Issue 14, 2013
From the journal:

Organic & Biomolecular Chemistry

Specific recognition of cytosine by hypoxanthine in pyrrolidinyl peptide nucleic acid†

Chotima Vilaivan,a   Wimonmas Srinarang,a   Nattawut Yotapan,a   Woraluk Mansawat,a   Chalothorn Boonlua,a   Junji Kawakami,bc   Yoshie Yamaguchi,bc   Yuko Tanakabc  and  Tirayut Vilaivan*a  

* Corresponding authors

a Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
E-mail: vtirayut@chula.ac.th
Fax: +66-2-2187598

b Department of Nanobiochemistry, FIRST, Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan

c Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan

Abstract

Hypoxanthine is an unnatural base that can potentially pair with all natural nucleobases. While hypoxanthine in DNA exhibits marginal preference for pairing with cytosine (C), little is known about its pairing behavior in other DNA analogues. In this study, we synthesized a hypoxanthine-containing monomer and incorporated it into pyrrolidinyl peptide nucleic acid with α/β-peptide backbone derived from D-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid (acpcPNA). DNA binding studies clearly revealed that hypoxanthine in acpcPNA behaves like G-analogue because it can specifically form a stable base pair with dC in DNA. The ability to replace G by hypoxanthine without affecting the base pairing properties of acpcPNA can solve a number of problems associated with G-rich acpcPNA including difficult synthesis, formation of secondary structures and fluorescence quenching.

Graphical abstract: Specific recognition of cytosine by hypoxanthine in pyrrolidinyl peptide nucleic acid

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Article information

DOI
https://doi.org/10.1039/C3OB27129C
Article type
Paper
Submitted
31 Oct 2012
Accepted
30 Jan 2013
First published
31 Jan 2013

Org. Biomol. Chem., 2013,11, 2310-2317

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Specific recognition of cytosine by hypoxanthine in pyrrolidinyl peptide nucleic acid

C. Vilaivan, W. Srinarang, N. Yotapan, W. Mansawat, C. Boonlua, J. Kawakami, Y. Yamaguchi, Y. Tanaka and T. Vilaivan, Org. Biomol. Chem., 2013, 11, 2310 DOI: 10.1039/C3OB27129C

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