Introducing Bacteria and Synthetic Biomolecules along Engineered DNA Fibers

Jonathan R Burns

doi:10.1002/smll.202100136

Abstract

Deoxyribonucleic acid (DNA) nanotechnology enables user-defined structures to be built with unrivalled control. The approach is currently restricted across the nanoscale, yet the ability to generate macroscopic DNA structures has enormous potential with applications spanning material, physical, and biological science. To address this need, I employed DNA nanotechnology and developed a new macromolecular nanoarchitectonic assembly method to produce DNA fibers with customizable properties. The process involves coalescing DNA nanotubes under high salt conditions to yield filament superstructures. Using this strategy, fibers over 100 microns long, with stiffnesses 10 times greater than cytoskeletal actin filaments can be fabricated. The DNA framework enables fibers to be functionalized with advanced synthetic molecules, including, aptamers, origami, nanoparticles, and vesicles. In addition, the fibers can act as bacterial extracellular scaffolds and adhere Escherichia coli cells in a controllable fashion. These results showcase the opportunities offered from DNA nanotechnology across the macroscopic scale. The new biophysical approach should find widespread use, from the generation of hybrid-fabric materials, smart analytical devices in biomedicine, and platforms to study cell-cell interactions.

Highlights

Deoxyribonucleic acid (DNA) nanotechnology enables user-defined strucorigami blocks are able to combine into spherical superstructures,[8] organized tures to be built with unrivalled control
I employed DNA nanotechnology and developed a new macromolecular nanoarchitectonic assembly method and plate arrays which assemble on 2D surfaces to mimic famous artwork.[10]
A new macromolecular nanoarchitectonic approach has been developed which can be functionalized with synthetic biomolecules and E. coli cells

Summary

Structural Characterization of DNA Nanotubes and Fibers

The DNA framework must be sufficiently stable and rigid across the micron range for macroscopic applications. At high divalent metal ion concentrations the DNA nanotubes coalesced to form highly rigid fibers (Figure 2b; Figures S9–S11, Supporting Information). CLSM identified the longest fibers’ increased to over 40 μm, whilst the persistence length increased to over 200 μm (Figure 2b-iii, Table 1; Figure S14, Supporting Information), which is an order of magnitude stiffer than cytoskeletal actin filaments.[27] The results imply the Cy3 dyes interact constructively in the nanotube bundle with adjacent dyes via π-stacking interactions. Thermal UV absorbance and corresponding CLSM analysis confirmed all DNA constructs remain structurally stable at physiological temperatures (Figure 2e, Table 1; Figure S17, Supporting Information). 3× seed-annealing cycles improved the fibers’ stiffness further, with fibers over 100 μm long and 300 nm wide observed (Table 1; Figures S12–S14, Supporting Information). The fibers remain stable when resuspended into deionized water

Functionalizing DNA Fibers with Synthetic Biomolecules

Escherichia coli Cells Adhere Along DNA Fibers

Summary and Perspective

Experimental Section

Data Availability Statement