Mapping the Morphology of DNA on Carbon Nanotubes in Solution Using X-ray Scattering Interferometry

Rosenberg, Daniel J.; Cunningham, Francis J.; Hubbard, Joshua D.; Goh, Natalie S.; Wang, Jeffrey Wei-Ting; Nishitani, Shoichi; Hayman, Emily B.; Hura, Greg L.; Landry, Markita P.; Pinals, Rebecca L.

doi:10.1021/jacs.3c09549

Mapping the Morphology of DNA on Carbon Nanotubes in Solution Using X-ray Scattering Interferometry

Journal Article · Fri Dec 29 00:00:00 EST 2023 · Journal of the American Chemical Society

DOI:https://doi.org/10.1021/jacs.3c09549· OSTI ID:2323407

^[1]; Cunningham, Francis J. ^[2]; Hubbard, Joshua D. ^[2]; Goh, Natalie S. ^[2]; Wang, Jeffrey Wei-Ting ^[2]; ^[2]; Hayman, Emily B. ^[3]; ^[4]; ^[5]; ^[6]

Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States); SLAC
Univ. of California, Berkeley, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of California, Santa Cruz, CA (United States)
Univ. of California, Berkeley, CA (United States); Chan-Zuckerberg Biohub, San Francisco, CA (United States); Innovative Genomics Institute (IGI), Berkeley, CA (United States)
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

Single-walled carbon nanotubes (SWCNTs) with adsorbed single-stranded DNA (ssDNA) are applied as sensors to investigate biological systems, with potential applications ranging from clinical diagnostics to agricultural biotechnology. Unique ssDNA sequences render SWCNTs selectively responsive to target analytes such as (GT)n-SWCNTs recognizing the neuromodulator, dopamine. It remains unclear how the ssDNA conformation on the SWCNT surface contributes to functionality, as observations have been limited to computational models or experiments under dehydrated conditions that differ substantially from the aqueous biological environments in which the nanosensors are applied. 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 (GT)_n ssDNA oligomer lengths (n = 6, 15) that are used on SWCNTs in the context of dopamine sensing and measure the ssDNA conformational changes as a function of ionic strength and during dopamine interaction. Here, we show that the shorter oligomer, (GT)₆, adopts a more periodically ordered ring structure along the SWCNT axis (inter-ssDNA distance of 8.6 ± 0.3 nm), compared to the longer (GT)₁₅ oligomer (most probable 5'-to-5' distance of 14.3 ± 1.1 nm). During molecular recognition, XSI reveals that dopamine elicits simultaneous axial elongation and radial constriction of adsorbed ssDNA on the SWCNT surface. Our approach using XSI to probe solution-phase morphologies of polymer-functionalized SWCNTs can be applied to yield insights into sensing mechanisms and inform future design strategies for nanoparticle-based sensors.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); National Science Foundation (NSF); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-05CH11231; AC02-76SF00515

OSTI ID:: 2323407

Journal Information:: Journal of the American Chemical Society, Journal Name: Journal of the American Chemical Society Journal Issue: 1 Vol. 146; ISSN 0002-7863

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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