Kinetic adsorption profile and conformation evolution at the DNA-gold nanoparticle interface probed by dynamic light scattering

DNA Hairpins and Stabilization of Gold Nanoparticles: Effect of Stem Length and Toehold Composition

This study investigates the effect of DNA hairpins on the stabilization of gold nanoparticles (AuNPs) against salt-induced aggregation (SIA) in label-free colorimetric biosensors. AuNPs were incubated with DNA hairpins of varying stem lengths and toehold sequences, followed by the addition of NaCl, before being subjected to ultraviolet-visible (UV-vis) measurement. Results showed that hairpins with longer stems generally provide better stabilization of AuNPs (18-bp >14-bp >10-bp). No improvement was observed for 14- and 18-bp hairpins with a toehold beyond 8A, which may be attributed to saturated adsorption of hairpins on the gold surface. For 14-bp hairpins with an 8-mer homopolymeric toehold, we observed a stabilization trend of A > C > G > T, similar to the reported trend of ssDNA. For variants containing ≥50% adenine as terminal bases, introducing cytosine or guanine as preceding bases could also result in strong stabilization. As the proportion of adenine decreases, variants with guanine or thymine provide less protection against SIA, especially for guanine-rich hairpins (≥6G) that could form G-quadruplexes. Such findings could serve as guidelines for researchers to design suitable DNA hairpins for label-free AuNP-based biosensors.

Non-Invasive, Reliable, and Fast Quantification of DNA Loading on Gold Nanoparticles by a One-Step Optical Measurement

An exquisite, versatile, and reproducible quantification of DNA loading on gold nanoparticles (Au NPs) has long been pursued because this loading influences the analytical, therapeutic, and self-assembly behaviors of DNA-Au NPs. Nevertheless, the existing methods used thus far rely solely on the invasive detachment and subsequent spectroscopic quantification of DNA, which are error-prone and highly dependent on trained personnel. Here, we present a non-invasive optical framework that can determine the number of DNA strands on Au NPs by versatile one-step measurement of the visible absorption spectra of DNA-Au NP solutions without any invasive modifications or downstream processes. Using effective medium theory in conjunction with electromagnetic numerical calculation, the change in DNA loading density, resulting from varying the ion concentration, Au NP size, DNA strand length, and surrounding temperature, can be tracked in situ merely by the one-step measurement of visible absorption spectra, which is otherwise impossible to achieve. Moreover, the simplicity and robustness of this method promote reproducible DNA loading quantification regardless of experimental adeptness, which is in stark contrast with existing invasive and multistep methods. Overall, the optical framework outlined in this work can contribute to democratizing research on DNA-Au NPs and facilitating their rapid adoption in transformative applications.

A highly specific aptamer probe targeting PD-L1 in tumor tissue sections: Mutation favors specificity

Although DNA aptamers can show comparable affinity to antibodies and have the advantage of having high batch-to-batch consistency, they often suffer from unsatisfied specificity for complex samples. The limited library size used for aptamer in vitro isolation (SELEX) has been recognized as one of the major reasons. Programmed cell death-ligand 1 (PD-L1) is both a key protein in cancer diagnostics and also immunotherapy. We report here a DNA aptamer that highly specifically binds PD-L1 expressed on the surface of various cancer cells and multiple types of tissue sections. The aptamers were selected from a DNA library containing a type II restriction endonuclease Alu I recognition site in the middle of the 40-nt random sequences, against recombinant PD-L1 rather than the whole cell or tissue section. The library enrichment was achieved by Alu I mediated-SELEX, named as REase-SELEX, in which Alu I cut off the non-binders at the recognition site and, more importantly, induced library mutations to substantially increase the library diversity. 8-60, a representative aptamer with high affinity (K_D = 1.4 nM determined by SPR) successfully detected four types of cancer cells with PD-L1 expression levels from low to high by flow cytometry, normal human tonsil (gold standard for PD-L1 antibody evaluation), clinical non-small cell lung cancer (high PD-L1 expression level), and malignant melanoma (low PD-L1 expression level) tissue sections by fluorescence microscopy imaging, showing unprecedented high specificity. The results demonstrate that 8-60 is an advanced probe for PD-L1 cancer diagnostics and mutations in SELEX greatly favor aptamer specificity.

Novel BiOBr by compositing low-cost biochar for efficient ciprofloxacin removal: the synergy of adsorption and photocatalysis on the degradation kinetics and mechanism insight

C/BiOBr composite materials were synthesized via a simple one-step solvothermal method, with C derived from biochar, which was prepared from the low-cost straw. The samples were characterized by SEM, XRD, XPS and PL. The 2% C/BiOBr composite material showed a noticeable adsorption and photocatalysis synergistic effect to remove CIP. The adsorption rate and degradation rate were 1.45 times and 1.8 times that of BiOBr. The adsorption kinetics and isotherms of CIP on C/BiOBr were analyzed with the pseudo-second-order kinetic and Langmuir models. The degradation efficiency was 96.8% after 60 min of irradiation. High stability and degradability were still maintained after four cycles. The Bi-O-C bond accelerated electron transition and inhibited the rapid photogenerated electron pair recombination. In the degradation process of CIP, ˙O2 - and h+ played a significant role. Experiments proved that C/BiOBr is practical and feasible for the degradation of CIP under the synergistic effect of adsorption and photocatalysis.

PD-L1 aptamer isolation via Modular-SELEX and its applications in cancer cell detection and tumor tissue section imaging

PD-1/PD-L1 is an important pathway in immunotherapy and a high PD-L1 expression level in tumor tissues is an essential prerequisite for PD-1/PD-L1 blocking-based therapy. The PD-L1 expression level in tumor tissue sections is currently detected via immunohistochemistry (IHC) using anti-PD-L1 antibodies from various resources, which has the disadvantage of inconsistent results. As synthetic affinity ligands, aptamers have good batch-to-batch consistency and have been demonstrated to have great potential for use in biomedical applications. In this study, we isolated PD-L1 aptamers using a combination method, named Modular-SELEX (systematic evolution of ligands by exponential enrichment), which includes three sequentially performed modules: the affinity module, the specificity module, and the compatibility module. Three rounds of magnetic crosslinking precipitation (MCP)-SELEX, three rounds of Capture-SELEX, and two rounds of Tissue-SELEX were respectively performed in the corresponding three modules to significantly and efficiently improve the native affinity, specificity, and compatibility of the enriched library. The isolated aptamer Clon-3 had nanomolar binding affinity, as determined via both homogeneous and PD-L1 immobilized affinity assays. Clon-3 could be used to recognize various cancer cells with distinct PD-L1 expression levels using flow cytometry. The PD-L1 expression levels in normal human tonsils (the gold standard for anti-PD-L1 antibody) and non-small cell lung cancer tissue sections stained using Cy5.5-labeled Clon-3 were also successfully imaged using a confocal microscope. The fluorescence intensities of the tissue sections were in good agreement with their actual PD-L1 expression levels as confirmed via IHC.

Enhanced Sulfamerazine Removal via Adsorption–Photocatalysis Using Bi2O3–TiO2/PAC Ternary Nanoparticles

The presence of sulfonamides (SAs) in water has received increasing attention due to the risk to ecosystems. The adsorption and photocatalysis performance for sulfamerazine (SMZ) of Bi2O3–TiO2 supported on powdered activated carbon (Bi2O3–TiO2/PAC) nanoparticles was evaluated. The amount of doped Bi2O3 not only influenced the photocatalytic performance but also impacted the adsorption capacity. The adsorption mass transfer mechanism of Bi2O3–TiO2/PAC was elucidated and is further discussed in combination with the photocatalytic mechanism. It was indicated that Bi2O3–TiO2/PAC(10%–700 °C) performed best, and the SMZ removal by the adsorption–photocatalysis of Bi2O3–TiO2/PAC(10%–700 °C) reached 95.5%. Adsorption onto active sites was a major adsorption step, and external diffusion was assisted. Superoxide radical (●O2−) and hole (h+) were identified as the major reactive oxygen species (ROS) for SMZ removal. Benzene ring fracture, SO2 extrusion and nitrogenated SMZ were proposed as the main pathways for photocatalysis. Meanwhile, alkaline conditions enhanced photocatalytic performance, while contrary effects were observed for adsorption. The adsorption–photocatalysis removal performance for SMZ in lake water was better than that for river water. It can be generalized for the potential application of photocatalysis coupling with adsorption to remove refractory antibiotics in water.

Size Matters: Nano-Biochar Triggers Decomposition and Transformation Inhibition of Antibiotic Resistance Genes in Aqueous Environments

Antibiotic resistance genes (ARGs) are considered to be a type of emerging contaminant; their interaction with biochar (BC) could affect their dissemination and fate in the environment. Although adsorption of ARGs onto bulk-BC has been reported, the interaction with nanosized BC (nano-BC) is largely unknown. In this study, the interactions of a model extracellular DNA (eDNA, calf thymus DNA) and two typical ARGs (ampC and ermB) extracted from a natural river with bulk- and nano-BCs from two pyrolysis temperatures (400 and 700 °C) were investigated. Only adsorption was observed on bulk-BCs, while not only adsorption but also fragmentation of these eDNA molecules was found to occur on nano-BCs. Also, their replication was greatly inhibited by nano-BCs. The electron paramagnetic resonance results indicated that hydroxyl radicals produced from persistent free radicals (PFRs) on nano-BCs played a major role in the damage of eDNA. Moreover, the direct contact with nonradical reacting sites and PFRs on nano-BCs also contributed to the decay of eDNA. Comparatively, PFRs in bulk-BCs were difficult to be reached by eDNA because of steric hindrance and played a negligible role in destroying eDNA. These findings highlight the importance of the size effect in evaluating the reactivity and related environmental risks of PFRs on BC and improve our understanding on the interaction between ARGs and BC.

Laser-triggered collaborative chemophotothermal effect of gold nanoparticles for targeted colon cancer therapy

Nanotechnology has shown advantages for cancer treatment. Multimodal nanoparticles (NPs) combining chemotherapy and photothermal therapy are promising and elicit synergetic benefit. However, there were still less multifunctional nanomaterials with good targeting and anti-tumor property applied as the colon cancer therapeutic strategy. In this study, we designed the gold NPs modified with AS1411 and DNA riched of GC intercalation (hairpin DNA) with doxorubicin (DOX) for targeted chemotherapy and NIR laser-triggered chemo-photothermal effect (PTT). We took advantage of PTT effect to realize DOX release from hairpin DNA. We also demonstrated AS1411 based NPs exhibited remarkable targeted binding towards SW480 colon cancer cells in vitro and enhanced uptake inside the cells. Strikingly, AS1411 based NPs exhibited the most efficient cytotoxicity and markedly enhanced inhibition effect on cells proliferation to SW480 cells under laser exposure when compared to the NPs merely with PTT or chemotherapy. Our study appears to provide an alternative nanoplatform with good targeted and chemo-photothermal therapy against colon cancer.

Aptamer-Gold(III) Complex Nanoparticles: A New Way to Detect Cu, Zn SOD Glycoprotein

Aptamers are small biomolecules composed of 20-100 nucleotides that recognize target molecules in three-dimensional structures. These natural targeting molecules have attracted interest in the biomedical field as biomarkers for cancer diagnostics. In this study, we investigated the interaction of a characteristic aptamer with its target protein, Cu, Zn superoxide dismutase (SOD 4), on a gold nanoparticle (AuNP) surface under experimental conditions. For this purpose, we applied two protocols to coat SOD 4 aptamer (APT) on the nanoparticle surface: carbodiimide chemistry (EDC/NHS) (Method ON) and a complexation methodology (Method IN). The nano-aptamer's interactions with SOD 4 were detected by UV-vis absorption and Raman spectroscopy in a range of protein concentrations (from 1 μM to 50 nM). We believe that the interaction is heavily dependent on the nature of the biomarker (SOD 4) and also on the steric arrangement of the aptamer on the gold nanoparticle surface. The lowest detectable concentration (limit of detection, LOD) was about 2 nM for APT IN PEG-AuNPs and 8 nM for APT ON PEG-AuNPs. For the first time, we demonstrated a very sensitive detection of SOD 4 in the nanomolar concentration range with new ways of biosensor synthesis (APT IN and ON), providing a very strong tool to understand the effect of aptamer conformation to detect SOD 4.

Poly-adenine regulated DNA density on AuNPs to construct efficient DNA walker for microRNA-21 detection

DNA-modified gold nanoparticles (AuNPs) are useful nanomaterials for detecting multiple molecules. However, their performance is greatly dependent on the density of probe DNA on the surface of AuNPs. Here, we used Poly-adenine (PolyA) to regulate the surface density of probe DNA to achieve a highly efficient DNA walking biosensor system to detection miRNA-21. The movement track of the biosensor system consists of PolyA-DNA probe was connected to AuNPs, and exonuclease III (Exo III) acted as a motor driving the walker movement to achieve signal amplification. By optimizing the length of PolyA, the surface density of probe DNA was changed, thereby affecting the target binding and enzymatic processing of the bound probes, which ultimately enhanced the sensitivity and reduced timeliness of the DNA walker. Furthermore, the designed PolyA-DNA probe exhibits an outstanding sensitivity, due to the effect of density regulation, which is 7.9 times and 11.1 times lower than those of the SH-DNA and the free-DNA, respectively. In addition, the hairpin structure of DNA probe locates fluorophore at a zone adjacent to AuNPs surface, which reduces the background signal by 1.1 times compared with traditional straight probe. In this work, the biosensor system shows a high selectivity towards miRNA-21. Moreover, the biosensor system has been demonstrated to be potentially useful for the miRNA-21 detection in human serum with the recoveries of 93.2%-110.0% and has high repeatability. Considering these advantages, this PolyA-regulated DNA walking biosensor system has great potential as a routine tool for miRNA detection and has wide applications in the field of biomedical analysis.

Long-Term Functional Stability of Functional Nucleic Acid-Gold Nanoparticle Conjugates with Different Secondary Structures

Thiolated functional nucleic acid-gold nanoparticle conjugates (FNA-AuNPs) are the core recognition elements in biosensors. The long-term functional stability (LTFS) is critical for their practical applications and, however, has been overlooked. Here we report on the huge effects of multiple experimental factors on LTFS, including spacer- and buffer-composition, secondary structures of FNAs, and surface blocking. We quantitatively determined these effects by measuring the relative hybridization capacity (RHC, the relative amount of complementary DNA hybridized with the same amount of conjugates) for linear DNA-AuNP or the relative signal change generated by their function (RSC-F) for molecular beacon (MB) and G-quadruplex (G4)-AuNPs. There is a positive relationship between the spacer affinity [oligoadenine (A₁₀) > oligothymine (T₁₀) > oligoethlyene glycol (EG₁₈)] of the linear DNA probes and the LTFS. The LTFS of linear DNA-AuNP in phosphate buffer (PB) was much better than that in Good's buffers such as HEPES, Tris, and MES. The secondary structure of FNAs also strongly impacted the LTFS, showing the substantially decreased LTFS from G4- to linear DNA- to MB-AuNPs, where EG₁₈ spacer was used for all these conjugates. The surface blocking of FNA-AuNPs greatly improved the LTFS. We experimentally determined that the LTFS of FNA-AuNPs was directly related to the dissociation of DNAs caused by the in situ generated H₂O₂ due to the oxidase activity of AuNP and thereby oxidation of Au-thiol bonds. The oxidase activity of AuNP was favored at high temperature, low pH, high AuNP concentration, high Good's buffer concentration, and high salt concentration, corresponding well with the positive effects of high affinity spacer, PB, and surface blocking on the LTFS of FNA-AuNPs. Our study has implications on both fundamental surface science and practical applications.

A nitrile-mediated aptasensor for optical anti-interference detection of acetamiprid in apple juice by surface-enhanced Raman scattering

Currently, the detection of pesticide is critical for food safety assurance, but it is still challenging due to the presence of biological interferents from complex food matrix. In this study, we developed an optical anti-interference surface-enhanced Raman scattering (SERS) aptasensor system for trace detection of acetamiprid. 4-(Mercaptomethyl) benzonitrile (MMBN) containing CN bond was used as Raman tag to provide a sharp peak (2227 cm^-1) in the Raman-silent spectral window (1800-2800 cm^-1) where no Raman signal existed for most of molecules. Gold nanoparticles (AuNPs) bonded with polyadenine (polyA)-mediated aptamer and Raman tag (MMBN-AuNPs-aptamer) was synthesized as Raman probe, while the complementary DNA (cDNA) conjugated with AgNPs-decorated silicon wafer (AgNPs@Si) was used as SERS substrate. As acetamiprid molecule could specifically combine with aptamer, preventing the formation of MMBN-AuNPs-aptamer-cDNA-AgNPs@Si (expressed as "Au-AgNPs@Si") hybrid through DNA sequence linking, Raman signal intensities of MMBN in Au-AgNPs@Si decreased when the concentration of acetamiprid increased. Under the optimum assay condition, the proposed method displayed a linear response for acetamiprid detection in the range of 25-250 nM with a low detection limit of 6.8 nM. Finally, the developed aptasensor was successfully used to determine acetamiprid content in apple juice. Accordingly, this novel anti-interference SERS aptasensor could be a promising acetamiprid sensor for food safety assurance.

A label-free colorimetric aptasensor based on controllable aggregation of AuNPs for the detection of multiplex antibiotics

We devise a novel colorimetric aptasensor for multiplex antibiotics based on an ss-DNA fragment coordinately controlling gold nanoparticles (AuNPs) aggregation. The multifunctional aptamer (Apt) was elaborately designed to be adsorbed on AuNPs surfaces acting as a binding element for antibiotics and a molecular switch. Chloramphenicol (CAP) and tetracycline (TET) were selected as the model antibiotics. When one kind of antibiotics was added, the specifically recognized fragment of Apt can bind to it and dissociated, and the non-specific one coordinately controls AuNPs aggregation under high-salt conditions. Hence, different color changes of AuNPs solution can be used as the signal readout. The aptasensor exhibited remarkable selectivity and sensitivity for separate detection of TET and CAP, and the detection limits are estimated to be 32.9 and 7.0 nM, respectively. The analysis with the absorption spectroscopy and the smartphone are applied to detect antibiotics in real samples with consistent results and desirable recoveries.

Enhanced degradation of ciprofloxacin by graphitized mesoporous carbon (GMC)-TiO2 nanocomposite: Strong synergy of adsorption-photocatalysis and antibiotics degradation mechanism

In order to achieve remarkable synergy between adsorption and photocatalysis for antibiotics elimination from water, in this study, a graphitized mesoporous carbon (GMC)-TiO₂ nanocomposite was successfully synthesized by an extended resorcinol-formaldehyde (R-F) method. In the composite, the lamellar GMC nanosheets possessed large specific surface area and mesoporous structure, and could adsorb and enrich antibiotics effectively. This could not only reduce the antibiotic concentration in water shortly, but also greatly increase the chances for antibiotics to contact with and be degraded by photocatalysts and active species. Interestingly, GMC could also facilitate the transportation of photogenerated electrons to further improve the photocatalytic efficiency of TiO₂, and 15 mg/L ciprofloxacin (CIP) could be totally mineralized in 1.5 h. Meanwhile, the biological inhibition of reaction solution on luminescence bacteria decreased obviously with antibiotics degradation until non-toxicity, reinforcing the thorough elimination of antibiotics. Besides, from the viewpoint of organic chemistry, several plausible CIP degradation pathways were established using HPLC-MS technique, and an interesting intermediate with five-membered ring structure was firstly proposed, which is helpful to deeply understand CIP degradation. Strong synergy between adsorption and photocatalysis, along with quick and efficient antibiotics elimination, double confirm the great potential of GMC-TiO₂ nanocomposite for practical antibiotic wastewater purification.

Heterogeneous Kinetics in the Functionalization of Single Plasmonic Nanoparticles

The functionalization of gold nanoparticles with DNA has been studied extensively in solution; however, these ensemble measurements do not reveal particle-to-particle differences. Here we study the functionalization of gold nanorods with thiolated single-stranded DNA (ssDNA) at the single-particle level. We exploit the sensitivity of the plasmon resonance to the local refractive index to study the functionalization in real time using single-particle spectroscopy. We find particle-to-particle variations of the plasmon shift that are attributed to the particle size distribution and variations in ssDNA coverage. We find that the ssDNA coverage varies by ∼10% from particle to particle, beyond the expected variation due to Poisson statistics. Surprisingly, we find binding rates that differ from particle to particle by an order of magnitude, even though the buffer conditions are identical. We ascribe this heterogeneity to a distribution of activation energies caused by particle-to-particle variations in effective surface charge. These results yield insight into the kinetics of biofunctionalization at the single particle level and highlight that significant kinetic heterogeneity has to be taken into account in applications of functional particles. The presented methodology is easily extended to any nanoparticle coating and can be used to optimize functionalization protocols.

Polyadenine-Modulated DNA Conformation Monitored by Surface-Enhanced Raman Scattering (SERS) on Multibranched Gold Nanoparticles and Its Sensing Application

This work proposes a facile way to modulate the conformation of DNA from the "Lie-Down" to the "Stand-Up" conformation on the surface of multibranched gold nanoparticles (AuNPs). This is realized by regulating the length of polyadenine (polyA) linked to the DNA sequence and/or the hybridization of this sequence with the target DNA, and can be monitored by the Raman signal owing to the excellent performance of multibranched AuNPs (AuNSs) as a surface-enhanced Raman scattering (SERS) substrate and the distance change between the Raman reporter and the substrate. The probable mechanism, which depends on the repulsion of polyA from the sequence and the tip assembly, has also been probed through theoretical simulation using the finite difference time domain method. By virtue of this strategy, a conformation-transformation-based DNA@AuNS sensor is constructed for the identification of a specific oligonucleotide, which has been used for the detection of DNA sequences associated with Severe Acute Respiratory Syndrome (SARS). This strategy leads to a novel sensing platform with good extendibility for DNA analysis, and provides a powerful protocol for facilitating the cognition of DNA conformation on metal surfaces.

Satellite-like Gold Nanocomposites for Targeted Mass Spectrometry Imaging of Tumor Tissues

We have developed a simple, rapid, high-throughput cancer diagnosis system using functional nanoparticles (NPs) consisting of poly(catechin) capped-gold NPs (Au@PC NPs) and smaller nucleolin-binding aptamer (AS1411) conjugated gold NPs (AS1411-Au NPs). The AS1411-Au NPs/Au@PC NP is used as a targeting agent in laser desorption/ionization mass spectrometry (LDI-MS)-based tumor tissue imaging. Self-assembled core-shell Au@PC NPs are synthesized by a simple reaction of tetrachloroaurate(III) with catechin. Au@PC NPs with a well-defined and dense poly(catechin) shell (~40-60 nm) on the surface of each Au core (~60-80 nm) are obtained through careful control of the ratio of catechin to gold ions, as well as the pH of the reaction solution. Furthermore, we have shown that AS1411-conjugated Au NPs (13-nm) self-assembled on Au@PC NP can from a satellite-like gold nanocomposite. The high density of AS1411-Au NPs on the surface of Au@PC NP enhances multivalent binding with nucleolin molecules on tumor cell membranes. We have employed LDI-MS to detect AS1411-Au NPs/Au@PC NPs labeled nucleolin-overexpressing MCF-7 breast cancer cells through the monitoring of Au cluster ions ([Au_n]⁺; 1 ≤ n ≤ 3). The ultrahigh signal amplification from Au NPs through the formation of a huge number of [Au_n]⁺ ions results in a sensing platform with a limit of detection of 100 MCF-7 cells mL^-1. Further, we have applied the satellite-like AS1411-Au NPs/Au@PC NP nanocomposite as a labeling agent for tumor tissue imaging by LDI-MS. Our nanocomposite-assisted LDI-MS imaging platform can be extended for simultaneous analysis of different tumor markers on cell membranes when using different ligand-modified metal nanoparticles.

Utilization of unmodified gold nanoparticles for label-free detection of mercury (II): Insight into rational design of mercury-specific oligonucleotides

Colorimetric detection of mercury (II) with the use of DNA oligonucleotides and unmodified gold nanoparticles (AuNPs) as indicators has been extensively studied. This study provides in-depth insights into the rational design of mercury-specific oligonucleotides (MSO) in the biosensing system. The leftover bases of MSO, as a result of the formation of T-Hg²⁺-T base pairs, can adsorb on the AuNPs and hinder their aggregation at concentrations of salt. This phenomenon was directly verified by the changes in particle sizes characterized by dynamic light scattering for the first time. Based on these findings, we proposed a rational design for the MSO with approximately 20-fold improvement in detection sensitivity. The detection limit of the proposed assay decreased to 15nM with a linear working range from 50nM to 300nM for Hg²⁺. The cross-reactivity against eight other metal ions was negligible compared with the response to Hg²⁺. Considering the diverse applications of AuNPs with oligonucleotides, this study can serve as a good reference and provides important implications in sensing and DNA-directed nanoparticle assembly.

Rapid, Surfactant-Free, and Quantitative Functionalization of Gold Nanoparticles with Thiolated DNA under Physiological pH and Its Application in Molecular Beacon-Based Biosensor

The controlled attachment of thiolated DNA to gold nanoparticles (AuNPs) dictates many applications. This is typically achieved by either "aging-salting" processes or low-pH method, where either Na⁺ or H⁺ is used to minimize charge repulsion and facilitate attachment of thiolated DNA onto AuNPs. However, the "aging-salting" process takes a long time, and is prone to aggregation when used with larger AuNPs. Surfactants are needed to precoat and thereby enhance the stability of AuNPs. The low-pH method can disrupt the structural integrity of DNAs. We report here an oligoethylene glycol (OEG) spacer-assisted method that enables quantitative and instantaneous attachment at physiological pH without the need for surfactants. The method is based on our finding that an uncharged OEG spacer as short as six EG units can effectively shield against repulsion between AuNPs and DNAs, substantially enhancing both the adsorption kinetics and thermodynamics of thiolated DNAs. We applied this to thiolated DNAs of various lengths and thiol modification positions and to large AuNPs. Importantly, our method also allows for the direct immobilization of thiolated molecular beacons (MB), and avoids particle aggregation due to intermolecular hydrogen bonding. The prepared MB-AuNPs were successfully used for the fluorescent detection of target DNA at nanomolar concentrations. The OEG spacer appears to offer a highly effective parameter for tuning DNA adsorption kinetics and thermodynamics besides pH and salt, providing a novel means for highly controllable and versatile functionalization of AuNPs.

Interaction of new kinase inhibitors cabozantinib and tofacitinib with human serum alpha-1 acid glycoprotein. A comprehensive spectroscopic and molecular Docking approach

In the current study we have investigated the interaction of newly approved kinase inhibitors namely Cabozantinib (CBZ) and Tofacitinib (TFB) with human Alpha-1 acid glycoprotein (AAG) under simulated physiological conditions using fluorescence quenching measurements, circular dichroism, dynamic light scattering and molecular docking methods. CBZ and TFB binds to AAG with significant affinity and the calculated binding constant for the drugs lie in the order of 10(4). With the increase in temperature the binding constant values decreased for both CBZ and TFB. The fluorescence resonance energy transfer (FRET) from AAG to CBZ and TFB suggested the fluorescence intensity of AAG was quenched by the two studied drugs via the formation of a non-fluorescent complex in the static manner. The molecular distance r value calculated from FRET is around 2 nm for both drugs, fluorescence spectroscopy data was employed for the study of thermodynamic parameters, standard Gibbs free energy change at 300 K was calculated as -5.234 kcal mol(-1) for CBZ-AAG interaction and -6.237 kcal mol(-1) for TFB-AAG interaction, standard enthalpy change and standard entropy change for CBZ-AAG interaction are -9.553 kcal mol(-1) and -14.618 cal mol(-1) K(-1) respectively while for AAG-TFB interaction, standard enthalpy and standard entropy change was calculated as 4.019 kcal mol(-1) and 7.206 cal mol(-1) K(-1) respectively. Protein binding of the two drugs caused the tertiary structure alterations. Dynamic light scattering measurements demonstrated the reduction in the hydrodynamic radii of the protein. Furthermore molecular docking results suggested the Hydrophobic interaction and hydrogen bonding were the interactive forces in the binding process of CBZ to AAG while in case of TFB only hydrophobic interactions were found to be involved, overlap of the binding site for two studied drugs on the AAG molecule was revealed by docking results.

Gold nanoparticles modified with self-assembled hybrid monolayer of triblock aptamers as a photoreversible anticoagulant

We demonstrated that thrombin-binding aptamer-conjugated gold nanoparticles (TBA-Au NPs), prepared from a self-assembled hybrid monolayer (SAHM) of triblock aptamers on Au NPs (13 nm), can effectively inhibit thrombin activity toward fibrinogen. The first block poly(adenine) at the end of the triblock TBA was used for the self-assembly on Au NP surface. The second block, in the middle of TBA, was composed of oligonucleotides that could hybridize with each other. The third block, containing TBA15 (15-base, binding to the exosite I of thrombin) and TBA29 (29-base, binding to the exosite II of thrombin) provided bivalent interaction with thrombin. The SAHM triblock aptamers have optimal distances between TBA15 and TBA29, aptamer density, and orientation on the Au NP surfaces. These properties strengthen the interactions with thrombin (Kd=1.5 × 10(-11)M), resulting in an extremely high anticoagulant potency. The thrombin clotting time mediated by SAHM TBA15/TBA29-Au NPs was >10 times longer than that of four commercially available drugs (heparin, argatroban, hirudin, or warfarin). In addition, the rat-tail bleeding assay time further demonstrated that the SAHM TBA15/TBA29-Au NPs were superior to heparin. The SAHM TBA15/TBA29-Au NPs exhibited excellent stability in the human plasma (half-life >14 days) and good biocompatibility (low cytotoxicity and hemolysis). Most interestingly, the inhibition by SAHM TBA15/TBA29-Au NPs was controllable by the irradiation of green laser, via heat transfer-induced TBA release from Au NPs. Therefore, these easily prepared (self-assembled), low cost (non-thiolated aptamer), photo-controllable, multivalent TBA15/TBA29-Au NPs (high density of TBA15/TBA29 on Au NPs) show good potential for the treatment of various diseases related to blood-clotting disorders. Our study opens up the possibility of regulation of molecule binding, protein recognition, and enzyme activity using SAHM aptamer-functionalized nanomaterials.

Nanoprobe-Enhanced, Split Aptamer-Based Electrochemical Sandwich Assay for Ultrasensitive Detection of Small Molecules

It is quite challenging to improve the binding affinity of antismall molecule aptamers. We report that the binding affinity of anticocaine split aptamer pairs improved by up to 66-fold by gold nanoparticles (AuNP)-attached aptamers due to the substantially increased local concentration of aptamers and multiple and simultaneous ligand interactions. The significantly improved binding affinity enables the detection of small molecule targets with unprecedented sensitivity, as demonstrated in nanoprobe-enhanced split aptamer-based electrochemical sandwich assays (NE-SAESA). NE-SAESA replaces the traditional molecular reporter probe with AuNPs conjugated to multiple reporter probes. The increased binding affinity allowed us to use 1,000-fold lower reporter probe concentrations relative to those employed in SAESA. We show that the near-elimination of background in NE-SAESA effectively improves assay sensitivity by ∼1,000-100,000-fold for ATP and cocaine detection, relative to equivalent SAESA. With the ongoing development of new strategies for the selection of aptamers, we anticipate that our sensor platform should offer a generalizable approach for the high-sensitivity detection of diverse targets. More importantly, we believe that NE-SAESA represents a novel strategy to improve the binding affinity between a small molecule and its aptamer and potentially can be extended to other detection platforms.

Bovine thrombin enhances the efficiency and specificity of polymerase chain reaction

The polymerase chain reaction (PCR) has become one of the central techniques in molecular biology since its invention. However, PCR can be fraught with difficulties in various situations, and it is desirable to find novel PCR enhancers suitable for universal applications. Here we show that bovine thrombin (BT), a well-known coagulation protein, is exceptionally effective at preventing the formation of primer dimers and enhancing the formation of the desired PCR products. The PCR enhancement effects of BT were demonstrated by testing various types of samples, including low-copy synthetic single-stranded DNAs (ssDNAs), synthetic ssDNA pools, human genomic DNA, and hepatitis B virus genomic DNA. In addition, BT was also able to effectively relieve PCR inhibition by nanomaterial inhibitors such as gold nanoparticles (AuNPs) and graphene oxide (GO). Compared with BSA, one of the most popular PCR enhancers, BT was more effective and required concentrations 18-178 times less than that of BSA to achieve a similar level of PCR enhancement.