Quenching of fluorescently labeled pyrrolidinyl peptide nucleic acid by oligodeoxyguanosine and its application in DNA sensing

Organic & Biomolecular Chemistry
Chayan Charoenpakdee, Tirayut Vilaivan

Abstract

Quenching by nucleobases can significantly affect the fluorescence properties of many fluorophores. The quenching efficiency depends on the electronic properties of the fluorophore and adjacent nucleobases. In this study, we present a hitherto unreported high-efficiency quenching (up to 90%) of various fluorescently labeled pyrrolidinyl peptide nucleic acid (acpcPNA) probes by oligodeoxyguanosine (dGX). The quenching principle relies on the electrostatic interaction between the positively charged lysine-modified acpcPNA probe and the negatively charged oligodeoxyguanosine. The addition of stoichiometric quantities of a DNA target with the sequence complementary to the PNA probe restored the fluorescence to the original level. This was explained by the binding of the DNA to the PNA via a specific base pairing, which resulted in the separation of the oligodeoxyguanosine quencher from the fluorophore. Much less fluorescence restoration was observed in the DNA containing one or more mismatched bases. Applications of the oligodeoxyguanosine-quenched PNA probes for DNA sequence determination, including in multiplex formats, are demonstrated. The performance in terms of sensitivity and mismatch discrimination is comparable to classica...Continue Reading

References

Mar 1, 1996·Nature Biotechnology·S Tyagi, F R Kramer
May 8, 2002·Analytical Sciences : the International Journal of the Japan Society for Analytical Chemistry·M TorimuraR Kurane
Jul 13, 2006·The Journal of Physical Chemistry. a·Shunichi FukuzumiTomoyoshi Suenobu
Oct 31, 2007·Methods : a Companion to Methods in Enzymology·Sattanathan ParamasivanPhilip H Bolton
Mar 26, 2008·Chemical Society Reviews·Natarajan VenkatesanByeang Hyean Kim
May 29, 2009·Angewandte Chemie·Chun-Hua LuGuo-Nan Chen
May 29, 2009·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Sören DooseMarkus Sauer
Nov 4, 2010·Analytical and Bioanalytical Chemistry·Bernard Juskowiak
Mar 2, 2012·Organic Letters·Woraluk MansawatTirayut Vilaivan
Jul 4, 2012·Nucleic Acids Research·Adrien PadiracYannick Rondelez
Sep 27, 2012·Chemical Communications : Chem Comm·Hui ZhouGuo-Li Shen
Apr 20, 2013·The Analyst·Shuang GuoGuo-Jun Zhang
Apr 16, 2014·Analytical Chemistry·Rong HuWeihong Tan
Oct 7, 2014·Langmuir : the ACS Journal of Surfaces and Colloids·Joon Soo ParkDong-Eun Kim
Oct 8, 2014·The Journal of Physical Chemistry. a·Bishnu Thapa, H Bernhard Schlegel
Mar 18, 2015·Chemical Society Reviews·Jing ZhengWeihong Tan
May 30, 2015·Accounts of Chemical Research·Tirayut Vilaivan
Feb 20, 2016·Bioconjugate Chemistry·Nicole KretschyMark M Somoza
Mar 11, 2016·Accounts of Chemical Research·Felix Hövelmann, Oliver Seitz
Sep 27, 2016·Langmuir : the ACS Journal of Surfaces and Colloids·Chang LuJuewen Liu
Jan 21, 2017·Analytical Chemistry·Yan Du, Shaojun Dong
Aug 3, 2017·Journal of Biotechnology·Anjali GuptaNidhi Puri
Nov 21, 2017·ACS Chemical Biology·David L Wilson, Eric T Kool
Jan 11, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Gil Tae Hwang
Feb 7, 2018·Scientific Reports·Gonca BülbülSilvana Andreescu
Mar 7, 2018·Beilstein Journal of Organic Chemistry·Tirayut Vilaivan
Jun 4, 2019·Biosensors·Aditya BalajiJin Zhang
Sep 19, 2019·Organic & Biomolecular Chemistry·Boonsong DitmangkloTirayut Vilaivan
Sep 22, 2019·Current Opinion in Chemical Biology·Jacques SaarbachNicolas Winssinger

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Methods Mentioned

BETA
fluorescence
fluorescence studies
electrophoresis

Software Mentioned

Waters Empower

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