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. 2019 Oct 21;32(10):2118-2124.
doi: 10.1021/acs.chemrestox.9b00299. Epub 2019 Sep 30.

Reactivity of N3-Methyl-2'-Deoxyadenosine in Nucleosome Core Particles

Kun Yang  1 , Huabing Sun  1 , Leah Lowder  2 , Sridhar Varadarajan  2 , Marc M Greenberg  1
Affiliations

Reactivity of N3-Methyl-2'-Deoxyadenosine in Nucleosome Core Particles

Kun Yang et al. Chem Res Toxicol. .

Abstract

N3-Methyl-2'-deoxyadenosine (MdA) is the major dA methylation product in duplex DNA. MdA blocks DNA replication and undergoes depurination at significantly higher rates than the native nucleotide from which it is derived. Recent reports on the effects of the nucleosome core particle (NCP) environment on the reactivity of N7-methyl-2'-deoxyguanosine (MdG) inspired this investigation concerning the reactivity of MdA in NCPs. NCPs containing MdA at selected positions were produced using a strategy in which the minor groove binding Me-Lex molecule serves as a sequence specific methylating agent. Hydrolysis of the glycosidic bond in MdA to form abasic sites (AP) is suppressed in a NCP. Experiments using histone variants indicate that the proximal, highly basic N-terminal tails are partially responsible for the decreased depurination rate constant. MdA also forms cross-links with histone proteins. The levels of MdA-histone DNA-protein cross-links (DPCMdA) decrease significantly over time and are replaced by those involving AP. The time dependent decrease in DPCMdA is attributed to the reversibility of their formation and the relatively rapid rate of AP formation from MdA. Overall, MdA reactivity in NCPs qualitatively resembles that of MdG.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Chart 1
Chart 1. DNA Methylating Agents
Scheme 1
Scheme 1. Formation and Reactivity of Methylated Purines
Figure 1
Figure 1
Me-Lex alkylation of free 601 DNA. The length of the lines is proportional to the amount of strand damage detected.
Scheme 2
Scheme 2. Selective Introduction of MdA into DNA Using Me-Lex
Scheme 3
Scheme 3. Distinguishing MdA from AP
Figure 2
Figure 2
Nucleosome core particle structure in the vicinity of MdA58, MdA59, MdA234, and MdA235. (A) Major region damaged by Me-Lex showing histone H3 (blue) and H4 (green) N-terminal tails. (B) Zoomed in region showing C2-positions (red arrows) of alkylated dAs. The structure is generated by superimposing two NCP structures (pdb: 1kx5 and 3lz0).
Scheme 4
Scheme 4. Distinguishing DPCs Formed from MdA and AP
Figure 3
Figure 3
Distribution of DPCs as a function of time from (A) MdA58, (B) MdA59, (C) MdA234, and (D) MdA235.
See this image and copyright information in PMC

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