Thermodynamic versus Kinetic Products of DNA Alkylation as Modeled by Reaction of Deoxyadenosine

Veldhuyzen, Willem F.; Shallop, Anthony J.; Jones, R. A. C.; Rokita, Steven E.

doi:10.1021/ja011686d

Cited by 87 publications

(137 citation statements)

References 63 publications

Supporting

Mentioning

127

Contrasting

Order By: Relevance

“…A recent appreciation for the reversible nature of quinone methide alkylation (31,32) suggested that its transient adducts with DNA might function as effective delivery agents for this highly reactive intermediate just as a malondialdehyde adduct of deoxyguanosine (dG) efficiently transports malondialdehyde in vivo (33,34). Our laboratory had traditionally relied on a fluoride dependent deprotection of O-silylated precursors (QMP) and their site-directed conjugates for inducible alkylation by an ortho-benzoquinone methide intermediate (QM) (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Our laboratory had traditionally relied on a fluoride dependent deprotection of O-silylated precursors (QMP) and their site-directed conjugates for inducible alkylation by an ortho-benzoquinone methide intermediate (QM) (Fig. 2) (32,(35)(36)(37)(38)(39). However, a self-adduct formed within the oligonucleotide conjugate by its QM has now demonstrated a capacity for target-promoted QM transfer as described below.…”

Section: Resultsmentioning

confidence: 99%

“…The only nucleotide that does not readily form an adduct with QM is thymidine (32,37), and therefore a QMP conjugate containing only thymidine (T 10 -QMP) was synthesized. Incubation of this conjugate with KF for 24 h as described above yielded a single product in 98% as detected by HPLC.…”

Section: Addition Of Water To the Quinone Methide Is Not Competitive mentioning

confidence: 99%

See 2 more Smart Citations

A general strategy for target-promoted alkylation in biological systems

Zhou

Rokita²

2003

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

115

View full text Add to dashboard Cite

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

A general strategy for target-promoted alkylation in biological systems

Zhou

Rokita²

2003

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

115

View full text Add to dashboard Cite

“…Molecular modeling and the inherent nucleophilicity of N1 in dA lead us to suggest that 3 is the initial cross-linked product formed in duplex DNA from syn-5-(2′-deoxyuridinyl)-methyl radical (1) or the methide (20). 10,35 The disappearance of the cross-link product in the presence of azide can be explained via ratelimiting formation of an ion pair (IP, Scheme 5) or direct attack by the nucleophile on 3. In principle, these mechanisms are distinguishable from one another by measuring the observed rate constant for the disappearance of ISC as a function of azide concentration.…”

Section: What Is the Structure Of The Cross-linked Product?mentioning

confidence: 99%

Oxygen Independent DNA Interstrand Cross-Link Formation by a Nucleotide Radical

2005

View full text Add to dashboard Cite

A 5-(2′-Deoxyuridinyl)methyl radical (1) was independently generated from three photochemical precursors and is the first example of a DNA radical that forms interstrand cross-links. Oxygen labeling experiments support generation of 1 by all precursors. Interstrand cross-links are produced upon irradiation of DNA containing any of the precursors. Cross-linking occurs via reaction with the opposing 2′-deoxyadenosine and is independent of O 2 . The independence of cross-link formation on O 2 is explained by kinetic analysis, which shows that the radical reacts reversibly with O 2 . Examination of the effects of glutathione on cross-link formation under anaerobic conditions suggests that adoption of the syn-conformation by 1 is the rate-limiting step in the process. Interstrand crosslink formation is reversible in the presence of a good nucleophile. The stability of the interstrand cross-link suggests that the isolated molecule is a rearrangement product of that formed in solution. The rearrangement is a consequence of the isolation procedure but also occurs slowly in solution. Oxygen independent cross-link formation may be useful for the purposeful damage of DNA in hypoxic tumor cells, where O 2 is deficient.The biological importance of DNA damage is evident in many ways. The double sword nature of these chemical transformations is illustrated by their involvement in the etiology and treatment of cancer. 1-3 In addition, there is a growing appreciation of the importance of DNA damage in aging. 4-6 DNA radicals are an important family of reactive intermediates that give rise to modified intact polymers and also lead to single-and double-strand breaks. 7-9 Recently, we reported that an independently generated 5-(2′-deoxyuridinyl)methyl radical (1) produced interstrand cross-links (ISCs) with an opposing 2′-deoxyadenosine (dA) (Scheme 1). 10 The radical is derived from formal hydrogen atom abstraction from the methyl group of thymidine and is not believed to be formed in large amounts by ionizing radiation despite the low bond dissociation energy (BDE) of the carbon-hydrogen bonds and their accessibility in the major groove. The preliminary report concerning 1 was the first explicit example of DNA interstrand cross-link (ISC) formation through a nucleic acid radical. ISCs are often responsible for the cytotoxic effects of DNA damaging agents. 11,12 Hence, ISC formation by a radical produced in even small amounts (e.g., 1) by agents such as γ-radiolysis could be biologically significant. Our interest in the radical-mediated cross-link formation is enhanced by the observation that the process involving 1 is independent of O 2 . This suggests that, in addition to being chemically novel, the formation of interstrand cross-links from 1 may be useful in hypoxic cells, such as those present in tumors. In addition to arising from direct hydrogen atom abstraction, the 5-(2′-deoxyuridinyl)methyl radical (1) can be formed from a two-step process, such as that induced by the direct effect of γ-radiolysis (Scheme 1). In a...

show abstract

“…1-meG is a major lesion generated when tRNA is treated with MeI but is also repaired slowly compared to 1-meA or 3-meC [42]. The 3-meC and 1-meA are drawn as positively charged in solution; however, they could also exist as the neutral 6-imino (for 1-meA) or 4-imino (for 3-meC) forms, respectively, after isomerization and release of one proton from the exocyclic amino groups [62,63]. The imino nitrogen could serve as a hydrogen bond acceptor or a ligand to the active site metal, which may facilitate recognition of these two substrates.…”

Section: Substratesmentioning

confidence: 99%

Oxidative dealkylation DNA repair mediated by the mononuclear non-heme iron AlkB proteins

Mishina

2006

Journal of Inorganic Biochemistry

View full text Add to dashboard Cite

DNA can be damaged by various intracellular and environmental alkylating agents to produce alkylation base lesions. These base damages, if not repaired promptly, may cause genetic changes that lead to diseases such as cancer. Recently, it was discovered that some of the alkylation DNA base damage can be directly removed by a family of proteins called the AlkB proteins that utilize a mononuclear non-heme iron(II) and α-ketoglutarate as cofactor and cosubstrate. These proteins activate dioxygen and perform an unprecedented oxidative deal-kylation of the alkyl adducts on DNA heteroatoms. This review summarizes the discovery of this activity and the recent research advances in studying this unique DNA repair pathway. The focus is placed on the chemical mechanism and function of these proteins. KeywordsDNA repair; AlkB; ABH; Direct repair; Mononuclear non-heme iron; Dioxygenase; Oxidative dealkylation; Demethylation Direct repair of alkylation DNA damageCellular DNA is subject to nonenzymatic alkylation (methylation) by environmental or chemical mutagens, resulting in adducts that are toxic and mutagenic [1][2][3][4][5][6]. Organisms have evolved a variety of mechanisms to repair these mutagenic damages. Escherichia coli (E. coli) responds to this threat by activating an adaptive responsive pathway, mediated by the E. coli Ada protein [7]. Upon receiving a methyl group from the damaged DNA, Ada turns into a transcriptional activator and activates its own expression and that of the alkB gene and two other genes, alkA and aidB ( Fig. 1(a)) [4,7,8]. The upregulated Ada is a bifunctional protein, which uses a N-terminal Cys38 residue to remove a methyl group fromS p -methylphosphotriester and a C-terminal Cys321 residue to remove a methyl adduct from O 6 -methylguanaine ( Fig. 1(b)) [9][10][11]. Both repair functions are irreversible and represent rare examples of direct repair of DNA damage. AlkA is a glycosylase that cleaves methylated bases from DNA and performs the first step of the well-known base excision repair of base lesions [12][13][14]. The precise function of AidB is still unknown. The function of the last member of this adaptive response, AlkB, also remained unknown until recently despite extensive research efforts. E. coli AlkBSince the first genetic study in 1983 isolating the E. coli mutant with specific sensitivity to the alkylating agent methylmethane sulfonate, MMS [15], the activity of AlkB was undisclosed The Fe II /αKG-dependent dioxygenase superfamily is widespread from bacteria to humans [19] and is the largest known non-heme iron protein family [20][21][22][23]. It represents a wide diversity of enzymes that catalyze the hydroxylation of unactivated C-H groups of a variety of substrates by coupling reductive activation of dioxygen with a decarbox-ylation of αKG, the co-substrate, to succinate. In the event of oxidation one of the oxygen atoms from O 2 is incorporated into the succinate and the other as a hydroxyl in the product [24]. This group of enzymes is known for their importance in ...

show abstract

Thermodynamic versus Kinetic Products of DNA Alkylation as Modeled by Reaction of Deoxyadenosine

Cited by 87 publications

References 63 publications

A general strategy for target-promoted alkylation in biological systems

A general strategy for target-promoted alkylation in biological systems

Oxygen Independent DNA Interstrand Cross-Link Formation by a Nucleotide Radical

Oxidative dealkylation DNA repair mediated by the mononuclear non-heme iron AlkB proteins

Contact Info

Product

Resources

About