Open AccessCharacterisation of an aptamer against the Runt domain of AML 1 ( RUNX 1) by NMR and mutational analyses
Author(s) -
Takada Kenta,
Amano Ryo,
Nomura Yusuke,
Tanaka Yoichiro,
Sugiyama Shigeru,
Nagata Takashi,
Katahira Masato,
Nakamura Yoshikazu,
Kozu Tomoko,
Sakamoto Taiichi
Publication year - 2018
Publication title -
febs open bio
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.718
H-Index - 31
ISSN - 2211-5463
DOI - 10.1002/2211-5463.12368
Subject(s) - aptamer , oligonucleotide , chemistry , systematic evolution of ligands by exponential enrichment , nuclear magnetic resonance spectroscopy , rna , selex aptamer technique , biochemistry , biology , dna , stereochemistry , microbiology and biotechnology , gene
Since the invention of systematic evolution of ligands by exponential enrichment, many short oligonucleotides (or aptamers) have been reported that can bind to a wide range of target molecules with high affinity and specificity. Previously, we reported an RNA aptamer that shows high affinity to the Runt domain (RD) of the AML 1 protein, a transcription factor with roles in haematopoiesis and immune function. From kinetic and thermodynamic studies, it was suggested that the aptamer recognises a large surface area of the RD, using numerous weak interactions. In this study, we identified the secondary structure by nuclear magnetic resonance spectroscopy and performed a mutational study to reveal the residue critical for binding to the RD. It was suggested that the large contact area was formed by a DNA ‐mimicking motif and a multibranched loop, which confers the high affinity and specificity of binding.