Corona exchange dynamics on carbon nanotubes by multiplexed fluorescence monitoring

Abstract

Noncovalent adsorption of DNA on nanoparticles has led to their widespread implementation as gene delivery tools and optical probes. Yet, the behavior and stability of DNA-nanoparticle complexes once applied in biomolecule-rich, in vivo environments remains unpredictable, whereby biocompatibility testing usually occurs in serum. Here, we demonstrate time-resolved measurements of exchange dynamics between solution-phase and adsorbed corona-phase DNA and protein biomolecules on single-walled carbon nanotubes (SWCNTs). We capture real-time binding of fluorophore-labeled biomolecules, utilizing the SWCNT surface as a fluorescence quencher, and apply this corona exchange assay to study protein corona dynamics on ssDNA-SWCNT-based dopamine sensors. We study exchange of two blood proteins, albumin and fibrinogen, adsorbing to and competitively displacing (GT)6 vs. (GT)15 ssDNA from ssDNA-SWCNTs. We find that (GT)15 binds to SWCNTs with a higher affinity than (GT)6 and that fibrinogen interacts with ssDNA-SWCNTs more strongly than albumin. Albumin and fibrinogen cause a 52.2% and 78.2% attenuation of the dopamine nanosensor response, coinciding with 0.5% and 3.7% desorption of (GT)6, respectively. Concurrently, the total surface-adsorbed fibrinogen mass is 168% greater than that of albumin. Binding profiles are fit to a competitive surface exchange model which recapitulates the experimental observation that fibrinogen has a higher affinity for SWCNTs than albumin, with a fibrinogen on-rate constant 1.61-fold greater and an off-rate constant 0.563-fold smaller than that of albumin. Our methodology presents a generic route to assess real-time corona exchange on nanoparticles in solution phase, and more broadly motivates testing of nanoparticle-based technologies in blood plasma rather than the more ubiquitously-tested serum conditions.

Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes

“…However, rational design methodologies for corona phase engineering would benefit from a systematic body of knowledge about how individual polymer properties, such as polymer length, sequence, and chemistry, relate to structural and kinetic properties of the resulting corona phase. As polymer corona cannot be directly visualized with atomic resolution in experiments, important characteristics of the corona phase, such as structural arrangement of polymers, corona thickness, dynamics of assembled polymers on different timescales, kinetic stability of polymer corona, and interactions with other molecules present in the suspension, have to be inferred from experiments with limited resolution [25][26][27][28][29] .…”

Distinguishing dopamine and calcium responses using XNA-nanotube sensors for improved neurochemical sensing

“…Recent work by Pinals et al demonstrated that protein adsorption onto the nanotube surface when sensors are placed in biologically complex solutions can attenuate the optical response of (GT) 6 -SWCNT sensors to dopamine 33 . This decrease was attributed to protein adsorption on the nanotube surface, which resulted in both an increase of the baseline fluorescence and decrease of the final fluorescence intensity post-dopamine addition.…”

Rapid SARS-CoV-2 Detection by Carbon Nanotube-Based Near-Infrared Nanosensors

“…The ssDNA sequence of (GT) 6 was chosen based on high SWCNT suspension yield. The short ssDNA sequence length (12 nucleotides) was informed by previous work demonstrating that shorter ssDNA desorbs faster, and to a greater extent, from SWCNTs in the presence of proteins ( 33, 34 ). (GT) 6 -SWCNTs (2.5 mg/L final concentration) were incubated with ACE2 sensing protein (6.25 mg/L final concentration) in 0.1 M phosphate-buffered saline (PBS) solution to noncovalently passivate the SWCNT surface with protein, schematically represented in Figure 1A ( 34 ).…”

“…The affinity of ACE2 for the ssDNA-wrapped SWCNT surface was assessed by the corona exchange assay ( 33 ). For this assay, Cy5-labeled (GT) 6 ssDNA was tracked as it desorbed from the SWCNT surface and thus de-quenched in the presence of ACE2.…”

“…Corona dynamic studies were done as described previously ( 33 ). Briefly, the same ssDNA-SWCNT suspension protocol was employed, instead using fluorophore-labeled ssDNA-Cy5 (3’ Cy5-labeled custom ssDNA oligos with HPLC purification, Integrated DNA Technologies, Inc.).…”