Hirao I

Success probability of high-affinity DNA aptamer generation by genetic alphabet expansion

Nucleic acid aptamers are single-stranded DNA or RNA molecules that bind specifically to a wide variety of targets, such as small molecules, sugars, proteins and cells. Aptamers are generated by an evolutionary engineering method called SELEX (systematic evolution of ligands by exponential enrichment), through repetitive processes of selection and amplification using nucleic acid libraries with randomized sequences [1,2]. Once the aptamer sequences have been determined by SELEX, the aptamers and their modifications are manufactured by solid-phase chemical synthesis and can be used as antibody alternatives. However, one main issue is the aptamers' insufficient affinities to targets, because of the limited chemical diversity, especially the low hydrophobicity, of the nucleic acid components, A, G, C and T/U, for interactions with hydrophobic regions of target proteins. Thus, the practical applications of nucleic acid aptamers are still limited, and many improved methods for modified aptamer generation have been reported [3–8]. Especially, the use of a chemically expanded library is widely considered to be advantageous for generating high-affinity aptamers, but few studies have experimentally or theoretically confirmed the validity of this strategy [9].