An electrochemical biosensor based on the Y-endonuclease system and hybridization chain reaction amplification for the investigation of the cell density of Akashiwo sanguinea

As one of the significant algal bloom species, Akashiwo sanguinea has long brought challenges to controlling red tide. Red tide outbreaks are often accompanied by the mass propagation of various algal bloom species, which brings problems to investigating red tides using traditional optical methods. Electrochemical biosensing technology has high sensitivity and specificity, yet its use in detecting A. sanguinea DNA in sea areas is insufficient. Here, the amplification system combining Nt.BbvCI endonuclease-assisted and hybridization chain reaction (HCR) has a detection limit of the same or even lower magnitude than other HCR systems. More importantly, the auxiliary short strands from the Nt.BbvCI system activates HCR, reducing the steric hindrance of long DNA molecules and enhancing HCR’s activity. Thus, the portable electrochemical biosensor based on this system successfully detected simulated A. sanguinea DNA samples, with a limit of detection (LOD) at 1.53 fg/μL and a limit of quantification (LOQ) at 4.27 fg/μL, far better than traditional optical-based methods. Also, the predicted cell density of A. sanguinea generally matches that of optical microscopy. This portable biosensor is expected to conduct an on-site investigation of A. sanguinea ’s cell density. It can provide data support for early warnings of red tide outbreaks and reduce the time needed for investigations.