Mapping the Morphology of DNA on Carbon Nanotube-Based Sensors in Solution using X-ray Scattering Interferometry

Rosenberg, D. J.; Cunningham, F. J.; Hubbard, J. D.; Goh, N. S.-Y.; Wang, J. W.-T.; Hayman, E. B.; Hura, G. L.; Landry, M. P.; Pinals, R. L.

doi:10.1101/2023.05.04.539504

bioRxiv · 10.1101/2023.05.04.539504

Mapping the Morphology of DNA on Carbon Nanotube-Based Sensors in Solution using X-ray Scattering Interferometry

Rosenberg, D. J.·Cunningham, F. J.·Hubbard, J. D.·Goh, N. S.-Y.·Wang, J. W.-T.·Hayman, E. B.·Hura, G. L.·Landry, M. P.·Pinals, R. L.

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Abstract

Single-walled carbon nanotubes (SWCNTs) with adsorbed single-stranded DNA (ssDNA) are applied as sensors to investigate biological systems, with applications ranging from clinical diagnostics to agricultural biotechnology. Unique ssDNA sequences render SWCNTs selectively responsive to target analytes. However, it remains unclear how the ssDNA conformation on the SWCNT surface contributes to their ultimate functionality, as observations have been constrained to computational models or experiments under dehydrated states that differ substantially from the aqueous biological environments in which the nanosensors are applied. Herein, we demonstrate a direct mode of measuring in-solution ssDNA geometries on SWCNTs via X-ray scattering interferometry (XSI), which leverages the interference pattern produced by AuNP tags conjugated to ssDNA on the SWCNT surface. We employ XSI to quantify distinct surface-adsorbed morphologies for two ssDNA oligomer lengths, conformational changes as a function of ionic strength, and the mechanism of dopamine sensing for a previously established ssDNA-SWCNT nanosensor, with corresponding ab initio modeling for visualization. We show that the shorter oligomer, (GT)6, adopts a highly ordered structure of stacked rings along the SWCNT axis, compared to the longer, less periodic (GT)15 wrapping. The presence of dopamine elicits a simultaneous axial elongation and radial constriction of the ssDNA closer to the SWCNT surface. Application of XSI to probe solution-phase morphologies of nanoparticle-based tools will yield insights into sensing mechanisms and inform future design strategies for polymer-functionalized SWCNT technologies.

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Rosenberg, D. J., Cunningham, F. J., Hubbard, J. D., Goh, N. S.-Y., Wang, J. W.-T., Hayman, E. B., Hura, G. L., Landry, M. P., Pinals, R. L.. 2023-05-06. Mapping the Morphology of DNA on Carbon Nanotube-Based Sensors in Solution using X-ray Scattering Interferometry. https://doi.org/10.1101/2023.05.04.539504

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