Near-Infrared Fluorescent Biosensors Based on Covalent DNA Anchors

Abstract

Semiconducting single-walled carbon nanotubes (SWCNTs) are versatile near-infrared (NIR) fluorophores. They are noncovalently modified to create sensors that change their fluorescence when interacting with biomolecules. However, noncovalent chemistry has several limitations and prevents a consistent way to molecular recognition and reliable signal transduction. Here, we introduce a widely applicable covalent approach to create molecular sensors without impairing the fluorescence in the NIR (>1000 nm). For this purpose, we attach single-stranded DNA (ssDNA) via guanine quantum defects as anchors to the SWCNT surface. A connected sequence without guanines acts as flexible capture probe allowing hybridization with complementary nucleic acids. Hybridization modulates the SWCNT fluorescence and the magnitude increases with the length of the capture sequence (20 > 10 ≫ 6 bases). The incorporation of additional recognition units via this sequence enables a generic route to NIR fluorescent biosensors with improved stability. To demonstrate the potential, we design sensors for bacterial siderophores and the SARS CoV-2 spike protein. In summary, we introduce covalent guanine quantum defect chemistry as rational design concept for biosensors.

Stochastic Formation of Quantum Defects in Carbon Nanotubes

“…Additionally, Weisman et al developed a protocol to covalently attach guanine bases to the lattice of SWCNTs. − These defects cause quantum light emission from the coupled defect states. This approach can also be used directly for biosensing or conjugation of larger recognition motifs to create sensors for bacterial or viral motifs. , Diazonium chemistry also offers to conjugate more complex entities such as biomolecules. , It is useful to directly attach, for example, nanobodies or grow peptide chains on the SWCNT lattice, which expands the toolbox for many applications such as sensing with quantum defects. , The concentration of diazonium salt affects the reaction and, most likely, the density of quantum defects. The fluorescence intensity ratio I E 11 * / I E 11 between the quantum-defect-related emission (E 11 *) and the bandgap emission (E 11 ) of SWCNTs is regarded as an approximate measure for defect density .…”

“…This approach can also be used directly for biosensing or conjugation of larger recognition motifs to create sensors for bacterial or viral motifs. 38,39 Diazonium chemistry also offers to conjugate more complex entities such as biomolecules. 40,41 It is useful to directly attach, for example, nanobodies or grow peptide chains on the SWCNT lattice, which expands the toolbox for many applications such as sensing with quantum defects.…”

Aptamer-based kinetically controlled DNA reactions coupled with metal–organic framework nanoprobes for sensitive detection of SARS-CoV-2 spike protein

“…As shown in Table S2, † the method had better performance in terms of both detection limit and linear range. [15][16][17][18][19][20] At the same time, the method used easily accessed materials and required no additional design of the aptamer segment, so it could be easily extended to the detection of other protein markers by simply changing the aptamer segment. Of course, the method also had some limitations.…”

“…Emerging aptamers with good binding affinity and speci-city provide opportunities for the establishment of detection methods for SARS-CoV-2 spike protein. [13][14][15][16][17][18][19][20] For example, Metternich et al made use of two aptamers targeting SARS-CoV-2 spike protein to develop a uorescence detection method based on covalent guanine quantum defect chemistry; 15 Luo et al demonstrated the usability of aptamer-functionalized MXene nanosheets as a novel sensor that allowed detection of SARS-CoV-2 spike protein down to 38.9 fg mL −1 ; 17 Xue et al reported an electrochemical method based on aptamer-binding induced multiple hairpin assembly and successfully applied it to detect as low as 9.79 fg mL −1 SARS-CoV-2 spike protein. 20 Although these methods have shown promising feasibility, they still have some limitations.…”

Surfactant-Aided Stabilization of Individual Carbon Nanotubes in Water around the Critical Micelle Concentration

“…Dispersion of carbon nanotubes (CNTs), especially single-walled CNTs (SWCNTs), in water with the aid of surfactants is a well-established strategy used in many fundamental studies and technological applications. − Ever since O’Connell et al first discovered that SWCNTs could be stabilized in water as individual nanotubes by the anionic surfactant sodium dodecyl sulfate (SDS) in 2002, many types of surfactants have been explored to form aqueous SWCNT solutions, including the anionic surfactant sodium dodecylbenzene­sulfonate (SDBS), the cationic surfactant cetyltrimethyl­ammonium bromide (CTAB), and the anionic bile salt surfactants sodium cholate (SC) and sodium deoxycholate (DOC). , Not surprisingly, the surfactant type and the surfactant assembly onto the nanotube can affect the surface potential of the surfactant–SWCNT complexes, resulting in different dispersion efficiencies . Many advanced studies of SWCNTs are thereby enabled, including nanotube sorting, ,, chemical reaction engineering, , fabrication of high-performance nanoelectronics devices, − and the exploration of SWCNTs as biomedical drug/gene carriers − and color center hosts. , …”