Spatiotemporal Monitoring of Subcellular mRNAs In Situ via Polyadenine-Mediated Dual-Color Sticky Flares

Preadsorbed Particles with Cross-Shaped DNA Scaffolds Enable Spherical Nucleic Acid to Directly Respond to Protein in Complex Matrices

Spherical nucleic acids (SNAs) usually suffer from an undesired protein corona and disrupt the function of nucleic acids (e.g., aptamer), thereby compromising recognition and response to proteins in the biological environment. To overcome the unexpected protein interference, specific proteins were initially adsorbed onto magnetic particles (MPs) as a customized protein corona "shield" with fabricated nucleic acid scaffolds, forming a preadsorbed particle-based spherical nucleic acid (pap-SNA). By comparing with AuNPs-SNA or COOH-MPs, it was found that such a protein corona "shield" of pap-SNA significantly eliminated the adsorption of nonspecific proteins or other biomolecules onto the MPs' interface, thereby enabling the SNA to directly respond to proteins in complex matrices. To further reduce the interference of protein on SNA performance, a series of nucleic acid scaffolds (Z-type, dsDNA type, circle type, T-type, and cross-shaped type) were designed by changing the rigidity and thermal stability of functional nucleic acids on the MPs. As a consequence, the pap-SNA with a cross-shaped scaffold improved the sensitivity of the pap-SNA-based detection platform in that the orderly arrangement of functional nucleic acids provides a steric hindrance to interferents. Moreover, the presence of the cross-shaped scaffold not only enables pap-SNA to exhibit a proportional response to varied protein concentrations but also enhances the detection sensitivity of pap-SNA by 160% in serum and by 190% in urine. Therefore, incorporating optimized DNA scaffolds maintained and facilitated the function of a probe (aptamer) on the surface of SNA. This approach offers a pathway for creating SNA with direct response and anti-interference capability applicable to detecting diverse biomolecules such as nucleic acids and proteins in biological matrices.

Improved Catalytic Activity of Spherical Nucleic Acid Enzymes by Hybridization Chain Reaction and Its Application for Sensitive Analysis of Aflatoxin B1

Conventional spherical nucleic acid enzymes (SNAzymes), made with gold nanoparticle (AuNPs) cores and DNA shells, are widely applied in bioanalysis owing to their excellent physicochemical properties. Albeit important, the crowded catalytic units (such as G-quadruplex, G4) on the limited AuNPs surface inevitably influence their catalytic activities. Herin, a hybridization chain reaction (HCR) is employed as a means to expand the quantity and spaces of G4 enzymes for their catalytic ability enhancement. Through systematic investigations, we found that when an incomplete G4 sequence was linked at the sticky ends of the hairpins with split modes (3:1 and 2:2), this would significantly decrease the HCR hybridization capability due to increased steric hindrance. In contrast, the HCR hybridization capability was remarkably enhanced after the complete G4 sequence was directly modified at the non-sticky end of the hairpins, ascribed to the steric hindrance avoided. Accordingly, the improved SNAzymes using HCR were applied for the determination of AFB1 in food samples as a proof-of-concept, which exhibited outstanding performance (detection limit, 0.08 ng/mL). Importantly, our strategy provided a new insight for the catalytic activity improvement in SNAzymes using G4 as a signaling molecule.