Conjugation of two RNA aptamers improves binding affinity to AML1 Runt domain

Yusuke Nomura; Kaori Yamazaki; Ryo Amano; Kenta Takada; Takashi Nagata; Naohiro Kobayashi; Yoichiro Tanaka; Junichi Fukunaga; Masato Katahira; Tomoko Kozu; Yoshikazu Nakamura; Yuji Haishima; Hidetaka Torigoe; Taiichi Sakamoto

doi:10.1093/jb/mvx049

Conjugation of two RNA aptamers improves binding affinity to AML1 Runt domain

J Biochem. 2017 Dec 1;162(6):431-436. doi: 10.1093/jb/mvx049.

Authors

Yusuke Nomura^{1

2}, Kaori Yamazaki¹, Ryo Amano³, Kenta Takada³, Takashi Nagata⁴, Naohiro Kobayashi⁵, Yoichiro Tanaka⁶, Junichi Fukunaga⁶, Masato Katahira⁴, Tomoko Kozu⁶, Yoshikazu Nakamura^{7

8}, Yuji Haishima², Hidetaka Torigoe¹, Taiichi Sakamoto³

Affiliations

¹ Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku 162-8601, Tokyo, Japan.
² Division of Medical Devices, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan.
³ Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan.
⁴ Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
⁵ Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
⁶ Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806, Japan.
⁷ RIBOMIC Inc, 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan.
⁸ Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

PMID: 28992043
DOI: 10.1093/jb/mvx049

Abstract

To develop a high-affinity aptamer against AML1 Runt domain, two aptamers were conjugated based on their structural information. The newly designed aptamer Apt14 was generated by the conjugation of two RNA aptamers (Apt1 and Apt4) obtained by SELEX against AML1 Runt domain, resulting in improvement in its binding performance. The residues of AML1 Runt domain in contact with Apt14 were predicted in silico and confirmed by mutation and NMR analyses. It was suggested that the conjugated internal loop renders additional contacts and is responsible for the enhancement in the binding affinity. Conjugation of two aptamers that bind to different sites of the target protein is a facile and robust strategy to develop an aptamer with higher performance.

Keywords: AML; RNA; aptamer; design; structure.

MeSH terms

Aptamers, Nucleotide / chemistry*
Binding Sites
Core Binding Factor Alpha 2 Subunit / chemistry*
Core Binding Factor Alpha 2 Subunit / genetics
Surface Plasmon Resonance

Substances

Aptamers, Nucleotide
Core Binding Factor Alpha 2 Subunit