Tailed-Hoogsteen triplex DNA silver nanoclusters as potential pH and miRNA sensors

S. PARK , H.  C. YADAVALLI, T. H. KIM, P. SHAH, S. W. YANG
Department of Biology, Duke University, Durham, NC 27008, USA  Department of Systems Biology, Yonsei University, Seoul, 03722, Republic of Korea

MicroRNAs (miRNAs) are a class of non-coding RNA, typically 21-22 nucleotides in size, that play a crucial role in regulating gene expression. Extracellular pH also changes dynamically in response to environmental cues and physiological conditions. The role of miRNA and pH in various biological processes such as plant development, defense processes, and stress responses has led to considerable interest in their potential as biomarkers and sensor development. We have developed a novel method for sensing target miRNA and changes in pH in vitro using Tailed-Hoogsteen triplex DNA-encapsulated Silver Nanoclusters (DNA/AgNCs). Upon the hybridization of the target miRNA with the tail, the Tailed-Hoogsteen triplex DNA/AgNCs exhibited a pronounced red fluorescence, effectively turning on the signal. This red fluorescence signal was also shown to be reversibly pH-dependent, as more alkaline conditions turned off the signal while more acidic conditions turned on the signal. Furthermore, in-gel fluorescence assays and small angle x-ray scattering (SAXS) analysis revealed that the formation of a non-canonical head-to-head triplex dimer structure and stabilization of the Hoogsteen triplex DNA was essential for the turn-on miRNA sensing. Our DNA/AgNCs-based method utilizes the attractive photochemical properties of AgNCs and demonstrates their potential as practical sensors for pH and small RNAs.