Lipid Membrane Binding of Computationally-Designed DNA Aptamers Specific for Phosphatidylserine

Abstract

Recently we applied an entropy based seed-and-grow strategy to design a set of short DNA aptamers (Chem. Biol. Drug Des. 78:1-13). Each member consisting upto 12 nucleotides binds specifically with phospholipid phosphatidylserine (PS). The PS binding aptamers can be used e.g., to diagnose the PS externalization in cells undergoing apoptosis which is an important biomarker to be used in anti-cancer treatment. The in vitro fluorescence measurements on the PS bound aptamers primarily validate the applicability of the mentioned computational aptamer designing methodology. We have further studied the binding properties of the designed aptamers with phospholipid vesicles using a direct detection (non-fluorescence) methodology to measure concentrations of relative PS bound aptamers versus unbound ones. A novel technique has been proposed to analyze the phospholipid binding properties of aptamers without fluorescent tags attached to them. Our results suggest that the PS binding of aptamers is very much sequence specific and depends also on the number of nucleotides in the sequence with shorter aptamers showing better binding. Finally, we have been able to properly rank the aptamers considering the best binding properties with PS and thus have found a set of candidates for preclinical trials. This may open up the possibility of discovering aptamer based diagnostic tools to be used in treatments of many diseases including cancer.