Lipo-oligo/polysaccharide biorecognition at the nano-bio interface: insights into LA27 aptamer binding to biomimetic bacterial membranes

Gram-negative bacteria feature an asymmetric outer membrane, composed of phospholipids in the inner leaflet and lipopolysaccharides (LPS) or lipooligosaccharides (LOS) in the outer leaflet, which underpins virulence and antibiotic resistance. Conventional LPS assays like the Limulus amebocyte lysate test face ethical and practical challenges, motivating the development of aptamer-based detection. Here, we probe the interaction of the LA27 DNA aptamer (Kd ≈ 46 nM) with biomimetic membranes incorporating LOS/LPS from Akkermansia muciniphila, Flavobacterium sp. Root935, and Paenalcaligenes hominis strains. Asymmetric supported lipid bilayers (SLBs) and symmetric large unilamellar vesicles (LUVs) were characterized by neutron reflectometry (NR), small-angle neutron scattering (SANS), and dynamic light scattering (DLS). NR confirmed preserved bilayer asymmetry and revealed that LA27 deeply penetrates Akkermansia LOS bilayers, evidenced by increased core hydration and structural disruption, whereas interactions with Flavobacterium LOS are moderate, and those with Paenalcaligenes LPS are confined to surface adhesion due to extensive LPS O-antigen chains. SANS and DLS of LUVs corroborated these modes: Akkermansia vesicles showed negligible changes in lamellar thickness and hydrodynamic radius, consistent with insertion, while those containing Flavobacterium LOS and Paenalcaligenes LPS exhibited significant increases in both size-related metrics, indicative of surface binding for those latter cases. These results elucidate how polysaccharide composition and supramolecular architecture of LOS/LPS govern aptamer affinity and specificity, providing a rigorous framework for nano-bio interface studies and laying the groundwork for selective, aptamer-based endotoxin sensing platforms.