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DNA tetrahedron

Professor Andrew Turberfield

Professor of Biological Physics

Research theme

  • Biological physics

Sub department

  • Condensed Matter Physics

Research groups

  • Nucleic acid nanotechnology
Andrew.Turberfield@physics.ox.ac.uk
  • About
  • Publications

A new architecture for DNA-templated synthesis in which abasic sites protect reactants from degradation

Angewandte Chemie International Edition Wiley 63:14 (2024) e202317482

Authors:

Jennifer Frommer, Robert Oppenheimer, Benjamin M Allott, Samuel Núñez-Pertíñez, Thomas R Wilks, Liam R Cox, Jonathan Bath, Rachel K O'Reilly, Andrew Turberfield

Abstract:

The synthesis of artificial sequence-defined polymers that match and extend the functionality of proteins is an important goal in materials science. One way of achieving this is to program a sequence of chemical reactions between precursor building blocks by means of attached oligonucleotide adapters. However, hydrolysis of the reactive building blocks has so far limited the length and yield of product that can be obtained using DNA-templated reactions. Here, we report an architecture for DNA-templated synthesis in which reactants are tethered at internal abasic sites on opposite strands of a DNA duplex. We show that an abasic site within a DNA duplex can protect a nearby thioester from degradation, significantly increasing the yield of a DNA-templated reaction. This protective effect has the potential to overcome the challenges associated with programmable sequence-controlled synthesis of long non-natural polymers by extending the lifetime of the reactive building blocks.
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Coarse-grained modelling of DNA-RNA hybrids

arXiv (2023) 1-15

Authors:

Eryk J Ratajczyk, Petr Šulc, Andrew J Turberfield, Jonathan PK Doye, Adriaan A Louis

Abstract:

We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension characteristics. By parameterising the DNA-RNA hydrogen bonding interaction we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability we provide three examples of its use—calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami.
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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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Designing the self-assembly of arbitrary shapes using minimal complexity building blocks

ACS Nano American Chemical Society 17:6 (2023) 5387-5398

Authors:

Joakim Bohlin, Andrew J Turberfield, Ard A Louis, Petr Šulc

Abstract:

The design space for self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. We develop a pipeline to explore the design spaces for a set of structures of various sizes and complexities. To understand the implications of the different solutions, we analyze their assembly dynamics using patchy particle simulations and study the influence of the number of distinct building blocks, and the angular and spatial tolerances on their interactions, on the kinetics and yield of the target assembly. We show that the resource-saving solution with a minimum number of distinct blocks can often assemble just as well (or faster) than designs where each building block is unique. We further use our methods to design multifarious structures, where building blocks are shared between different target structures. Finally, we use coarse-grained DNA simulations to investigate the realization of multicomponent shapes using DNA nanostructures as building blocks.
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