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Systematic Selection of High-Affinity ssDNA Sequences to Carbon Nanotubes.

ABSTRACT: Single-walled carbon nanotubes (SWCNTs) have gained significant interest for their potential in biomedicine and nanoelectronics. The functionalization of SWCNTs with single-stranded DNA (ssDNA) enables the precise control of SWCNT alignment and the development of optical and electronic biosensors. This study addresses the current gaps in the field by employing high-throughput systematic selection, enriching high-affinity ssDNA sequences from a vast random library. Specific base compositions and patterns are identified that govern the binding affinity between ssDNA and SWCNTs. Molecular dynamics simulations validate the stability of ssDNA conformations on SWCNTs and reveal the pivotal role of hydrogen bonds in this interaction. Additionally, it is demonstrated that machine learning could accurately distinguish high-affinity ssDNA sequences, providing an accessible model on a dedicated webpage (http://service.k-medai.com/ssdna4cnt). These findings open new avenues for high-affinity ssDNA-SWCNT constructs for stable and sensitive molecular detection across diverse scientific disciplines.

SUBMITTER: Lee D

PROVIDER: S-EPMC11348070 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

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Systematic Selection of High-Affinity ssDNA Sequences to Carbon Nanotubes.

Lee Dakyeon D Lee Jaekang J Kim Woojin W Suh Yeongjoo Y Park Jiwoo J Kim Sungjee S Kim YongJoo Y Kwon Sunyoung S Jeong Sanghwa S

Advanced science (Weinheim, Baden-Wurttemberg, Germany) 20240625 32

Single-walled carbon nanotubes (SWCNTs) have gained significant interest for their potential in biomedicine and nanoelectronics. The functionalization of SWCNTs with single-stranded DNA (ssDNA) enables the precise control of SWCNT alignment and the development of optical and electronic biosensors. This study addresses the current gaps in the field by employing high-throughput systematic selection, enriching high-affinity ssDNA sequences from a vast random library. Specific base compositions and ...[more]

PMID: 38932669

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Project description:Surface oxidation improves the dispersion of carbon nanotubes in aqueous solutions and plays a key role in the development of biosensors, electrochemical detectors and polymer composites. Accurate characterization of the carbon nanotube surface is important because the development of these nano-based applications depends on the degree of functionalization, in particular the amount of carboxylation. Affinity capillary electrophoresis is used to characterize the oxidation of multi-walled carbon nanotubes. A polytryptophan peptide that contains a single arginine residue (WRWWWW) serves as a receptor in affinity capillary electrophoresis to assess the degree of carboxylation. The formation of peptide-nanotube receptor-ligand complex was detected with a UV absorbance detector. Apparent dissociation constants (KD) are obtained by observing the migration shift of the WRWWWW peptide through background electrolyte at increasing concentrations of multi-walled carbon nanotubes. A 20% relative standard deviation in method reproducibility and repeatability is determined with triplicate analysis within a single sample preparation and across multiple sample preparations for a commercially available carbon nanotube. Affinity capillary electrophoresis is applied to assess differences in degree of carboxylation across two manufacturers and to analyze acid treated carbon nanotubes. The results of these studies are compared to X-ray photoelectron spectroscopy and zeta potential. Affinity capillary electrophoresis comparisons of carbon nanotube samples prepared by varying acid treatment time from 30 min to 3 h yielded significant differences in degree of carboxylation. X-ray photoelectron spectroscopy analysis was inconclusive due to potential acid contamination, while zeta potential showed no change based on surface charge. This work is significant to research involving carbon nanotube-based applications because it provides a new metric to rapidly characterize carbon nanotubes obtained from different vendors, or synthesized in laboratories using different procedures.

Dataset Information

Systematic Selection of High-Affinity ssDNA Sequences to Carbon Nanotubes.

Publications

Systematic Selection of High-Affinity ssDNA Sequences to Carbon Nanotubes.

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