Enrichment and Fluorogenic Labelling of 5-formyluracil in DNA

Overview

Journal Chem Sci

Publisher Royal Society of Chemistry

Specialty Chemistry

Date 2017 Jun 30

PMID 28660064

Citations 8

Authors

Chaoxing Liu

Yafen Wang

Xiong Zhang

Fan Wu

Wei Yang

Guangrong Zou

Qian Yao

Jiaqi Wang

Yuqi Chen

Shaoru Wang

Xiang Zhou

Affiliations

Soon will be listed here.

Abstract

Recently, the detection of natural thymine modified 5-formyluracil has attracted widespread attention. Herein, we introduce a new insight into designing reagents for both the selective biotin enrichment and fluorogenic labelling of 5-formyluracil in DNA. Biotinylated -phenylenediamine directly tethered to naphthalimide can switch on 5-formyluracil, under physiological conditions, which can then be used in cell imaging after exposure to γ-irradiation. In addition, its labelling property caused the polymerase extension to stop in the 5-formyluracil site, which gave us more information than the fluorescence did itself. The idea of detecting 5-formyluracil might be used in the synthesis of other modified diaminofluoresceins.

Citing Articles

Oxime formation coordination-directed detection of genome-wide thymine oxides with nanogram-scale sample input.

Xiao F, Wang Q, Zhang K, Liu C, Zou G, Zhou X Chem Sci. 2022; 13(31):9074-9078.

PMID: 36091206 PMC: 9365094. DOI: 10.1039/d2sc03013f.

Epigenetic Pyrimidine Nucleotides in Competition with Natural dNTPs as Substrates for Diverse DNA Polymerases.

Pospisil S, Panattoni A, Gracias F, Sykorova V, Vankova Hausnerova V, Vitovska D ACS Chem Biol. 2022; 17(10):2781-2788.

PMID: 35679536 PMC: 9594043. DOI: 10.1021/acschembio.2c00342.

Quantification and mapping of DNA modifications.

Dai Y, Yuan B, Feng Y RSC Chem Biol. 2021; 2(4):1096-1114.

PMID: 34458826 PMC: 8341653. DOI: 10.1039/d1cb00022e.

Ultrasensitive recognition of AP sites in DNA at the single-cell level: one molecular rotor sequentially self-regulated to form multiple different stable conformations.

Feng B, Wang K, Yang Y, Wang G, Zhang H, Liu Y Chem Sci. 2020; 10(44):10373-10380.

PMID: 32110326 PMC: 6988597. DOI: 10.1039/c9sc04140k.

Polymerization retardation isothermal amplification (PRIA): a strategy enables sensitively quantify genome-wide 5-methylcytosine oxides rapidly on handy instruments with nanoscale sample input.

Chen D, Wang Y, Mo M, Zhang J, Zhang Y, Xu Y Nucleic Acids Res. 2019; 47(19):e119.

PMID: 31418020 PMC: 6821303. DOI: 10.1093/nar/gkz704.

References

Yu H, Xiao Y, Jin L . A lysosome-targetable and two-photon fluorescent probe for monitoring endogenous and exogenous nitric oxide in living cells. J Am Chem Soc. 2012; 134(42):17486-9. DOI: 10.1021/ja308967u. View

Raiber E, Beraldi D, Ficz G, Burgess H, Branco M, Murat P . Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase. Genome Biol. 2012; 13(8):R69. PMC: 3491369. DOI: 10.1186/gb-2012-13-8-r69. View

Pfaffeneder T, Hackner B, Truss M, Munzel M, Muller M, Deiml C . The discovery of 5-formylcytosine in embryonic stem cell DNA. Angew Chem Int Ed Engl. 2011; 50(31):7008-12. DOI: 10.1002/anie.201103899. View

Kamiya H, Murata-Kamiya N, Karino N, Ueno Y, Matsuda A, Kasai H . Induction of T --> G and T --> A transversions by 5-formyluracil in mammalian cells. Mutat Res. 2001; 513(1-2):213-22. DOI: 10.1016/s1383-5718(01)00312-6. View

Sasaki E, Kojima H, Nishimatsu H, Urano Y, Kikuchi K, Hirata Y . Highly sensitive near-infrared fluorescent probes for nitric oxide and their application to isolated organs. J Am Chem Soc. 2005; 127(11):3684-5. DOI: 10.1021/ja042967z. View

Chan J, Dodani S, Chang C . Reaction-based small-molecule fluorescent probes for chemoselective bioimaging. Nat Chem. 2012; 4(12):973-84. PMC: 4096518. DOI: 10.1038/nchem.1500. View

Samanta B, Seikowski J, Hobartner C . Fluorogenic Labeling of 5-Formylpyrimidine Nucleotides in DNA and RNA. Angew Chem Int Ed Engl. 2015; 55(5):1912-6. DOI: 10.1002/anie.201508893. View

Kawasaki F, Murat P, Li Z, Santner T, Balasubramanian S . Synthesis and biophysical analysis of modified thymine-containing DNA oligonucleotides. Chem Commun (Camb). 2017; 53(8):1389-1392. PMC: 5759927. DOI: 10.1039/c6cc08670e. View

Hardisty R, Kawasaki F, Sahakyan A, Balasubramanian S . Selective Chemical Labeling of Natural T Modifications in DNA. J Am Chem Soc. 2015; 137(29):9270-2. PMC: 4521287. DOI: 10.1021/jacs.5b03730. View

10.

Gabe Y, Urano Y, Kikuchi K, Kojima H, Nagano T . Highly sensitive fluorescence probes for nitric oxide based on boron dipyrromethene chromophore-rational design of potentially useful bioimaging fluorescence probe. J Am Chem Soc. 2004; 126(10):3357-67. DOI: 10.1021/ja037944j. View

11.

Tang Y, Xiong J, Jiang H, Zheng S, Feng Y, Yuan B . Determination of oxidation products of 5-methylcytosine in plants by chemical derivatization coupled with liquid chromatography/tandem mass spectrometry analysis. Anal Chem. 2014; 86(15):7764-72. DOI: 10.1021/ac5016886. View

12.

Jeffet J, Kobo A, Su T, Grunwald A, Green O, Nilsson A . Super-Resolution Genome Mapping in Silicon Nanochannels. ACS Nano. 2016; 10(11):9823-9830. DOI: 10.1021/acsnano.6b05398. View

13.

Rogstad D, Liu P, Burdzy A, Lin S, Sowers L . Endogenous DNA lesions can inhibit the binding of the AP-1 (c-Jun) transcription factor. Biochemistry. 2002; 41(25):8093-102. DOI: 10.1021/bi012180a. View

14.

Hong H, Wang Y . Derivatization with Girard reagent T combined with LC-MS/MS for the sensitive detection of 5-formyl-2'-deoxyuridine in cellular DNA. Anal Chem. 2006; 79(1):322-6. PMC: 2531228. DOI: 10.1021/ac061465w. View

15.

Pfaffeneder T, Spada F, Wagner M, Brandmayr C, Laube S, Eisen D . Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA. Nat Chem Biol. 2014; 10(7):574-81. DOI: 10.1038/nchembio.1532. View

16.

Hu J, Xing X, Xu X, Wu F, Guo P, Yan S . Selective chemical labelling of 5-formylcytosine in DNA by fluorescent dyes. Chemistry. 2013; 19(19):5836-40. DOI: 10.1002/chem.201300082. View

17.

Howorka S, Siwy Z . Nanopores and Nanochannels: From Gene Sequencing to Genome Mapping. ACS Nano. 2016; 10(11):9768-9771. DOI: 10.1021/acsnano.6b07041. View

18.

Guo P, Xu X, Qiu X, Zhou Y, Yan S, Wang C . Synthesis and spectroscopic properties of fluorescent 5-benzimidazolyl-2'-deoxyuridines 5-fdU probes obtained from o-phenylenediamine derivatives. Org Biomol Chem. 2013; 11(10):1610-3. DOI: 10.1039/c3ob27519a. View

19.

Hirose W, Sato K, Matsuda A . Selective detection of 5-formyl-2'-deoxyuridine, an oxidative lesion of thymidine, in DNA by a fluorogenic reagent. Angew Chem Int Ed Engl. 2010; 49(45):8392-4. DOI: 10.1002/anie.201004087. View

20.

Klungland A, Paulsen R, Rolseth V, Yamada Y, Ueno Y, Wiik P . 5-Formyluracil and its nucleoside derivatives confer toxicity and mutagenicity to mammalian cells by interfering with normal RNA and DNA metabolism. Toxicol Lett. 2001; 119(1):71-8. DOI: 10.1016/s0378-4274(00)00308-8. View