Fluorescence ratiometric DNA detection by peptide nucleic acid-pyrene binary probes

Koki Ishii; Sakura Tsuchitani; Miyu Toyama; Hajime Shigeto; Shohei Yamamura; Takashi Ohtsuki; Yoshitane Imai; Mizuki Kitamatsu

doi:10.1016/j.bmcl.2022.128838

Fluorescence ratiometric DNA detection by peptide nucleic acid-pyrene binary probes

Bioorg Med Chem Lett. 2022 Sep 1:71:128838. doi: 10.1016/j.bmcl.2022.128838. Epub 2022 May 30.

Authors

Koki Ishii¹, Sakura Tsuchitani¹, Miyu Toyama¹, Hajime Shigeto², Shohei Yamamura², Takashi Ohtsuki³, Yoshitane Imai¹, Mizuki Kitamatsu⁴

Affiliations

¹ Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan.
² Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan.
³ Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan.
⁴ Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan. Electronic address: kitamatu@apch.kindai.ac.jp.

PMID: 35654301
DOI: 10.1016/j.bmcl.2022.128838

Abstract

We developed a method for detecting DNA by excimer fluorescence from two peptide nucleic acids (PNAs) modified with a pyrene (Pyr). The two PNA-Pyr probes were prepared by solid-phase peptide synthesis, and we assessed fluorescence from the mixture of probes with DNA. From the results, excimer fluorescence derived from the two PNA-Pyr probes forming hybrids with the complementary DNA was observed, and the two probes showed the maximum excimer/monomer ratio when the probes and DNA were hybridized at a 1:1:1 ratio, indicating that the PNA-Pyr probes can detect target DNA. Furthermore, we adjusted the spatial arrangement between the two PNA-Pyr hybrids formed on the DNA to promote optimal excimer formation. As a result, optimal excimer formation was achieved by spacing the two nucleobases between the formed two hybrids and further inserting a hexamethylene linker (C6) between the PNA and Pyr of the PNA-Pyr probe on one side.

Keywords: DNA; Excimer; Fluorescence; Peptide nucleic acid; Pyrene.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA
DNA Probes
Peptide Nucleic Acids*
Peptides
Pyrenes
Spectrometry, Fluorescence

Substances

DNA Probes
Peptide Nucleic Acids
Peptides
Pyrenes
DNA