Binding affinity of a peptide nucleic acid containing pyrimido[4,5-d]pyrimidine-2,4,5,7-(1H,3H,6H,8H)-tetraone as a nucleobase for oligonucleotides.
In order to examine the potentiality as a universal nucleobase of pyrimido[4,5-d]pyrimidine-2,4,5,7-(1H,3H,6H,8H)-tetraone (PPT) incorporated in a peptide-nucleic acid (PNA), we synthesized a PNA with PPT, that is H-Gly-CCT(PPT)TCC-Lys-NH2, and investigated the duplex-formation ability of this PNA for the oligodeoxyribonucleotide, (5')GGAXAGG(3') (X = A, G, C or T) on the basis of the Tmvalue of a 1:1 mixture of the PNA and the oligonucleotide. As a result, we found that H-Gly-CCT(PPT)TCC-Lys-NH2 has good binding affinity for all the tested oligonucleotides, i.e., (5')GGAAAGG(3'), (5')GGAGAGG(3'), (5')GGACAGG(3') and (5')GGATAGG(3') and forms stable duplexes with these nucleotides. Thus, it was revealed that PPT serves as an excellent universal base in PNA to discriminate all natural nucleobases.
Hirano
Taisuke
T
Graduate School of Information Science, Nagoya University, Chikusa, Nagoya 4648601, Japan.
Kuroda
Kenji
K
Kataoka
Masanori
M
Hayakawa
Yoshihiro
Y
D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D020135:Peptide Nucleic Acids / Q000737:chemistry*; D011744:Pyrimidinones / Q000737:chemistry*
D009838:Oligodeoxyribonucleotides; D020135:Peptide Nucleic Acids; D011744:Pyrimidinones; C520194:pyrimido(4,5-d)pyrimidine-2,4,5,7-(1H,3H,6H,8H)-tetraone