programmably engineered FRET-nanoflare for ratiometric live-cell ATP imaging with anti-interference capability

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.

DNA-Modulated and Mechanoresponsive Excitonic Couplings Reveal Chiroptical Correlation of Conformation, Tension, and Dynamics of DNA Self-Assembly

Study of the conformational and mechanical behaviors of biomolecular assemblies is vital to the rational design and realization of artificial molecular architectures with biologically relevant functionality. Here, we revealed DNA-modulated and mechanoresponsive excitonic couplings between organic chromophores and verified strong correlations between the excitonic chiroptical responses and the conformational and mechanical states of DNA self-assemblies irrespective of fluorescence background interference. Besides, the excitonic chiroptical effect allowed sensitive monitoring of DNA self-assembled nanostructures due to small molecule bindings or DNA strand displacement reactions. Moreover, we developed a new chiroptical reporter, a DNA-templated dimer of an achiral cyanine5 and an intrinsically chiral BODIPY, that exhibited unique multiple-split spectral line shape of exciton-coupled circular dichroism, largely separated response wavelengths, and enhanced anisotropy dissymmetry factor (g-factor). These results shed light on a promising chiroptical spectroscopic tool for studying biomolecular recognition and binding, conformation dynamics, and soft mechanics in general.

A fuel-initiated DNA molecular machine for microRNA detection in serum via poly-adenine-mediated spherical nucleic acids

MicroRNAs (miRNAs) have been identified as promising disease diagnostic biomarkers. However, it is challenging to sensitively detect miRNAs, especially in complex biological environments, due to their low abundance and small size. Herein, we have developed a DNA-fueled molecular machine for sensitive detection of miRNA-22 (miR-22) in undiluted serum by combining poly-adenine-mediated spherical nucleic acids (polyA-SNAs) with a toehold mediated strand displacement reaction (TMSDR). The polyA-SNAs are constructed by the assembly of diblock DNA probes on a AuNP surface through the high binding affinity of polyA to AuNPs. The surface density of the diblock DNA probe can be controlled by tuning the length of the polyA block, and the orientation of the diblock DNA probe can adopt an upright conformation, which is beneficial to target hybridization and TMSDRs. TMSDR is an enzyme-free target recycling amplification approach. Taking advantage of polyA-mediated SNAs and TMSDR, the operation of the molecular machine based on two successive TMSDRs on polyA20-SNAs is rapid and efficient, which can significantly amplify the fluorescence response for detection of miR-22 in an undiluted complex matrix. The developed sensor can detect as low as 10 pM of target miRNA/DNA in undiluted fetal bovine serum within 30 min. The synergetic effect of polyA-mediated SNAs and TMSDR presents a potential alternative tool for the detection of biomarkers in real biological samples.

Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids

Owing to the versatile photophysical and chemical properties, spherical nucleic acids (SNAs) have been widely used in biosensing. However, traditional SNAs are formed by self-assembly of thiolated DNA on the surface of a gold nanoparticle (AuNP), where it is challenging to precisely control the orientation and surface density of DNA. As a new SNA, a polyadenine (polyA)-mediated SNA using the high binding affinity of consecutive adenines to AuNPs shows controllable surface density and configuration of DNA, which can be used to improve the performance of a biosensor. Herein, we first introduce the properties of polyA-mediated SNAs and fundamental principles regarding the polyA-AuNP interaction. Then, we provide an overview of current representative synthesis methods of polyA-mediated SNAs and their advantages and disadvantages. After that, we summarize the application of polyA-mediated SNAs in biosensing based on fluorescence and colorimetric methods, followed by discussion and an outlook of future challenges in this field.