Selection of a biofilm-degrading aptamer against Edwardsiella tarda using Inhibition-SELEX and investigation of degradation factors and binding affinity

ABSTRACT Edwardsiella tarda is an important pathogen whose biofilm formation significantly enhances virulence and antibiotic resistance, posing serious threats to food safety and public health. Using an Inhibition-SELEX approach, the aptamer ET6 was screened for its ability to target and degrade E. tarda biofilms. Within 2 h, ET6 achieved a biofilm degradation rate of 71.51%, whereas degradation rates for non-target bacteria ( Nocardia salmonicola , Vibrio harveyi , Pseudomonas aeruginosa , Escherichia coli , Aeromonas hydrophila , and Pseudomonas plecoglossicida ) remained below 20%. Six factors influencing the biofilm degradation rate were systematically investigated, including biofilm preparation conditions, aptamer concentration, aptamer volume, and the interaction time between the aptamer and the biofilm. ET6 exhibited an affinity constant (Kd) of 169.36 ± 24.69 nmol/L and a maximum binding capacity (Bmax) of 467.75 ± 34.17 nmol/L for E. tarda biofilm. Compared with planktonic cells, Kd increased and Bmax decreased in biofilms, indicating reduced binding affinity of the aptamer. Finally, analysis of secondary and tertiary structures of ET6 revealed that both the 5’ and 3’ ends consist of unpaired strands, conferring relatively high conformational flexibility. These findings provide a basis for the prevention and control of diseases caused by E. tarda and support the development of aptamer-based strategies targeting bacterial biofilms.