Cleavage at 5-methylcytosine in DNA by photosensitized oxidation with 2-methyl-1,4-naphthoquinone tethered oligodeoxynucleotides

Yamada, Hisatsugu; Tanabe, Kazuhito; Nishimoto, Sei‐ichi

doi:10.1016/j.bmcl.2004.11.038

Cited by 17 publications

(21 citation statements)

References 17 publications

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“…Coupling of N ‐hydroxysuccinimidyl ester 1 with ODN N gave the desired ODN F1 29. 30 The crude ODN F1 was purified by reversed phase HPLC and the incorporation of d F1 U was confirmed by enzymatic digestion and ESI‐TOF mass spectrometry.…”

Section: Resultsmentioning

confidence: 99%

Probing DNA Mismatched and Bulged Structures by Using ¹⁹F NMR Spectroscopy and Oligodeoxynucleotides with an ¹⁹F‐Labeled Nucleobase

Tanabe

Tsuda

Itô

et al. 2013

Chemistry A European J

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In this study, DNA local structures with bulged bases and mismatched base pairs as well as ordinary full-matched base pairs by using (19)F NMR spectroscopy with (19)F-labeled oligodeoxynucleotides (ODNs) were monitored. The chemical shift change in the (19) F NMR spectra allowed discrimination of the DNA structures. Two types of ODNs possessing the bis(trifluoromethyl)benzene unit (F-unit) at specified uridines were prepared and hybridized with their complementary or noncomplementary strands to form matched, mismatched, or bulged duplexes. By using ODN F1, in which an F-unit was connected directly to a propargyl amine-substituted uridine, three local structures, that is, full-matched, G-U mismatch, and A-bulge could be analyzed, whereas other structures could not be discriminated. A molecular modeling study revealed that the F-unit in ODN F1 interacted little with the nucleobases and sugar backbone of the opposite strand because the linker length between the F-unit and the uridine base was too short. Therefore, the capacity of ODN F1 to discriminate the DNA local structures was limited. Thus, ODN F2 was designed to improve this system; aminobenzoic acid was inserted between the F-unit and uridine base so the F-unit could interact more closely with the opposite strand. Eventually, the G-bulge and T-U mismatch and the three aforementioned local structures could be discriminated by using ODN F2. In addition, the dissociation processes of these duplexes could be monitored concurrently by (19)F NMR spectroscopy.

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Section: Resultsmentioning

confidence: 99%

Probing DNA Mismatched and Bulged Structures by Using ¹⁹F NMR Spectroscopy and Oligodeoxynucleotides with an ¹⁹F‐Labeled Nucleobase

Tanabe

Tsuda

Itô

et al. 2013

Chemistry A European J

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“…This is a major pathway for the radical cations of T and 5-methylcytosine . Recently, similar reactions were implicated in the formation of breaks in AQ− and menadione−DNA duplexes . Thus, it is reasonable to propose that T methyl radicals in AQ−DNA duplexes react with AQ semi-quinone radicals to give cross-links.…”

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confidence: 94%

Near-UV Induced Interstrand Cross-Links in Anthraquinone−DNA Duplexes

2006

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Anthraquinone (AQ) has been extensively used as a photosensitizer to study charge transfer in DNA. Near-UV photolysis of AQ induces electron abstraction in oligonucleotides leading to AQ radical anions and base radical cations. In general, this reaction is followed by the transport of base radical cations to sites of low oxidation potential, that is, GG, and conversion of G radical cations to DNA breaks. Here, we show that AQ also produces interstrand cross-links in DNA duplexes. About half of the cross-links collapse to single strands in hot piperidine treatment. The structure of stable interstrand cross-links was deduced by MS, NMR, and sequence substitution. The cross-links consist of a covalent link between the methyl group of T on one strand with either C6 or C7 of AQ on the other strand. The formation of interstrand cross-links decreased in O2 compared to deoxygenated solutions. In the presence of O2, the yield of breaks at GG doublets was 10-fold greater than that of cross-links for end tethered AQ, while cross-links exceeded breaks for centrally located AQ. The formation of stable cross-links can be explained by initial charge transfer from T to excited AQ, deprotonation of T radical cations, and condensation of the latter species with AQ radicals. These studies reveal a novel pathway of damage in the photolysis of AQ-DNA duplexes.

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“…The presence of a substituent at C3 of this MQ derivative may have limited its reactivity toward the formation of cross-links by charge transfer and radical condensation. Interestingly, Yamada and co-workers used a similar oligonucleotide construct in which DNA was attached to MQ via a spacer at C3 to investigate charge transfer in DNA (62). In this work, the authors reported charge transfer at a distance leading to cleavage at 5-methylcytosine in the oligonucleotide, but they did not report the formation of cross-links.…”

Section: Discussionmentioning

confidence: 98%

Near-UV Photolysis of 2-Methyl-1,4-naphthoquinone−DNA Duplexes: Characterization of Reversible and Stable Interstrand Cross-Links between Quinone and Adenine Moieties

Bergeron

Klarskov

Hunting

et al. 2007

Chem. Res. Toxicol.

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Near-UV photolysis of 2-methyl-1,4-naphthoquinone (MQ, menadione) tethered DNA induces initial charge transfer followed by either transport of the damage to G or the formation of interstrand cross-links between MQ and DNA bases. In this work, the products responsible for interstrand cross-links have been characterized by mass spectrometry, NMR, and comparison with model compounds. Three major products were formed in the photolysis of MQ-DNA duplexes. Two of the products (isomers) have a cross-link between C2 of a 2,3-saturated MQ moiety and N6 of a dAdo moiety. These products readily convert back to MQ and dAdo upon heating in neutral solution, and thus, they lead to reversible cross-links in MQ-DNA duplexes. The third product has a cross-link between C3 of a 2,3-unsaturated MQ moiety and N6 of an dAdo moiety. This product was stable in neutral solution. The formation of MQ to A cross-links in DNA may be explained by the coupling of MQ radicals that arise from the protonation of MQ radical anions, together with adenin-N6-yl radicals that arise from the deprotonation of A radical cations.

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Cleavage at 5-methylcytosine in DNA by photosensitized oxidation with 2-methyl-1,4-naphthoquinone tethered oligodeoxynucleotides

Cited by 17 publications

References 17 publications

Probing DNA Mismatched and Bulged Structures by Using ¹⁹F NMR Spectroscopy and Oligodeoxynucleotides with an ¹⁹F‐Labeled Nucleobase

Probing DNA Mismatched and Bulged Structures by Using ¹⁹F NMR Spectroscopy and Oligodeoxynucleotides with an ¹⁹F‐Labeled Nucleobase

Near-UV Induced Interstrand Cross-Links in Anthraquinone−DNA Duplexes

Near-UV Photolysis of 2-Methyl-1,4-naphthoquinone−DNA Duplexes: Characterization of Reversible and Stable Interstrand Cross-Links between Quinone and Adenine Moieties

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Cleavage at 5-methylcytosine in DNA by photosensitized oxidation with 2-methyl-1,4-naphthoquinone tethered oligodeoxynucleotides

Cited by 17 publications

References 17 publications

Probing DNA Mismatched and Bulged Structures by Using 19F NMR Spectroscopy and Oligodeoxynucleotides with an 19F‐Labeled Nucleobase

Probing DNA Mismatched and Bulged Structures by Using 19F NMR Spectroscopy and Oligodeoxynucleotides with an 19F‐Labeled Nucleobase

Near-UV Induced Interstrand Cross-Links in Anthraquinone−DNA Duplexes

Near-UV Photolysis of 2-Methyl-1,4-naphthoquinone−DNA Duplexes: Characterization of Reversible and Stable Interstrand Cross-Links between Quinone and Adenine Moieties

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Probing DNA Mismatched and Bulged Structures by Using ¹⁹F NMR Spectroscopy and Oligodeoxynucleotides with an ¹⁹F‐Labeled Nucleobase

Probing DNA Mismatched and Bulged Structures by Using ¹⁹F NMR Spectroscopy and Oligodeoxynucleotides with an ¹⁹F‐Labeled Nucleobase