A study of DNA design dependency of segmented DNA-induced gold nanoparticle aggregation towards versatile bioassay development

Abstract

DNA-decorated gold nanoparticles (AuNPs) are important sensing probes for designing versatile assays for detecting DNA hybridization, DNA binders and DNA associated biological processes. In this study, we report DNA design rules for a pair of segmented DNA-conjugated AuNPs that can undergo “transient” aggregation due to cooperative base-pairing force of sticky ends on DNA and salt screening. A wildtype estrogen receptor response element (ERE) was used as a model DNA which is segmented into two half-sites, each carrying a complementary sticky end and a half-site DNA, were conjugated onto AuNPs to form two sets of complementary DNA–AuNPs conjugates. A number of DNA design parameters are studied for their effects on the aggregation kinetics, namely DNA conformation (i.e., mixed structure of ssDNA and dsDNA), number of sticky-ends bases, spacer length, as well as the symmetrical and asymmetrical interplay between the complementary set of segmented DNA–AuNPs conjugates. Firstly, we found that dsDNA serves as a more effective spacer than ssDNA in preventing base coordination of the nucleotides to the AuNPs surface due to its rigidity that in turn helps to improve the accessibility of sticky-ends for faster aggregation. Secondly, base-pairing force in facilitating the salt-induced AuNPs aggregation is tunable by the number of sticky-ends, which is closely related to the length and structural composition of the DNA spacer. Thirdly, symmetrically spaced sticky-ends enable quicker non-crosslinking aggregation than the asymmetrical combination due to their closer initial interparticle distance. Based on the optimized DNA design, we appended the efficient aggregation that leads to transient formation of a full ERE sequence for detecting estrogen receptor β (ER β) by exploiting protein binding retarded particle aggregation. With a competition assay, binding affinity of ERβ to different DNA sequences can be easily screened using a single set of complementary segmented DNA–AuNPs probes. The DNA design dependency of the DNA–AuNPs aggregation studied herein has enabled potential applications for rapid and highly specific DNA-binding protein detection, which could be extended to detect a wide range of DNA binders and its related biological processes.