Design of Tail-Clamp Peptide Nucleic Acid Tethered with Azobenzene Linker for Sequence-Specific Detection of Homopurine DNA

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
Shinjiro SawadaKunihiro Kaihatsu

Abstract

DNA carries genetic information in its sequence of bases. Synthetic oligonucleotides that can sequence-specifically recognize a target gene sequence are a useful tool for regulating gene expression or detecting target genes. Among the many synthetic oligonucleotides, tail-clamp peptide nucleic acid (TC-PNA) offers advantages since it has two homopyrimidine PNA strands connected via a flexible ethylene glycol-type linker that can recognize complementary homopurine sequences via Watson-Crick and Hoogsteen base pairings and form thermally-stable PNA/PNA/DNA triplex structures. Here, we synthesized a series of TC-PNAs that can possess different lengths of azobenzene-containing linkers and studied their binding behaviours to homopurine single-stranded DNA. Introduction of azobenzene at the N-terminus amine of PNA increased the thermal stability of PNA-DNA duplexes. Further extension of the homopyrimidine PNA strand at the N-terminus of PNA-AZO further increased the binding stability of the PNA/DNA/PNA triplex to the target homopurine sequence; however, it induced TC-PNA/DNA/TC-PNA complex formation. Among these TC-PNAs, 9W5H-C4-AZO consisting of nine Watson-Crick bases and five Hoogsteen bases tethered with a beta-alanine conjugated...Continue Reading

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Citations

Jan 3, 2019·The Analyst·Tatiana A LyalinaDmitry M Kolpashchikov
Nov 16, 2019·Beilstein Journal of Organic Chemistry·Lei ZhangOlalla Vázquez
Feb 15, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Kenji TakagiKunihiro Kaihatsu
Aug 12, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Roberto Corradini
Jul 11, 2021·Biosensors & Bioelectronics·Marcello MasciniSylvia Daunert

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Methods Mentioned

BETA
electrophoresis
gel
gel mobility shift assay

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