Synthesis and Enzymatic Incorporation of a Responsive Ribonucleoside Probe That Enables Quantitative Detection of Metallo-Base Pairs

Overview

Journal Org Lett

Publisher American Chemical Society

Specialties Biochemistry
Chemistry

Date 2019 Jun 12

PMID 31184159

Citations 3

Authors

Sudeshna Manna

Seergazhi G Srivatsan

Affiliations

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Abstract

Synthesis of a highly responsive fluorescent ribonucleoside analogue based on a 5-methoxybenzofuran uracil core, enzymatic incorporation of its triphosphate substrate into RNA transcripts, and its utility in the specific detection and estimation of Hg-ion-mediated metallo-base pair formation in DNA-RNA and RNA-RNA duplexes are described.

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References

Schmidt O, Mata G, Luedtke N . Fluorescent Base Analogue Reveals T-Hg-T Base Pairs Have High Kinetic Stabilities That Perturb DNA Metabolism. J Am Chem Soc. 2016; 138(44):14733-14739. DOI: 10.1021/jacs.6b09044. View

Dziuba D, Jurkiewicz P, Cebecauer M, Hof M, Hocek M . A Rotational BODIPY Nucleotide: An Environment-Sensitive Fluorescence-Lifetime Probe for DNA Interactions and Applications in Live-Cell Microscopy. Angew Chem Int Ed Engl. 2016; 55(1):174-8. DOI: 10.1002/anie.201507922. View

Tanaka Y, Oda S, Yamaguchi H, Kondo Y, Kojima C, Ono A . 15N-15N J-coupling across Hg(II): direct observation of Hg(II)-mediated T-T base pairs in a DNA duplex. J Am Chem Soc. 2007; 129(2):244-5. DOI: 10.1021/ja065552h. View

Ono A, Togashi H . Highly selective oligonucleotide-based sensor for mercury(II) in aqueous solutions. Angew Chem Int Ed Engl. 2004; 43(33):4300-2. DOI: 10.1002/anie.200454172. View

Ma D, He H, Leung K, Zhong H, Chan D, Leung C . Label-free luminescent oligonucleotide-based probes. Chem Soc Rev. 2013; 42(8):3427-40. DOI: 10.1039/c2cs35472a. View

Ono A, Torigoe H, Tanaka Y, Okamoto I . Binding of metal ions by pyrimidine base pairs in DNA duplexes. Chem Soc Rev. 2011; 40(12):5855-66. DOI: 10.1039/c1cs15149e. View

Sinkeldam R, Greco N, Tor Y . Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev. 2010; 110(5):2579-619. PMC: 2868948. DOI: 10.1021/cr900301e. View

Liu S, Clever G, Takezawa Y, Kaneko M, Tanaka K, Guo X . Direct conductance measurement of individual metallo-DNA duplexes within single-molecule break junctions. Angew Chem Int Ed Engl. 2011; 50(38):8886-90. DOI: 10.1002/anie.201102980. View

Zhang X, Li Y, Su H, Zhang S . Highly sensitive and selective detection of Hg2+ using mismatched DNA and a molecular light switch complex in aqueous solution. Biosens Bioelectron. 2009; 25(6):1338-43. DOI: 10.1016/j.bios.2009.10.023. View

10.

Tanpure A, Srivatsan S . A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site. Chemistry. 2011; 17(45):12820-7. DOI: 10.1002/chem.201101194. View

11.

Blanchard D, Manderville R . An internal charge transfer-DNA platform for fluorescence sensing of divalent metal ions. Chem Commun (Camb). 2016; 52(61):9586-8. DOI: 10.1039/c6cc04613d. View

12.

Pawar M, Srivatsan S . Synthesis, photophysical characterization, and enzymatic incorporation of a microenvironment-sensitive fluorescent uridine analog. Org Lett. 2011; 13(5):1114-7. DOI: 10.1021/ol103147t. View

13.

Pawar M, Nuthanakanti A, Srivatsan S . Heavy atom containing fluorescent ribonucleoside analog probe for the fluorescence detection of RNA-ligand binding. Bioconjug Chem. 2013; 24(8):1367-77. DOI: 10.1021/bc400194g. View

14.

Tanaka K, Clever G, Takezawa Y, Yamada Y, Kaul C, Shionoya M . Programmable self-assembly of metal ions inside artificial DNA duplexes. Nat Nanotechnol. 2008; 1(3):190-4. DOI: 10.1038/nnano.2006.141. View

15.

Kim S, Kool E . Sensing metal ions with DNA building blocks: fluorescent pyridobenzimidazole nucleosides. J Am Chem Soc. 2006; 128(18):6164-71. PMC: 2533741. DOI: 10.1021/ja0581806. View

16.

Wang Y, Geng F, Xu H, Qu P, Zhou X, Xu M . A label-free oligonucleotide based thioflavin-T fluorescent switch for Ag+ detection with low background emission. J Fluoresc. 2012; 22(3):925-9. DOI: 10.1007/s10895-011-1031-z. View

17.

Hollenstein M, Hipolito C, Lam C, Dietrich D, Perrin D . A highly selective DNAzyme sensor for mercuric ions. Angew Chem Int Ed Engl. 2008; 47(23):4346-50. DOI: 10.1002/anie.200800960. View

18.

Jakobsen U, Shelke S, Vogel S, Sigurdsson S . Site-directed spin-labeling of nucleic acids by click chemistry: detection of abasic sites in duplex DNA by EPR spectroscopy. J Am Chem Soc. 2010; 132(30):10424-8. DOI: 10.1021/ja102797k. View

19.

Liu C, Huang C, Chang H . Highly selective DNA-based sensor for lead(II) and mercury(II) ions. Anal Chem. 2009; 81(6):2383-7. DOI: 10.1021/ac8022185. View

20.

Doose S, Neuweiler H, Sauer M . Fluorescence quenching by photoinduced electron transfer: a reporter for conformational dynamics of macromolecules. Chemphyschem. 2009; 10(9-10):1389-98. DOI: 10.1002/cphc.200900238. View