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5‘ Modification of Duplex DNA with a Ruthenium Electron Donor−Acceptor Pair Using Solid-Phase DNA Synthesis

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California Institute of Technology, The Beckman Institute 139-74, Pasadena, California 91125
Cite this: Inorg. Chem. 2003, 42, 4, 1039–1044
Publication Date (Web):January 21, 2003
Copyright © 2003 American Chemical Society

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    Incorporation of metalated nucleosides into DNA through covalent modification is crucial to measurement of thermal electron-transfer rates and the dependence of these rates with structure, distance, and position. Here, we report the first synthesis of an electron donor−acceptor pair of 5‘ metallonucleosides and their subsequent incorporation into oligonucleotides using solid-phase DNA synthesis techniques. Large-scale syntheses of metal-containing oligonucleotides are achieved using 5‘ modified phosporamidites containing [Ru(acac)2(IMPy)]2+ (acac is acetylacetonato; IMPy is 2‘-iminomethylpyridyl-2‘-deoxyuridine) (3) and [Ru(bpy)2(IMPy)]2+ (bpy is 2,2‘-bipyridine; IMPy is 2‘-iminomethylpyridyl-2‘-deoxyuridine) (4). Duplexes formed with the metal-containing oligonucleotides exhibit thermal stability comparable to the corresponding unmetalated duplexes (Tm of modified duplex = 49 °C vs Tm of unmodified duplex = 47 °C). Electrochemical (3, E1/2 = −0.04 V vs NHE; 4, E1/2 = 1.12 V vs NHE), absorption (3, λmax = 568, 369 nm; 4, λmax = 480 nm), and emission (4, λmax = 720 nm, τ = 55 ns, Φ = 1.2 × 10-4) data for the ruthenium-modified nucleosides and oligonucleotides indicate that incorporation into an oligonucleotide does not perturb the electronic properties of the ruthenium complex or the DNA significantly. In addition, the absence of any change in the emission properties upon metalated duplex formation suggests that the [Ru(bpy)2(IMPy)]2+[Ru(acac)2(IMPy)]2+ pair will provide a valuable probe for DNA-mediated electron-transfer studies.

     Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700. E-mail:  [email protected]. Phone:  (206) 543-9835. Fax:  (206) 685-8665.


     To whom correspondence should be addressed. Department of Chemistry, Department of Biochemistry, Molecular Biology and Cell Biology, Department of Neurobiology and Physiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113. E-mail:  [email protected]. Phone:  (847) 491-2481. Fax:  (847) 491-3832.

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    1. Mikael Madsen, Kurt V. Gothelf. Chemistries for DNA Nanotechnology. Chemical Reviews 2019, 119 (10) , 6384-6458.
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    3. Seann P. Mulcahy, Shan Li, Ricarda Korn, Xiulan Xie and Eric Meggers. Solid-Phase Synthesis of Tris-heteroleptic Ruthenium(II) Complexes and Application to Acetylcholinesterase Inhibition. Inorganic Chemistry 2008, 47 (12) , 5030-5032.
    4. Lihui Wei,, John Babich,, William C. Eckelman, and, Jon Zubieta. Rhenium Tricarbonyl Core Complexes of Thymidine and Uridine Derivatives. Inorganic Chemistry 2005, 44 (7) , 2198-2209.
    5. Alfredo M. Angeles-Boza,, Patricia M. Bradley,, Patty K.-L. Fu,, Sara E. Wicke,, John Bacsa,, Kim R. Dunbar, and, Claudia Turro. DNA Binding and Photocleavage in Vitro by New Dirhodium(II) dppz Complexes:  Correlation to Cytotoxicity and Photocytotoxicity. Inorganic Chemistry 2004, 43 (26) , 8510-8519.
    6. Aisling Byrne, Christopher S. Burke, Tia E. Keyes. Precision targeted ruthenium( ii ) luminophores; highly effective probes for cell imaging by stimulated emission depletion (STED) microscopy. Chemical Science 2016, 7 (10) , 6551-6562.
    7. Yeng Ying Lee, Stephen G. Parker, Abbas Barfidokht, Muhammad Tanzirul Alam, D. Barney Walker, Barbara A. Messerle, J. Justin Gooding. A Ruthenium Based Organometallic Complex for Biosensing that is both a Stable Redox Label and a Homobifunctional Linker. Electroanalysis 2015, 27 (5) , 1078-1085.
    8. Yeng Ying Lee, D. Barney Walker, J. Justin Gooding, Barbara A. Messerle. Ruthenium( ii ) complexes containing functionalised β-diketonate ligands: developing a ferrocene mimic for biosensing applications. Dalton Trans. 2014, 43 (33) , 12734-12742.
    9. Carl P. Myers, Mary Elizabeth Williams. Directed self-assembly of inorganic redox complexes with artificial peptide scaffolds. Coordination Chemistry Reviews 2010, 254 (19-20) , 2416-2428.
    10. Amanda L. Eckermann, Daniel J. Feld, Justine A. Shaw, Thomas J. Meade. Electrochemistry of redox-active self-assembled monolayers. Coordination Chemistry Reviews 2010, 254 (15-16) , 1769-1802.
    11. Kristmann Gislason, Snorri T. Sigurdsson. Synthesis of a 5′‐6‐Locked, 1,10‐Phenanthroline‐Containing Nucleoside and Its Incorporation into DNA. European Journal of Organic Chemistry 2010, 2010 (24) , 4713-4718.
    12. Peijiao Wang, Jeremiah E. Miller, Lawrence M. Henling, Charlotte L. Stern, Natia L. Frank, Amanda L. Eckermann, Thomas J. Meade. Synthesis and Characterization of Ruthenium and Rhenium Nucleosides. Inorganic Chemistry 2007, 46 (23) , 9853-9862.
    13. Megan M. Knagge, Jonathan J. Wilker. Ligand-based backbone modifications for metal-chelating nucleic acids. Chemical Communications 2007, 12 (32) , 3356.

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