Affinity Improvement of a VEGF Aptamer by in Silico Maturation for a Sensitive VEGF-Detection System

作者：Nonaka Yoshihiko; Yoshida Wataru; Abe Koichi; Ferri Stefano; Schulze Holger; Bachmann Till T; Ikebukuro Kazunori^*

来源：Analytical Chemistry, 2013, 85(2): 1132-1137.

DOI：10.1021/ac303023d

Systematic evolution of ligands by exponential enrichment (SELEX) is an efficient method to identify aptamers; however, it sometimes fails to identify aptamers that bind to their target with high affinity. Thus, post-SELEX optimization of aptamers is required to improve aptamer binding affinity. We developed in silica maturation based on a genetic algorithm(1) as an efficient mutagenesis method to improve aptamer binding affinity. In silica maturation was performed to improve a VEGF-binding DNA aptamer (VEap121). The VEap121 aptamer is considered to fold into a G-quadruplex structure and this structure may be important for VEGF recognition. Using in silica maturation, VEap121 was mutated with the exception of the guanine tracts that are considered to form the G-quartet. As a result, four aptamers were obtained that showed higher affinity compared with VEap121. The dissociation constant (K-d) of the most improved aptamer (3R02) was 300 pM. The affinity of 3R02 was 16-fold higher than that of VEap121. Moreover, a bivalent aptamer was constructed by connecting two identical 3R02s through a 10-mer thymine linker for further improvement of affinity. The bivalent aptamer (3R02 Bivalent) bound to VEGF with a K-d value of 30 pM. Finally, by constructing a VEGF-detection system using a VEGF antibody as the capture molecule and monovalent 3R02 as the detection molecule, a more sensitive assay was developed compared with the system using VEap121. These results indicate that in silica maturation could be an efficient method to improve aptamer affinity for construction of sensitive detection systems.

• 出版日期2013-1-15