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

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

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	128838
Journal	Bioorganic and Medicinal Chemistry Letters
Volume	71
DOIs	https://doi.org/10.1016/j.bmcl.2022.128838
Publication status	Published - Sept 1 2022

Keywords

DNA
Excimer
Fluorescence
Peptide nucleic acid
Pyrene

ASJC Scopus subject areas

Biochemistry
Molecular Medicine
Molecular Biology
Pharmaceutical Science
Drug Discovery
Clinical Biochemistry
Organic Chemistry

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10.1016/j.bmcl.2022.128838

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title = "Fluorescence ratiometric DNA detection by peptide nucleic acid-pyrene binary probes",

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",

author = "Koki Ishii and Sakura Tsuchitani and Miyu Toyama and Hajime Shigeto and Shohei Yamamura and Takashi Ohtsuki and Yoshitane Imai and Mizuki Kitamatsu",

note = "Funding Information: This work was supported by JST, CREST Grant Number JPMJCR2001 (to Y. I.). Publisher Copyright: {\textcopyright} 2022 Elsevier Ltd",

year = "2022",

month = sep,

day = "1",

doi = "10.1016/j.bmcl.2022.128838",

language = "English",

volume = "71",

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T1 - Fluorescence ratiometric DNA detection by peptide nucleic acid-pyrene binary probes

AU - Ishii, Koki

AU - Tsuchitani, Sakura

AU - Toyama, Miyu

AU - Shigeto, Hajime

AU - Yamamura, Shohei

AU - Ohtsuki, Takashi

AU - Imai, Yoshitane

AU - Kitamatsu, Mizuki

PY - 2022/9/1

Y1 - 2022/9/1

N2 - 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.

AB - 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.

KW - DNA

KW - Excimer

KW - Fluorescence

KW - Peptide nucleic acid

KW - Pyrene

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ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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