Unusual sequence length-dependent gold nanoparticles aggregation of the ssDNA sticky end and its application for enzyme-free and signal amplified colorimetric DNA detection.

Hongfei He,Dan Xiao Dan Xiao,Yan Meng,Baozhan Zheng,Jianyuan Dai,Zhijuan Duan,Yong Guo

doi:10.1038/srep30878

Abstract

It is known that the adsorption of short single-stranded DNA (ssDNA) on unmodified gold nanoparticles (AuNPs) is much faster than that for long ssDNA, and thus leads to length-dependent AuNPs aggregation after addition of salt, the color of the solutions sequentially changed from red to blue in accordance with the increase of ssDNA length. However, we found herein that the ssDNA sticky end of hairpin DNA exhibited a completely different adsorption behavior compared to ssDNA, an inverse blue-to-red color variation was observed in the colloid solution with the increase of sticky end length when the length is within a certain range. This unusual sequence length-dependent AuNPs aggregation might be ascribed to the effect of the stem of hairpin DNA. On the basis of this unique phenomenon and catalytic hairpin assembly (CHA) based signal amplification, a novel AuNPs-based colorimetric DNA assay with picomolar sensitivity and specificity was developed. This unusual sequence length-dependent AuNPs aggregation of the ssDNA sticky end introduces a new direction for the AuNPs-based colorimetric assays.

Highlights

Sensitive and selective detection of DNA is increasingly important in clinical diagnostics, forensic investigations, environmental and food safety monitoring[1]
DNAs with 18 base-pair stem and different lengths of single-stranded DNA (ssDNA) sticky ends, varying from 5- to 30-mer, were examined using unmodified AuNPs (DNA sequences were listed in Table S1 in the supporting information). ssDNAs with the same sequence to the sticky ends of hairpin DNAs were used as control
For the ssDNA, it exhibited length-dependent AuNPs aggregation and the color of the AuNPs solutions gradually changed from red to blue with the increase of ssDNA length (Fig. 1A), which is similar to the literature reported[21]

Summary

Results and Discussion

For the ssDNA, it exhibited length-dependent AuNPs aggregation and the color of the AuNPs solutions gradually changed from red to blue with the increase of ssDNA length (Fig. 1A), which is similar to the literature reported[21]. The repulsion between coiled sticky end and AuNPs plus the repulsion between stem and AuNPs will prevent sticky end to adsorb onto AuNPs (Fig. 2C), the color of the solutions gradually varied from red to blue with the increase of sticky end length (Fig. 1B) Further evidence for this hypothesis can be obtained by examining the interaction between AuNPs and hairpin DNAs with 10 and 14 bp stem. The high sequence specificity of the current strategy is attributed to the relatively long stem of the hairpin probes, which can make the hairpin structure thermodynamically stable, and it is unfavorable for the hybridization between mismatched target DNA and the hairpin probe[26]

Conclusions

Author Contributions

Additional Information