Comparison of classifications of aptamers against Vibrio alginolyticus based on their primary and secondary structure

Abstract

As a novel method to detect the pathogen Vibrio alginolyticus, 45 aptamers were previously selected and tested. In order to better understand the properties of these aptamers, it was essential to classify these aptamers based on appropriate criteria. The primary structure of 45 aptamers against V. alginolyticus was analyzed by the software DNAMAN and these aptamers were classified into 11 groups as the usual method according to their homogenous tree. However, the secondary structure of aptamers within each group varied greatly, which implies that the classification based on their primary structure is drastically different from that based on their secondary structure. Since the spacial structure like secondary structure is the basis for aptamers to bind to their targets, analysis on and classification by their secondary structure should be necessary and would be a good way to elucidate the mechanism of the specific identification of their targets. Further analysis on the secondary structure demonstrated that the fixed sequences were involved in the formation of the secondary structure of aptamers and contributed to the complexity of the structure, which makes it possible to increase their identification abilities.

Key words: Aptamer, primary structure, secondary structure, Vibrio alginolyticus, classification.