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Peng H, Vu S, Retes P, Ward S, Kumar A, Sevilla MD, Adhikary A, Greenberg MM. Photochemical and Single Electron Transfer Generation of 2'-Deoxycytidin- N4-yl Radical from Oxime Esters. J Org Chem 2023; 88:7381-7390. [PMID: 37220149 PMCID: PMC10308854 DOI: 10.1021/acs.joc.3c00646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A 2'-deoxycytidin-N4-yl radical (dC·), a strong oxidant that also abstracts hydrogen atoms from carbon-hydrogen bonds, is produced in a variety of DNA damaging processes. We describe here the independent generation of dC· from oxime esters under UV-irradiation or single electron transfer conditions. Support for this σ-type iminyl radical generation is provided by product studies carried out under aerobic and anaerobic conditions, as well as electron spin resonance (ESR) characterization of dC· in a homogeneous glassy solution at low temperature. Density functional theory (DFT) calculations also support fragmentation of the corresponding radical anions of oxime esters 2d and 2e to dC· and subsequent hydrogen atom abstraction from organic solvents. The corresponding 2'-deoxynucleotide triphosphate (dNTP) of isopropyl oxime ester 2c (5) is incorporated opposite 2'-deoxyadenosine and 2'-deoxyguanosine by a DNA polymerase with approximately equal efficiency. Photolysis experiments of DNA containing 2c support dC· generation and indicate that the radical produces tandem lesions when flanked on the 5'-side by 5'-d(GGT). These experiments suggest that oxime esters are reliable sources of nitrogen radicals in nucleic acids that will be useful mechanistic tools and possibly radiosensitizing agents when incorporated in DNA.
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Affiliation(s)
- Haihui Peng
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Son Vu
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Parker Retes
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Samuel Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Michael D Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
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Espinasse A, Lembke HK, Cao AA, Carlson EE. Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications. RSC Chem Biol 2020; 1:333-351. [PMID: 33928252 PMCID: PMC8081287 DOI: 10.1039/d0cb00078g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities. Although the impact of nucleobase alterations has predominantly been studied due to their importance for protein recognition, sugar and phosphate modifications have also been investigated. However, NTPs are cell impermeable due to their negatively charged phosphate tail, a major hurdle to achieving live bacterial studies. Herein, we review the recent advances made to investigate and evolve bacteria and their processes with the use of modified NTPs by exploring alterations in one of the three moieties: the nucleobase, the sugar and the phosphate tail. We also present the innovative methods that have been devised to internalize NTPs into bacteria for in vivo applications.
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Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Hannah K. Lembke
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Angela A. Cao
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
- Department of Medicinal Chemistry, University of Minnesota208 Harvard Street SEMinneapolisMinnesota 55454USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota321 Church St SEMinneapolisMinnesota 55454USA
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Matyašovský J, Hocek M. 2-Substituted 2'-deoxyinosine 5'-triphosphates as substrates for polymerase synthesis of minor-groove-modified DNA and effects on restriction endonuclease cleavage. Org Biomol Chem 2020; 18:255-262. [PMID: 31815989 DOI: 10.1039/c9ob02502b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Five 2-substituted 2'-deoxyinosine triphosphates (dRITP) were synthesized and tested as substrates in enzymatic synthesis of minor-groove base-modified DNA. Only 2-methyl and 2-vinyl derivatives proved to be good substrates for Therminator DNA polymerase, whilst all other dRITPs and other tested DNA polymerases did not give full length products in primer extension. The DNA containing 2-vinylhypoxanthine was then further modified through thiol-ene reactions with thiols. Cross-linking reaction between cysteine-containing minor-groove binding dodecapeptide and DNA proceeded thanks to the proximity effect between thiol and vinyl groups inside the minor groove. 2-Substituted dIRTPs and also previously prepared 2-substituted 2'-deoxyadenosine triphosphates (dRATP) were then used for enzymatic synthesis of minor-groove modified DNA to study the effect of minor-groove modifications on cleavage of DNA by type II restriction endonucleases (REs). Although the REs should recognize the sequence through H-bonds in the major groove, some minor-groove modifications also had an inhibiting effect on the cleavage.
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Affiliation(s)
- Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
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