Review—Engineering the Selectivity of the DNA-SWCNT Sensor

Abstract

Single-walled carbon nanotubes (SWCNTs) demonstrate a unique combination of optical, chemical, and physical properties that render them suitable for a variety of sensing applications. Their photostable near-infrared (nIR) fluorescence emissions are highly sensitive to perturbations in the surrounding SWCNT environment, enabling optical sensors with single-molecule detection limits. Despite these immanent advantages, SWCNTs lack the inherent molecular recognition capabilities required for selective sensing applications. One approach to tuning sensor selectivity is to engineer synthetic and biological wrappings that cover the nanotube's surface in a manner that limits chemical access to the surface to specific target analytes. Among the numerous possible wrappings, deoxyribonucleic acid (DNA) has emerged as the most studied polymeric wrapping. In addition to the sequence-dependent tunability DNA offers in engineering selectivity, DNA assumes a peculiar helical wrapping conformation along the SWCNT surface that has been the focus of many experimental and computational studies. In this review, we summarize some of the major findings in the field, focusing on the underlying molecular interactions responsible for the conformational and molecular recognition elements of the wrapping. Special focus is given to characterizing the nucleotide binding affinity, DNA sequence dependency, DNA length variation, SWCNT chirality, and sugar backbone (RNA vs. DNA) contributions to the wrapping conformation and SWCNT fluorescence. This article concludes with an assessment of the latest DNA-SWCNT-based sensing platforms used for the selective, single-and multi-modal detection of target analytes. Since their introduction in the early 60s, 1 biosensors have become an indispensable part of our daily lives, finding disparate applications in a variety of analytical fields ranging from biomedical diagnostics to environmental monitoring to food technology.2 Notably, optical biosensors based on fluorescent-light emission, which exploit diverse fluorescent probes as labeling agents for the recognition units, have emerged as highly sensitive, rapid, reproducible, and simple-to-operate analytical tools capable of quantitatively monitoring specific molecular interactions in real time.3,4 However, several drawbacks limit their application in more complex chemical and biological environments. For example, typical fluorescence-based sensors conventionally employ organic fluorophores that emit fluorescence with visible wavelengths that do not penetrate well through biological tissue.5 Furthermore, such fluorophores are often subject to rapid photobleaching, thus compromising their sensor lifetimes. These limitations are unfavorable for long-term in vivo sensing 6 for diagnostic applications. Recent research is thus focused on finding new technologies and materials to engineer novel sensing platforms with increased sensitivity and selectivity over extended periods of time.Single-walled carbon nanotubes (SWCNTs) have become widely used in a new genera...

Xeno Nucleic Acid Nanosensors for Enhanced Stability Against Ion-Induced Perturbations

“…Optical SWCNT sensors have already been successfully used for miRNA detection in urine and serum, real-time deep-tissue brain imaging, , and glucose detection both in whole blood and in vivo . Single-stranded DNA (ssDNA)-wrapped SWCNTs are among the most widely used SWCNT-based conjugates for optical biosensing. ,, The noncovalent functionalization of SWCNTs with ssDNA is based on π-stacking of the aromatic nucleotide bases with the hydrophobic side wall of carbon nanotubes. This functionalization preserves the optoelectronic properties and enhances biocompatibility in addition to greatly improving nanotube solubility in aqueous solutions.…”

Mapping Single Walled Carbon Nanotubes in Photosynthetic Algae by Single-Cell Confocal Raman Microscopy

“…Finally, shorten nanotubes were dried in oven at 60 °C for 24 h and the powder was treated as described below. The SWCNTs were dispersed by non-covalent functionalization with single strand DNA (ssDNA), a well-known dispersing agent, which facilitates the stable mono-dispersion of CNTs and enhances their compatibility with biological samples [ 29 , 30 ]. A previously described procedure was adopted[ 31 ] using autoclaved (20 min, 121 °C, 1 bar) powder of nanotubes.…”

Non-covalent Methods of Engineering Optical Sensors Based on Single-Walled Carbon Nanotubes

“…DNA is one of the most extensively studied wrappings for optical sensing applications based on Raman, fluorescence, and absorption spectroscopies (Zheng et al, 2003a; Heller et al, 2006; Enyashin et al, 2007; Zhang et al, 2011; Bansal et al, 2013; Kupis-Rozmysłowicz et al, 2016; Wu et al, 2018). The non-covalent functionalization of ssDNA is based on π-stacking of the aromatic nucleotide bases with the sp 2 -hybridized side-wall of carbon nanotubes (Zheng et al, 2003a).…”