Enzyme-Mediated Endogenous and Bioorthogonal Control of a DNAzyme Fluorescent Sensor for Imaging Metal Ions in Living Cells

Overview

Journal Angew Chem Int Ed Engl

Specialty Chemistry

Date 2019 Sep 19

PMID 31529664

Citations 23

Authors

Yao Lin

Zhenglin Yang

Ryan J Lake

Chengbin Zheng

Yi Lu

Affiliations

Soon will be listed here.

Abstract

Bioorthogonal control of metal-ion sensors for imaging metal ions in living cells is important for understanding the distribution and fluctuation of metal ions. Reported here is the endogenous and bioorthogonal activation of a DNAzyme fluorescent sensor containing an 18-base pair recognition site of a homing endonuclease (I-SceI), which is found by chance only once in 7×10 bp of genomic sequences, and can thus form a near bioorthogonal pair with I-SceI for DNAzyme activation with minimal effect on living cells. Once I-SceI is expressed inside cells, it cleaves at the recognition site, allowing the DNAzyme to adopt its active conformation. The activated DNAzyme sensor is then able to specifically catalyze cleavage of a substrate strand in the presence of Mg to release the fluorophore-labeled DNA fragment and produce a fluorescent turn-on signal for Mg . Thus I-SceI bioorthogonally activates the 10-23 DNAzyme for imaging of Mg in HeLa cells.

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References

Lu Y . New transition-metal-dependent DNAzymes as efficient endonucleases and as selective metal biosensors. Chemistry. 2002; 8(20):4588-96. DOI: 10.1002/1521-3765(20021018)8:20<4588::AID-CHEM4588>3.0.CO;2-Q. View

Wei W, Ba Z, Gao M, Wu Y, Ma Y, Amiard S . A role for small RNAs in DNA double-strand break repair. Cell. 2012; 149(1):101-12. DOI: 10.1016/j.cell.2012.03.002. View

Torabi S, Wu P, McGhee C, Chen L, Hwang K, Zheng N . In vitro selection of a sodium-specific DNAzyme and its application in intracellular sensing. Proc Natl Acad Sci U S A. 2015; 112(19):5903-8. PMC: 4434688. DOI: 10.1073/pnas.1420361112. View

Zhou W, Liang W, Li D, Yuan R, Xiang Y . Dual-color encoded DNAzyme nanostructures for multiplexed detection of intracellular metal ions in living cells. Biosens Bioelectron. 2016; 85:573-579. DOI: 10.1016/j.bios.2016.05.058. View

Nelson N . Metal ion transporters and homeostasis. EMBO J. 1999; 18(16):4361-71. PMC: 1171511. DOI: 10.1093/emboj/18.16.4361. View

Farris W, Mansourian S, Chang Y, Lindsley L, Eckman E, Frosch M . Insulin-degrading enzyme regulates the levels of insulin, amyloid beta-protein, and the beta-amyloid precursor protein intracellular domain in vivo. Proc Natl Acad Sci U S A. 2003; 100(7):4162-7. PMC: 153065. DOI: 10.1073/pnas.0230450100. View

Breaker R, Joyce G . A DNA enzyme that cleaves RNA. Chem Biol. 1994; 1(4):223-9. DOI: 10.1016/1074-5521(94)90014-0. View

Yang Z, Loh K, Chu Y, Feng R, Satyavolu N, Xiong M . Optical Control of Metal Ion Probes in Cells and Zebrafish Using Highly Selective DNAzymes Conjugated to Upconversion Nanoparticles. J Am Chem Soc. 2018; 140(50):17656-17665. PMC: 6473182. DOI: 10.1021/jacs.8b09867. View

Uhlenbeck O . Hammerhead ribozyme kinetics. RNA. 1998; 4(8):875-89. PMC: 1369666. DOI: 10.1017/s1355838298980876. View

10.

Katz S, Gimble F, Storici F . To nick or not to nick: comparison of I-SceI single- and double-strand break-induced recombination in yeast and human cells. PLoS One. 2014; 9(2):e88840. PMC: 3928301. DOI: 10.1371/journal.pone.0088840. View

11.

Domaille D, Que E, Chang C . Synthetic fluorescent sensors for studying the cell biology of metals. Nat Chem Biol. 2008; 4(3):168-75. DOI: 10.1038/nchembio.69. View

12.

Li J, Zheng W, Kwon A, Lu Y . In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme. Nucleic Acids Res. 1999; 28(2):481-8. PMC: 102519. DOI: 10.1093/nar/28.2.481. View

13.

Joyce G . Directed evolution of nucleic acid enzymes. Annu Rev Biochem. 2004; 73:791-836. DOI: 10.1146/annurev.biochem.73.011303.073717. View

14.

Wang W, Satyavolu N, Wu Z, Zhang J, Zhu J, Lu Y . Near-Infrared Photothermally Activated DNAzyme-Gold Nanoshells for Imaging Metal Ions in Living Cells. Angew Chem Int Ed Engl. 2017; 56(24):6798-6802. PMC: 5861726. DOI: 10.1002/anie.201701325. View

15.

Wu P, Hwang K, Lan T, Lu Y . A DNAzyme-gold nanoparticle probe for uranyl ion in living cells. J Am Chem Soc. 2013; 135(14):5254-7. PMC: 3644223. DOI: 10.1021/ja400150v. View

16.

Sakata T, Jackson D, Mao S, Marriott G . Optically switchable chelates: optical control and sensing of metal ions. J Org Chem. 2007; 73(1):227-33. PMC: 2518625. DOI: 10.1021/jo7019898. View

17.

Zhang J, Lan T, Lu Y . Molecular Engineering of Functional Nucleic Acid Nanomaterials toward In Vivo Applications. Adv Healthc Mater. 2019; 8(6):e1801158. PMC: 6426685. DOI: 10.1002/adhm.201801158. View

18.

Li Y, Sen D . Toward an efficient DNAzyme. Biochemistry. 1997; 36(18):5589-99. DOI: 10.1021/bi962694n. View

19.

Xiao L, Gu C, Xiang Y . Orthogonal Activation of RNA-Cleaving DNAzymes in Live Cells by Reactive Oxygen Species. Angew Chem Int Ed Engl. 2019; 58(40):14167-14172. DOI: 10.1002/anie.201908105. View

20.

Liu J, Brown A, Meng X, Cropek D, Istok J, Watson D . A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity. Proc Natl Acad Sci U S A. 2007; 104(7):2056-61. PMC: 1892917. DOI: 10.1073/pnas.0607875104. View