Engineering smart thioflavin T binders with switchable DNA topologies for constructing multiple label-free biosensors

Abstract

Thioflavin T (ThT) has been used as a sensitive fluorescence probe for lighting up nucleic acids. The binding of ThT is dependent on the structural topologies of DNA sequences. To date, most oligonucleotides interact with ThT through only a single topology, and this limits the applications of ThT as a sensing agent. Here, we modulated an HIV-1 integrase aptamer, 93del, to have switchable topologies by optimizing its 3′ flanking residues to enhance its ThT-binding capacity. Our data revealed that the sequences formed stem-loop hairpins and I-motif/G-quadruplex (G4) hybrids in Na+ buffer under alkaline and acidic conditions, respectively. Both topologies could bind ThT with high affinity (Kd ∼ 0.5 μM) and dramatically enhance the fluorescent signal of ThT. However, in the presence of K+, the sequences could be assembled into interlocked G4s, which had a low affinity for ThT but a high affinity for N-methyl mesoporphyrin IX (NMM). This allowed us to build highly sensitive fluorescent K+ sensors that were insusceptible to interference from Na+. Additionally, we found that the stacking of homologous base pairs in the hairpin loops was essential for ThT recognition and could be used as an indicator in the construction of label-free molecular beacons, allowing monitoring of microRNAs effectively in human serum spiked test. By employing external stimuli to induce the transformation of these topologies, we were able to sensitively detect adenosine triphosphate (ATP) molecules or Hg2+in vitro under specific acidic conditions. Our study provides a strategy for exploiting undiscovered functions of existing aptamers.