DNA Sequence Mediates Apparent Length Distribution in Single-Walled Carbon Nanotubes.

Mohammad Moein Safaee,Matthew Simmeth,Caroline Rocchio,Daniel Roxbury,Mitchell Gravely

doi:10.1021/acsami.8b16478

Mohammad Moein Safaee, Matthew Simmeth + Show 3 more

Open Access

https://doi.org/10.1021/acsami.8b16478

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Abstract

Single-walled carbon nanotubes (SWCNTs) functionalized with short single-stranded DNA have been extensively studied within the last decade for biomedical applications due to the high dispersion efficiency and intrinsic biocompatibility of DNA as well as the photostable and tunable fluorescence of SWCNTs. Characterization of their physical properties, particularly their length distribution, is of great importance regarding their application as a bioengineered research tool and clinical diagnostic agent. Conventionally, atomic force microscopy (AFM) has been used to quantify the length of DNA-SWCNTs by depositing the hybrids onto an electrostatically charged flat surface. Here, we demonstrate that hybrids of DNA-SWCNTs with different oligomeric DNA sequences ((GT)6 and (GT)30) differentially deposit on the AFM substrate, resulting in significant inaccuracies in the reported length distributions of the parent solutions. Using a solution-based surfactant exchange technique, we placed both samples into a common surfactant wrapping and found identical SWCNT length distributions upon surface deposition. Additionally, by spin-coating the surfactant-wrapped SWCNTs onto a substrate, thus mitigating effects of electrostatic interactions, we found length distributions that did not depend on DNA sequence but were significantly longer than electrostatic deposition methods, illuminating the inherent bias of the surface deposition method. Quantifying the coverage of DNA molecules on each SWCNT through both absorbance spectroscopy and direct observation, we found that the density of DNA per SWCNT was significantly higher in short (GT)6-SWCNTs (length < 100 nm) compared to long (GT)6-SWCNTs (length > 100 nm). In contrast, we found no dependence of the DNA density on SWCNT length in (GT)30-SWCNT hybrids. Thus, we attribute differences in the observed length distributions of DNA-SWCNTs to variations in electrostatic repulsion induced by sequence-dependent DNA density.

Highlights

Quantifying the coverage of DNA molecules on each SWCNT through both absorbance spectroscopy and direct observation, we found that the density of DNA per SWCNT was significantly higher in short (GT)6-SWCNTs compared to long (GT)6-SWCNTs
By transferring the hybrids into a common wrapping through the use of sodium deoxycholate (SDC)induced DNA displacement, we show that the length distributions of the two samples converge to a statistically identical value
In order to determine the length distribution of each sample, a solution of DNA-SWCNTs was exposed to an ultra-flat surface for 4 minutes, the surface was washed, and imaged with an atomic force microscope

Summary

Introduction

Single-walled carbon nanotubes (SWCNTs) with engineered wrappings[1,2,3,4] have recently been developed and utilized in various disparate fields ranging from additives that strengthen material composites[5,6,7,8] to biomedical applications including targeted anti-cancer drug delivery[9,10,11], nearinfrared (NIR) optical biosensing, 12-14 and biological imaging.[15,16,17,18] Of significant interest, SWCNTs exhibit intrinsic photoluminescence (fluorescence) that is photostable, tunable, and sensitive to its local environment.[19,20] covalent functionalization is known to negatively affect SWCNT electrical and optical properties,[21] alternative non-covalent methods are preferred. We demonstrate that hybrids of DNA-SWCNTs with different oligomeric DNA sequences ((GT)[6] and (GT)30) differentially deposit on the AFM substrate, resulting in significant inaccuracies in the reported length distributions of the parent solutions.

Results

Conclusion