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タイトル: | Sequence-specific DNA binding by long hairpin pyrrole–imidazole polyamides containing an 8-amino-3,6-dioxaoctanoic acid unit |
著者: | Sawatani, Yoshito Kashiwazaki, Gengo Chandran, Anandhakumar Asamitsu, Sefan Guo, Chuanxin Sato, Shinsuke Hashiya, Kaori Bando, Toshikazu Sugiyama, Hiroshi https://orcid.org/0000-0001-8923-5946 (unconfirmed) |
著者名の別形: | 佐藤, 慎祐 橋谷, かおり 板東, 俊和 杉山, 弘 |
キーワード: | DNA binder Py–Im polyamide Ethylene glycol unit SPR Bind-n-Seq |
発行日: | 15-Aug-2016 |
出版者: | Elsevier Ltd |
誌名: | Bioorganic and Medicinal Chemistry |
巻: | 24 |
号: | 16 |
開始ページ: | 3603 |
終了ページ: | 3611 |
抄録: | With the aim of improving aqueous solubility, we designed and synthesized five N-methylpyrrole (Py)–N-methylimidazole (Im) polyamides capable of recognizing 9-bp sequences. Their DNA-binding affinities and sequence specificities were evaluated by SPR and Bind-n-Seq analyses. The design of polyamide 1 was based on a conventional model, with three consecutive Py or Im rings separated by a β-alanine to match the curvature and twist of long DNA helices. Polyamides 2 and 3 contained an 8-amino-3, 6-dioxaoctanoic acid (AO) unit, which has previously only been used as a linker within linear Py–Im polyamides or between Py–Im hairpin motifs for tandem hairpin. It is demonstrated herein that AO also functions as a linker element that can extend to 2-bp in hairpin motifs. Notably, although the AO-containing unit can fail to bind the expected sequence, polyamide 4, which has two AO units facing each other in a hairpin form, successfully showed the expected motif and a K[D] value of 16 nM was recorded. Polyamide 5, containing a β-alanine–β-alanine unit instead of the AO of polyamide 2, was synthesized for comparison. The aqueous solubilities and nuclear localization of three of the polyamides were also examined. The results suggest the possibility of applying the AO unit in the core of Py–Im polyamide compounds. |
著作権等: | © 2016. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ The full-text file will be made open to the public on 15 August 2018 in accordance with publisher's 'Terms and Conditions for Self-Archiving'. この論文は出版社版でありません。引用の際には出版社版をご確認ご利用ください。 This is not the published version. Please cite only the published version. |
URI: | http://hdl.handle.net/2433/230868 |
DOI(出版社版): | 10.1016/j.bmc.2016.05.070 |
PubMed ID: | 27301681 |
出現コレクション: | 学術雑誌掲載論文等 |
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