Improvement of Aptamer Affinity by Dimerization

Hijiri Hasegawa; Ken-Ichi Taira; Koji Sode; Kazunori Ikebukuro

doi:10.3390/s8021090

Improvement of Aptamer Affinity by Dimerization

Sensors (Basel). 2008 Feb 19;8(2):1090-1098. doi: 10.3390/s8021090.

Authors

Hijiri Hasegawa¹, Ken-Ichi Taira¹, Koji Sode², Kazunori Ikebukuro³

Affiliations

¹ Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
² Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan. sode@cc.tuat.ac.jp.
³ Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan. ikebu@cc.tuat.ac.jp.

Abstract

To increase the affinities of aptamers for their targets, we designed an aptamerdimer for thrombin and VEGF. This design is based on the avidity of the antibody, whichenables the aptamer to connect easily since it is a single-strand nucleic acid. In this study,we connected a 15-mer thrombin-binding aptamer with a 29-mer thrombin-binding aptamer.Each aptamer recognizes a different part of the thrombin molecule, and the aptamer dimerhas a K_d value which is 1/10 of that of the monomers from which it is composed. Also, thedesigned aptamer dimer has higher inhibitory activity than the reported (15-mer) thrombin-inhibiting aptamer. Additionally, we connected together two identical aptamers againstvascular endothelial growth factor (VEGF₁₆₅), which is a homodimeric protein. As in thecase of the anti-thrombin aptamer, the dimeric anti-VEGF aptamer had a much lower K_d value than that of the monomer. This study demonstrated that the dimerization of aptamerseffectively improves the affinities of those aptamers for their targets.

Keywords: Aptamer; avidity; dimerization.