Interaction Mechanism of the LA27 Aptamer with the Endotoxins of Gram(-) Bacteria

Recently, a great interest was addressed to aptamers which have been used in the detection of lipopolysaccharides (LPS), which are complex molecules present in the outer membrane of the external envelope of Gram(-) bacteria. we are focusing on a short aptamer, named LA27 (3′-CGATAGATTGTTGTAAGACAATCTTCC-5′-NH), which has a great binding affinity towards LPS (Kd = 46.2 ± 9.5 nM). Theoretical studies indicate a possible selective affinity to the hydrophobic part of LPS. At the same time, any clear information on the affinity of the LA27 aptamer for LPS molecules deriving from different kinds of Gram(-) bacteria has not been investigated yet.
Previous investigations, through Neutron Reflectometry and Dynamic Light Scattering, proved the capability of this aptamer to bind with LPS extracted from different bacterial strains, particularly, it looks like the aptamer shows an affinity with the lipidic part of the LPSs. So, by exploiting the contrast-matching capabilities of SANS, using hydrogenated and deuterated DPPC as the main component of the membrane-biomimicking lipidic nanoaggregates, to prove the specific interaction of the LA27 aptamer with the hydrophobic part of LPSs.