The cell-SELEX method enables efficient selection of
aptamers that
bind whole bacterial cells. However, after selection, it is difficult
to determine their binding affinities using common screening methods
because of the large size of the bacteria. Here we propose a simple
surface plasmon resonance imaging method (SPRi) for aptamer characterization
using bacterial membrane vesicles, called nanosomes, instead of whole
cells. Nanosomes were obtained from membrane fragments after mechanical
cell disruption in order to preserve the external surface epitopes
of the bacterium used for their production. The study was conducted
on Bacillus cereus (B. cereus), a Gram-positive bacterium
commonly found in soil, rice, vegetables, and dairy products. Four
aptamers and one negative control were initially grafted onto a biochip.
The binding of B. cereus cells and nanosomes to immobilized
aptamers was then compared. The use of nanosomes instead of cells
provided a 30-fold amplification of the SPRi signal, thus allowing
the selection of aptamers with higher affinities. Aptamer SP15 was
found to be the most sensitive and selective for B. cereus ATCC14579 nanosomes. It was then truncated into three new sequences
(SP15M, SP15S1, and SP15S2) to reduce its size while preserving the
binding site. Fitting the results of the SPRi signal for B.
cereus nanosomes showed a similar trend for SP15 and SP15M,
and a slightly higher apparent association rate constant k
on
for SP15S2, which is the truncation
with a high probability of a G-quadruplex structure. These observations
were confirmed on nanosomes from B. cereus ATCC14579
grown in milk and from the clinical strain B. cereus J066. The developed method was validated using fluorescence microscopy
on whole B. cereus cells and the SP15M aptamer labeled
with a rhodamine. This study showed that nanosomes can successfully
mimic the bacterial membrane with great potential for facilitating
the screening of specific ligands for bacteria.