Rapid isolation of bacteria-specific aptamers with a non-SELEX-based method

Usually, isolation of bacteria-specific aptamers by SELEX is a time-consuming process due to the required repeated rounds of binding, separation, and amplification of the probes to target bacteria. Here, we show that it is possible to isolate bacteria-specific DNA aptamers omitting the repeated rounds of binding incubation, separation, and amplification that are indispensable for SELEX. The serial removal of unbound DNAs to the bacterial cells from an initial mixture of bacteria and DNA libraries through serial centrifugation, one-time separation, and further one-time amplification of DNA bound to the target bacterial cells applied in this non-SELEX-based method allows successful aptamer isolation. •Non-SELEX-based method for the isolation of aptamers to bacterial cells was proposed.•Centrifugation-based partitioning method can reduce the time remarkably to isolate aptamers to target bacteria.•The aptamers isolated by centrifugation-based partitioning method were comparable to the aptamers isolated by SELEX method.