Near-Infrared Fluorescence Modulation of Refolded DNA Aptamer-Functionalized Single-Walled Carbon Nanotubes for Optical Sensing

Abstract

Selective modulation of near-infrared (NIR) fluorescence of single-walled carbon nanotubes (SWNTs) is important for their applications as NIR optical sensors and devices. Here, we study the target-molecule-mediated NIR fluorescence modulation of refolded DNA aptamer-functionalized SWNTs, using platelet-derived growth factor (PDGF) and a PDGF-binding aptamer as a model system. The aptamer–SWNT complexes use SWNT as nanoscale NIR optical emitters and DNA aptamers as molecular recognition elements. The binding of target molecules, PDGFs in this study, to PDGF-binding aptamers on the surface of SWNTs induces a conformation change of the aptamers, which modulates the NIR fluorescence of SWNT emitters. This study suggests that PDGF-binding aptamers noncovalently assembled on the SWNT surface can undergo a temperature- and divalent-ion-induced conformational change into a folded structure through multiple stages, which renders aptamer-functionalized SWNTs optically responsive to target molecules. In addition, our experimental and theoretical results show that the aptamers have a nanotube-diameter-dependent affinity for SWNTs. We demonstrate that refolded aptamer-functionalized SWNTs reversibly modulate their NIR fluorescence in response to PDGF at the nanomolar range 0.1–10 nM with apparent dissociation constants of ∼0.71 nM (solution-phase complexes) and ∼3.1 nM (complexes in hydrogels). This study could open new opportunities to design label-free, reversible NIR optical sensors that can detect various target molecules upon availability or selection of their cognate aptamers.

Design of Refolding DNA Aptamer on Single-Walled Carbon Nanotubes for Enhanced Optical Detection of Target Proteins

“…Aptamers are synthetic single-stranded oligonucleotides without the periodic sequence and enable the recognition of a targeting protein through specific noncovalent interaction between the two entities, followed by partially structural conformation or 3-dimensional shape folding . High selectivity, specificity, and affinity of aptamers offer equal or superior biosensing capabilities to those of enzyme and antibodies which are relatively unstable with high production cost. − Regarding optical sensing, graphene or graphene oxide nanosheets with aptamers exhibit multiple imaging with strong loading ability using DNA/RNA aptamer probes because of high surface-to-thickness ratio, in which a biocompatible sensing platform with strong fluorescence quenching has been demonstrated through fluorescence resonance energy transfer (FRET) from the fluorophore constitutes. − Recently, label-free optical biosensor using Aptamer-SWNT hybrids platform demonstrates the detection of a target protein via large near-infrared fluorescent emission quenching or enhancing responses. − The aptamer-protein interaction enables the proximity of the protein to semiconducting SWNT to lead to the excited-electron transfer from the covalent band of SWNTs to LUMO of molecules/proteins for quenching effect and/or produces a change in the local dielectric environment of the SWNT for enhancing recognition. In this context, the allowance of aptamers folding on SWNTs is critical to the detection of a target protein without aptamer detachment from SWNTs.…”

“…In this context, the allowance of aptamers folding on SWNTs is critical to the detection of a target protein without aptamer detachment from SWNTs. It is recently reported that the refolding evolution of the Aptamer-SWNT hybrids through ligand exchange wrapping methods under the controlled conditions, including thermal-assisted denaturation for refolding aptamer on SWNT, incubation time allowing for appropriately refolded aptamer on SWNT to enhance optical biosensing, and reversible sensing modules within an alginate hydrogel matrix …”

SARS-CoV-2 detection with aptamer-functionalized gold nanoparticles

“…The disulfide bonds formed during storage are reduced with TCEP. Through a refolding process [ 44 ], these aptamers are returned to their 3D confirmation with a specific binding affinity to the spike protein. Subsequently, the aptamers are immobilized on a flat gold-coated glass slide.…”

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

“…Recent studies carried out by Landry et al and Lee et al have shown that DNA aptamers on SWCNT scaffolds can be used to detect certain biologically relevant proteins (Landry et al, 2017; Lee et al, 2018). This label-free fluorescence detection offers many advantages over conventional immunological analytical methods, such as enzyme-linked immunosorbent assays (ELISA) or mass spectroscopy, which lack temporal resolution for real-time quantification of protein levels.…”

“…Furthermore, this method obviates cumbersome purification and labeling steps typically required by more classical approaches. Both RAP1 and HIV-1 (Landry et al, 2017) and platelet-derived growth factor (PDGF) (Lee et al, 2018) were successfully detected using DNA aptamer-SWCNT complexes. Moreover, the RAP1 and HIV-1 sensors were also reported to selectively respond to their target proteins in molecularly complex environments, such as crude, unpurified cell lysates (Landry et al, 2017).…”