Cooperative Metal Ion-Mediated Adsorption of Spherical Nucleic Acids with a Large Hysteresis

Spherical Nucleic Acid Probes on Floating-Gate Field-Effect Transistor Biosensors for Attomolar-Level Analyte Detection

Field-effect transistor (FET) sensors are attractive for the label-free detection of target biomolecules, offering ultrahigh sensitivity and a rapid response. However, conventional methods for modifying biomolecular probes on sensors often involve intricate and time-consuming procedures that require specialized training. Herein, we propose a simple and versatile approach to functionalize floating-gate (FG) FET sensors by exploiting the strong binding ability of polyvalent interactions and the three-dimensional structure of densely functionalized spherical nucleic acids (SNAs). Crucially, the SNAs can be easily deposited onto a dielectric layer under mild conditions, ensuring stable immobilization of the probes. Further, the SNAs show efficient and robust immobilization on various dielectric layers including Y2O3, Ta2O5, and HfO2, forming conjugates that resist denaturation by various agents. By modifying the DNA sequence within the SNAs, we achieved highly sensitive FG-FET biosensors for DNA, adenosine triphosphate, and viral nucleic acids at the attomolar level. For clinical samples detection, unamplified enterovirus 71 RNA at levels as low as 0.13 copies μL-1 was detected within 100 s. Moreover, the sensor attained 100% accuracy for analyte detection in both positive and negative samples. Our findings provide a general and simple method for fabricating FET-based biochemical sensors and demonstrate that the SNA-modified FG-FET biosensor is a versatile and reliable integrated platform for ultrasensitive biomarker detection.

Metal-Mediated DNA Adsorption on Carboxylated, Hydroxylated, and Hydrogenated Nanodiamonds

Nanodiamonds (NDs) have attracted considerable attention owing to their quantum properties and versatility in biological applications. In this study, we systematically investigated the adsorption of DNA oligonucleotides onto NDs with three types of surface groups: carboxylated (COOH-), hydroxylated (OH-), and hydrogenated (H-). Among them, only the H-NDs showed fluorescence quenching property that is useful for real-time DNA adsorption kinetic studies. The effect of common metal ions on DNA adsorption was studied. In the presence of Na+, the order of DNA adsorption efficiency was H- > OH- > COOH-, whereas all the NDs showed a similar DNA adsorption efficiency in the presence of divalent metal ions such as Ca2+ and Zn2+. Desorption studies revealed that hydrogen bonding and metal-mediated interactions were dominant for the adsorption of DNA, and the H-NDs exhibited extraordinarily tight DNA adsorption. Finally, a fluorescently labeled DNA was adsorbed on NDs for DNA detection, and the COOH-NDs had the highest target specificity, and a detection limit of 1.4 nM was achieved. This study indicates the feasibility of using metal ions to mediate the physical adsorption of DNA to NDs and compares various NDs with graphene oxide for fundamental understanding.

Spherical DNA for Probing Wettability of Microplastics

Wettability of microplastics may change due to chemical or physical transformations at their surface. In this work, we studied the adsorption of spherical nucleic acids (SNAs) with a gold nanoparticle core and linear DNA of the same sequence to probe the wettability of microplastics. Soaking microplastics in water at room temperature for 3 months resulted in the enhancement of SNA adsorption capacity and affinity, whereas linear DNA adsorption was the same on the fresh and soaked microplastics. Drying of the soaked microplastics followed by rehydration decreased the adsorption of the SNA, suggesting that the effect of soaking was reversible and related to physical changes instead of chemical changes of the microplastics. Raman spectroscopy data also revealed no chemical transformations of the soaked microplastics. Heating of microplastics over a short period induced a similar effect to long-term soaking. We propose that soaking or heating removes air entrapped in the nanosized pores at the water-plastic interface, increasing the contact surface area of the SNA to afford stronger adsorption. However, such wetted porosity would not change the adsorption of linear DNA because of its much smaller size.

Adsorption of Linear and Spherical DNA Oligonucleotides onto Microplastics

Microplastic pollution of water and food chains can endanger human health. It has been reported that environmental DNA can be carried by microplastics and spread into the ecosystem. To better comprehend the interactions between microplastics and DNA, we herein investigated the adsorption of DNA oligonucleotides on a few important microplastics. The microplastics were prepared using common plastic objects made of polyethylene (PE), polypropylene (PP), polystyrene (PS), polyvinyl chloride (PVC), composite of PS/PVC, and polyethylene terephthalate (PET). The effect of environmentally abundant metal ions such as Na⁺, Mg²⁺, and Ca²⁺ on the adsorption was also studied. Among the microplastics, PET and PS had the highest efficiency for the adsorption of linear DNA, likely due to the interactions provided by their aromatic rings. The study of DNA desorption from PET revealed the important role of hydrogen bonding and metal-mediated adsorption, while van der Waals force and hydrophobic interactions were also involved in the adsorption mechanism. The adsorption of spherical DNA (SNA) made of a high density of DNA coated on gold nanoparticles (AuNPs) was also studied, where the adsorption affinity order was found to be PET > PS/PVC > PS. Moreover, a tighter DNA adsorption was achieved in the presence of Ca²⁺ and Mg²⁺ compared to Na⁺.

Metal-Doped Polydopamine Nanoparticles for Highly Robust and Efficient DNA Adsorption and Sensing

Controlling DNA adsorption on nanomaterials is crucial for a wide range of applications in analytical and biomedical sciences. Polydopamine (PDA) is a versatile material that can be coated on nearly any surface, and thus adsorbing DNA onto PDA can be a general method for indirect DNA functionalization of surfaces. Polyvalent metal ions were reported to promote DNA adsorption on PDA nanoparticles (NPs), but previous works added the metal ions after the formation of PDA. Herein, we compared the effect of polyvalent metal ions added during the synthesis of PDA NPs (called metal-doped) with the effect of polyvalent metal ions added after the synthesis (metal-adsorbed). A series of metal ions including Ca²⁺, Zn²⁺, Ni²⁺, Fe³⁺, and Gd³⁺ were tested, and Zn²⁺ was studied in detail due to its excellent ability for promoting DNA adsorption. With 100 μM Zn²⁺, metal-doped NPs were ∼30% more efficient than metal-adsorbed NPs for DNA adsorption in buffer attributable to a higher metal loading on the surface of the metal-doped NPs. Metal leaching was negligible from the metal-doped NPs, and they showed a remarkably higher robustness than the metal-adsorbed NPs, resulting in a 20-fold higher DNA extraction efficiency from serum. Based on the desorption studies, a higher adsorption affinity for the metal-doped NPs was confirmed. Finally, the Zn²⁺-doped PDA NPs were used for sensitive DNA detection with a limit of detection of 0.45 nM, and the sensor was highly resistant to nonspecific protein and phosphate displacement.

Spherical Nucleic Acid Mediated Functionalization of Polydopamine-Coated Nanoparticles for Selective DNA Extraction and Detection

Magnetic nanoparticles have been widely used for the separation of biomolecules for biological applications due to the mild and efficient separation process. In previous studies, core-shell magnetic nanoparticles (NPs) were designed for DNA extraction without much sequence specificity. In this work, to achieve highly selective DNA extraction, we designed a core-shell magnetic structure by coating polydopamine (PDA) on Fe₃O₄ NPs. Without divalent metal ions, PDA does not adsorb DNA at neutral pH. The Fe₃O₄@PDA NPs were then functionalized with spherical nucleic acids (SNA) to provide a high density of probe DNA. Fe₃O₄@PDA@SNA was also compared with when a linear SH-DNA was covalently attached to the NPs surface, showing a higher density of the probe SNA than SH-DNA can be loaded on the NPs in a remarkably shorter time. Nonspecific DNA extraction was thoroughly inhibited by both probes. DNA extraction by the Fe₃O₄@PDA@SNA was more effective as well as 5-fold faster than by the Fe₃O₄@PDA@SH-DNA, probably due to the favorable standing conformation of DNA strands in SNA. Moreover, extraction by Fe₃O₄@PDA@SNA showed high robustness in fetal bovine serum, and the same design can be used for selective detection of DNA. Finally, the method was also demonstrated on silica NPs and WS₂ nanosheets for coating with PDA and SNA. Altogether, our findings revealed an interesting and general surface modification strategy using PDA@SNA conjugates for sequence-specific DNA extraction.