for studying the cross-membrane translocation of ultralarge molecules and open new opportunities for analytical chemistry, synthetic biology, and nanomedicine.

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“…Single-molecule studies and nanoengineering have advanced to a stage towards attempting to engineer artificial lives. [1][2][3] One of the most critical parameters in this direction is to have a robust control in the orientation of molecules 4,5 as real-time structural biology is all about conformation and their dynamic heterogeneity. 6,7 The movement of the particles in a defined medium makes it difficult to hold single molecules inside a volume for detection, and sorting small biomolecules with a single-molecule level resolution is just as tough as catching the movement of dust mites in a closed space.…”

Section: Introductionmentioning

confidence: 99%

Orientation-dependent real-time single-molecule photobleaching inside uniform electrodynamic interfaces of nanofluidic confinement

Chinmaya

Ghosh

2022

Preprint

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The functioning of single molecules in nanofluidic confinement is a typical process in cell biology. The orientation of molecules is a critical parameter for this. We discern the orientation of a single molecule in a nanofluidic environment while it's functioning in an engineered solid-state device. Molecular properties depend on the electrodynamic interface. Our manufacturing ability of uniform electrodynamic interfaces at nanometric lengthscale opens the avenue of imitating biological abilities to handle single molecules with single-charge precision. We present a step-wise single-molecule fluorescence photobleaching study in a nanoconfined space of 25 nm to 45 nm. The uniform electrodynamics interfaces of silica-silica let us study the artefact-free dependence of molecular interface and its effect on step-wise photobleaching with a controlled environment of oxygen at room temperature.

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Sustained unidirectional rotation of a self-organized DNA rotor on a nanopore

Cited by 38 publications

References 32 publications

Mechanical DNA Origami to Investigate Biological Systems

Mechanical DNA Origami to Investigate Biological Systems

Functionalized DNA-Origami-Protein Nanopores Generate Large Transmembrane Channels with Programmable Size-Selectivity

Orientation-dependent real-time single-molecule photobleaching inside uniform electrodynamic interfaces of nanofluidic confinement

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