title: Specific recognition of cytosine by hypoxanthine in pyrrolidinyl peptide nucleic acid.
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.
authors: Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
authors: Chotima
authors: C
authors: Vilaivan
authors: Wimonmas
authors: W
authors: Srinarang
authors: Nattawut
authors: N
authors: Yotapan
authors: Woraluk
authors: W
authors: Mansawat
authors: Chalothorn
authors: C
authors: Boonlua
authors: Junji
authors: J
authors: Kawakami
authors: Yoshie
authors: Y
authors: Yamaguchi
authors: Yuko
authors: Y
authors: Tanaka
authors: Tirayut
authors: T
authors: Vilaivan
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D002942:Circular Dichroism; D003596:Cytosine / Q000737:chemistry*; D019271:Hypoxanthine / Q000737:chemistry*; D008969:Molecular Sequence Data; D015394:Molecular Structure; D020135:Peptide Nucleic Acids / Q000737:chemistry*; D011759:Pyrrolidines / Q000737:chemistry*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013816:Thermodynamics
chemical_list: D020135:Peptide Nucleic Acids; D011759:Pyrrolidines; D019271:Hypoxanthine; D003596:Cytosine