Effects of Small Molecules on DNA Adsorption by Gold Nanoparticles and a Case Study of Tris(2-carboxyethyl)phosphine (TCEP)

Mitigating dithiothreitol interference to gold/thiol interface in electrochemical detection of cathepsin B activity toward multiplex protease analysis

Proteases are overexpressed at various stages of conditions such as cancers and thus can serve as biomarkers for disease diagnosis. Electrochemical techniques to detect the activity of extracellular proteases have gained attraction due to their multiplexing capability. Here we employ an electrochemical approach based on a 3 × 3 gold (Au) microelectrode array (MEA) functionalized with (2-aminoethyl)ferrocene (AEF) tagged specific peptide substrates to monitor cathepsin B (CB) protease activity. Cleavage of these peptide substrates by proteases leads to an exponential decay in the alternating current voltammetry (ACV) signal. The protease activity is represented by the inverse of the decay time constant (1/τ), which is equal to (kcat/KM)[CB] based on the heterogeneous Michaelis-Menton model. However, the thiol/Au chemisorption linking AEF-peptide to gold electrodes is susceptible to interference by the protease activation reagent dithiothreitol (DTT), causing the peptides to desorb from the Au surface during continuous ACV measurement. This induces a false signal decay, masking the protease activity and reducing the sensor sensitivity. To address this, DTT is removed after activating CB using centrifugal filtration while EDTA is incorporated to maintain the enzyme activity. This allows accurate CB proteolysis kinetics and clarifies the roles of EDTA and DTT in activation. The intrinsic substrate-dependent cleavage by CB to three different peptide substrates has been demonstrated with the MEA chip, showcasing the potential for rapid activity profiling of multiple proteases. The study highlights the importance of understanding the interference of active bioreagents to the thiol/Au interface in broad redox-tagged electrochemical biosensors.

Plasmonic Imaging of Multivalent NTD-Nucleic Acid Interactions for Broad-Spectrum Antiviral Drug Analysis

The discovery and identification of broad-spectrum antiviral drugs are of great significance for blocking the spread of pathogenic viruses and corresponding variants of concern. Herein, we proposed a plasmonic imaging-based strategy for assessing the efficacy of potential broad-spectrum antiviral drugs targeting the N-terminal domain of a nucleocapsid protein (NTD) and nucleic acid (NA) interactions. With NTD and NA conjugated gold nanoparticles as core and satellite nanoprobes, respectively, we found that the multivalent binding interactions could drive the formation of core-satellite nanostructures with enhanced scattering brightness due to the plasmonic coupling effect. The core-satellite assembly can be suppressed in the presence of antiviral drugs targeting the NTD-NA interactions, allowing the drug efficacy analysis by detecting the dose-dependent changes in the scattering brightness by plasmonic imaging. By quantifying the changes in the scattering brightness of plasmonic nanoprobes, we uncovered that the constructed multivalent weak interactions displayed a 500-fold enhancement in affinity as compared with the monovalent NTD-NA interactions. We demonstrated the plasmonic imaging-based strategy for evaluating the efficacy of a potential broad-spectrum drug, PJ34, that can target the NTD-NA interactions, with the IC50 as 24.35 and 14.64 μM for SARS-CoV-2 and SARS-CoV, respectively. Moreover, we discovered that ceftazidime holds the potential as a candidate drug to inhibit the NTD-NA interactions with an IC50 of 22.08 μM from molecular docking and plasmonic imaging-based drug analysis. Finally, we validated that the potential antiviral drug, 5-benzyloxygramine, which can induce the abnormal dimerization of nucleocapsid proteins, is effective for SARS-CoV-2, but not effective against SARS-CoV. All these demonstrations indicated that the plasmonic imaging-based strategy is robust and can be used as a powerful strategy for the discovery and identification of broad-spectrum drugs targeting the evolutionarily conserved viral proteins.

Tackling breast cancer with gold nanoparticles: twinning synthesis and particle engineering with efficacy

The World Health Organization identifies breast cancer as the most prevalent cancer despite predominantly affecting women. Surgery, hormonal therapy, chemotherapy, and radiation therapy are the current treatment modalities. Site-directed nanotherapeutics, engineered with multidimensional functionality are now the frontrunners in breast cancer diagnosis and treatment. Gold nanoparticles with their unique colloidal, optical, quantum, magnetic, mechanical, and electrical properties have become the most valuable weapon in this arsenal. Their advantages include facile modulation of shape and size, a high degree of reproducibility and stability, biocompatibility, and ease of particle engineering to induce multifunctionality. Additionally, the surface plasmon oscillation and high atomic number of gold provide distinct advantages for tailor-made diagnosis, therapy or theranostic applications in breast cancer such as photothermal therapy, radiotherapy, molecular labeling, imaging, and sensing. Although pre-clinical and clinical data are promising for nano-dimensional gold, their clinical translation is hampered by toxicity signs in major organs like the liver, kidneys and spleen. This has instigated global scientific brainstorming to explore feasible particle synthesis and engineering techniques to simultaneously improve the efficacy and versatility and widen the safety window of gold nanoparticles. The present work marks the first study on gold nanoparticle design and maneuvering techniques, elucidating their impact on the pharmacodynamics character and providing a clear-cut scientific roadmap for their fast-track entry into clinical practice.

Probe-labeled electrochemical approach for highly selective detection of 5-carboxycytosine in DNA

5-carboxycytosine (5caC) plays a critical role as an intermediate form in DNA methylation and demethylation processes. Its distribution and quantity significantly influence the dynamic equilibrium of these processes, thereby impacting the normal physiological activities of organisms. However, the analysis of 5caC presents a significant challenge due to its low abundance in the genome, making it almost undetectable in most tissues. In response to this challenge, we propose a selective method for 5caC detection using differential pulse voltammetry (DPV) at glassy carbon electrode (GCE), hinging on probe labeling. The probe molecule Biotin LC-Hydrazide was introduced into the target base and the labeled DNA was immobilized onto the electrode surface with the help of T4 polynucleotide kinase (T4 PNK). Leveraging the precise and efficient recognition of streptavidin and biotin, streptavidin-horseradish peroxidase (SA-HRP) on the surface of the electrode catalyzed a redox reaction involving hydroquinone and hydrogen peroxide, resulting in an amplified current signal. This procedure allowed us to quantitatively detect 5caC based on variations in current signals. This method demonstrated good linearity ranging from 0.01 to 100 nM with a detection limit as low as 7.9 pM. We have successfully applied it to evaluate the 5caC levels in complex biological samples. The probe labeling contributes to a high selectivity for 5caC detection, while the sulfhydryl modification via T4 PNK efficiently circumvents the limitation of specific sequences. Encouragingly, no reports have been made about electrochemical methods for detecting 5caC in DNA, suggesting that our method offers a promising alternative for 5caC detection in clinical samples.

Empirical Optimization of Peptide Sequence and Nanoparticle Colloidal Stability: The Impact of Surface Ligands and Implications for Colorimetric Sensing

Surface ligands play a critical role in controlling and defining the properties of colloidal nanocrystals. These aspects have been exploited to design nanoparticle aggregation-based colorimetric sensors. Here, we coated 13-nm gold nanoparticles (AuNPs) with a large library of ligands (e.g., from labile monodentate monomers to multicoordinating macromolecules) and evaluated their aggregation propensity in the presence of three peptides containing charged, thiolate, or aromatic amino acids. Our results show that AuNPs coated with the polyphenols and sulfonated phosphine ligands were good choices for electrostatic-based aggregation. AuNPs capped with citrate and labile-binding polymers worked well for dithiol-bridging and π-π stacking-induced aggregation. In the example of electrostatic-based assays, we stress that good sensing performance requires aggregating peptides of low charge valence paired with charged NPs with weak stability and vice versa. We then present a modular peptide containing versatile aggregating residues to agglomerate a variety of ligated AuNPs for colorimetric detection of the coronavirus main protease. Enzymatic cleavage liberates the peptide segment, which in turn triggers NP agglomeration and thus rapid color changes in <10 min. The protease detection limit is 2.5 nM.

Surface hydrolysis-designed AuNPs-zwitterionic-glucose as a novel tool for targeting macrophage visualization and delivery into infarcted hearts

Macrophages, innate immune cells, are key players in the maintenance of myocardial homeostasis under normal conditions and tissue repair after injury. The infiltration of macrophages into the injured heart makes them a potentially appealing vehicle for noninvasive imaging and targeted drug delivery of myocardial infarction (MI). In this study, we demonstrated the use of surface hydrolysis-designed AuNPs-zwitterionic-glucose to label macrophages and track their infiltration into isoproterenol hydrochloride (ISO)-induced MI sites noninvasively using CT. The AuNPs-zwitterionic-glucose did not affect the viability or cytokine release of macrophages and were highly taken up by these cells. The in vivo CT images were obtained on Day 4, Day 6, Day 7, and Day 9, and the attenuation was seen to increase in the heart over time compared to the Day 4 scan. In vitro analysis also confirmed the presence of macrophages around injured cardiomyocytes. Additionally, we also addressed the concern of cell tracking or merely AuNP tracking, which is the inherent problem for any form of nanoparticle-labeled cell tracking by using zwitterionic and glucose-functionalized AuNPs. The glucose coated on the surface of AuNPs-zwit-glucose will be hydrolyzed in macrophages, forming only zwitterionic protected AuNPs that cannot be taken up again by endogenous cells in vivo. This will greatly improve the accuracy and precision of imaging and target delivery. We believe this is the first study to noninvasively visualize the infiltration of macrophages into MI hearts using CT, which could be used for imaging and evaluating the possibility of macrophage-mediated delivery in infarcted hearts.

Peptidic Sulfhydryl for Interfacing Nanocrystals and Subsequent Sensing of SARS-CoV-2 Protease

There is a need for surveillance of COVID-19 to identify individuals infected with SARS-CoV-2 coronavirus. Although specific, nucleic acid testing has limitations in terms of point-of-care testing. One potential alternative is the nonstructural protease (nsp5, also known as Mpro/3CLpro) implicated in SARS-CoV-2 viral replication but not incorporated into virions. Here, we report a divalent substrate with a novel design, (Cys)2-(AA)x-(Asp)3, to interface gold colloids in the specific presence of Mpro leading to a rapid and colorimetric readout. Citrate- and tris(2-carboxyethyl)phosphine (TCEP)-AuNPs were identified as the best reporter out of the 17 ligated nanoparticles. Furthermore, we empirically determined the effects of varying cysteine valence and biological media on the sensor specificity and sensitivity. The divalent peptide was specific to Mpro, that is, there was no response when tested with other proteins or enzymes. Furthermore, the Mpro detection limits in Tris buffer and exhaled breath matrices are 12.2 and 18.9 nM, respectively, which are comparable to other reported methods (i.e., at low nanomolar concentrations) yet with a rapid and visual readout. These results from our work would provide informative rationales to design a practical and noninvasive alternative for COVID-19 diagnostic testing-the presence of viral proteases in biofluids is validated.

Investigating the effect of 6-mercaptohexanol on the performance of a biosensor based on nanosurface energy transfer between gold nanoparticles and quantum dots

Nanosurface energy transfer (NSET)-based sensors have been widely developed using various pairs of nanomaterials including gold nanoparticles (AuNPs) and quantum dots (QDs). However, a low signal to background ratio is one of the most important problems that researchers are continually trying to solve. Herein, we present a 6-mercaptohexanol (MCH) modified MCH/DNA-Au-QD sensor for the detection of nucleic acids and MUC1. Interestingly, an unexpected effect of MCH was found in enhancing the fluorescence recovery ratio, therefore yielding a higher signal to background ratio. Through further investigation, we perceive the enhancement as a result of lowering of the NSET efficiency between free DNA-AuNPs and free DNA-QDs, which arises from the stretching of adsorbed DNA on the surface of AuNPs. The employment of MCH endowed the sensor with a wider linear range from 5 nM to 120 nM and a relatively lower LOD of 1.19 nM in nucleic acid detection, outperforming the original DNA-Au-QD sensor. Furthermore, the application of the sensor can be further extended to MUC1 detection. This study offers a better understanding of the NSET process between QDs and AuNPs and also initiates a new approach for the performance optimization of analogous NSET-based sensors.

In situ monitoring of the selective adsorption mechanism of small environmental pollutant molecules on aptasensor interface by attenuated total reflection surface enhanced infrared absorption spectroscopy (ATR-SEIRAS)

In situ monitoring of the interactions and properties of pollutant molecules at the aptasensor interface is being a very hot and interesting topic in environmental analysis since its charming molecule level understanding of the mechanism of environmental biosensors. Attenuated total reflection surface enhanced infrared absorption spectroscopy (ATR-SEIRAS) provides a unique and convenient technique for the in situ analysis, but is not easy for small molecules. Herein, an ATR-SEIRAS platform has been successfully developed to in situ monitor the selective adsorption mechanism of small pollutant molecule atrazine (ATZ) on the aptasensor interface by characteristic N‒H peak of ATZ for the first time. Based on the constructed ATR-SEIRAS platform, a thermodynamics model is established for the selective adsorption of ATZ on the aptasensor interface, described with Langmuir adsorption with a dissociation constant of 1.1 nM. The adsorption kinetics parameters are further obtained with a binding rate constant of 8.08×10⁵ M^-1 s^-1. A promising and feasible platform has therefore successfully provided for the study of the selective sensing mechanism of small pollutant molecules on biosensors interfaces, further broadening the application of ATR-SEIRAS technology in the field of small pollutant molecules.

Sensing Adenosine and ATP by Aptamers and Gold Nanoparticles: Opposite Trends of Color Change from Domination of Target Adsorption Instead of Aptamer Binding

The 27 mer DNA aptamer for adenosine and adenosine 5'-triphosphate (ATP) is a popular model system for designing biosensors. Various strategies have been reported for label-free colorimetric detection using gold nanoparticles (AuNPs). It is generally accepted that free aptamers can protect AuNPs against salt-induced aggregation, whereas target-bound aptamers cannot. However, these studies only considered the aptamer binding to its target, and the adsorption of the aptamer on AuNPs, but none considered the adsorption of target molecules by AuNPs. We herein report that the adsorption of adenosine destabilized citrate-capped AuNPs with an apparent K_d of just 7.7 μM adenosine, whereas that of ATP stabilized the AuNPs because of the negative charges from the triphosphate group. The adsorbed ATP inhibited the adsorption of DNA. Using the aptamer and a nonbinding mutant, ATP and guanosine 5'-triphosphate (GTP) had the same colorimetric response, and so did adenosine and guanosine, regardless of the DNA sequence, indicating that the color change mainly reflected the adsorption of the nucleosides and nucleotides instead of aptamer binding. The related literature examples using this aptamer were classified into three types and individually analyzed, where the reported color changes can all be explained by the adsorption of target analytes.

Dopamine and Melamine Binding to Gold Nanoparticles Dominates Their Aptamer-Based Label-Free Colorimetric Sensing

Target-directed aptamer adsorption by gold nanoparticles (AuNPs) has been widely used to develop label-free colorimetric biosensors. However, the potential interactions between target molecules and AuNPs have not been considered, which may lead to misinterpretation of analytical results. In this work, the detection of dopamine, melamine, and K⁺ was studied as model systems to address this problem. First, dopamine and two control molecules all induced the aggregation of citrate-capped AuNPs with apparent K_d's of 5.8 μM dopamine, 51.6 μM norepinephrine, and 142 μM tyramine. Isothermal titration calorimetry measured the aptamer K_d to be 1.9 μM dopamine and 16.8 μM norepinephrine, whereas tyramine cannot bind. Surface enhanced Raman spectroscopy confirmed direct adsorption of dopamine, and the adsorbed dopamine inhibited the adsorption of DNA. Using a typical salt-induced colorimetric detection protocol, a similar color response was observed regardless of the sequence of DNA, indicating the observed color change reflected the adsorption of dopamine by the AuNPs instead of the binding of dopamine by the aptamer. For this label-free sensor to work, the interaction between the target molecule and AuNPs should be very weak, while dopamine represents an example of strong interactions. For the other two systems, the melamine detection did not reflect aptamer binding either but the K⁺ detection did, suggesting melamine also strongly interacted with AuNPs, whereas K⁺ had very weak interactions with AuNPs. Since each target molecule is different, such target/AuNP interactions need to be studied case-by-case to ensure the sensing mechanism.

Attaching DNA to Gold Nanoparticles With a Protein Corona

DNA-functionalized gold nanoparticles (AuNPs) have been widely used in directed assembly of materials, biosensors, and drug delivery. This conjugate may encounter proteins in these applications and proteins may affect not only DNA adsorption but also the function of the attached DNA. Bovine serum albumin (BSA) with many cysteine residues can strongly adsorb on AuNPs and this conjugate showed high colloidal stability against salt, acid and base. Similar protection effects were also observed with a few other common proteins including catalase, hemoglobin, glucose oxidase, and horseradish peroxidase. DNA oligonucleotides without a thiol label can hardly displace adsorbed BSA, and BSA cannot displace pre-adsorbed DNA either, indicating a strongly kinetically controlled system. Thiolated DNA can be attached at a low density on the AuNPs with a BSA corona. The BSA corona did not facilitate the hybridization of the conjugated DNA, while a smaller peptide, glutathione allowed faster hybridization. Overall, proteins increase the colloidal stability of AuNPs, and they do not perturb the gold-thiol bond in the DNA conjugate, although a large protein corona may inhibit the hybridization function of DNA.

Interactions between gold, thiol and As(iii) for colorimetric sensing

Arsenite cannot crosslink glutathione-capped gold nanoparticles but a high concentration of arsenite can displace adsorbed glutathione, indicating that any two species from gold, thiol and arsenite can react.