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

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.

In vitro eradication of abasic site-mediated DNA–peptide/protein cross-links by Escherichia coli long-patch base excision repair

“…An AP site is one of the most abundant endogenous DNA lesions ( 2 ). It acts as an electrophile that can react with protein nucleophiles ( e.g., lysine and cysteine residues) to yield various types of covalent DPCs including Schiff base ( 16 , 17 , 18 , 22 , 24 , 25 , 45 , 46 ), thiazolidine ( 47 , 48 , 49 , 50 ), S -glycosidic ( 51 ), and N -glycosidic ( 52 , 53 ) bond-linked AP-protein adducts. These DPCs are either new types of DNA lesions or proposed to temporarily protect the lesions from the error-prone repair ( 17 , 49 ).…”

Proteomics Study of DNA–Protein Crosslinks in Methylmethanesulfonate and Fe2+-EDTA-Exposed Human Cells

“…Of the most concern among the different types of DNA crosslinks is the covalent linkage of DNA to proteins, which are known to pose adverse physiological effects in cells. , For example, the covalently bound DNA–protein cross-link (DPC) product 1 (see Figure ) was identified to originate from a lysine residue of human DNA polymerase β reacting with a 2-deoxyribonolactone unit found in a DNA molecule that suffered a C1′-oxidation damage, affecting the function of a key enzyme in the base excision repair machinery. − Another example involved 8-oxo-dG, which is one of the most abundant oxidative stress-induced DNA lesions, being further converted to reactive species and coupled with histone proteins in nucleosome core particles to produce DPC 2 (see Figure ). It was also reported that DPCs 3 and 4 (see Figure ) were produced when methylating agent-induced apurinic/apyrimidinic (AP) sites in DNA condensed with lysine and cysteine residues in proteins of human cells. − …”

“…In contrast, reversible and specific noncovalent interactions of DNA with proteins, mediated by van der Waals forces, hydrogen bonding, and ionic interactions, are ubiquitous in all organisms and are fundamental to many biological processes, particularly in regulating gene expression, replication, repair, and transcription. − Since the formation of covalently bound DPCs upon toxicant exposure would disrupt DNA–protein interactions that are part of normal cell physiology, they are extremely toxic. For example, DPCs can completely block DNA replication and transcription, and they can ultimately threaten genomic integrity and cell viability .…”

“…The resulting AP sites are reactive toward lysine and cysteine residues on proteins in their proximity to form DPCs (Figure ). − It was also found that the MMS-exposure-induced N7-methyl-2′-deoxyguanosine further reacts with histone proteins to form crosslinks . Results from previous studies showed an elevated concentration of DPCs in MMS-exposed cells without identifying the specific DPC-forming proteins .…”

“…9 It was also reported that DPCs 3 and 4 (see Figure 1) were produced when methylating agent-induced apurinic/ apyrimidinic (AP) sites in DNA condensed with lysine and cysteine residues in proteins of human cells. 10−14 In contrast, reversible and specific noncovalent interactions of DNA with proteins, mediated by van der Waals forces, hydrogen bonding, and ionic interactions, are ubiquitous in all organisms 12 and are fundamental to many biological processes, particularly in regulating gene expression, replication, repair, and transcription. 15−17 Since the formation of covalently bound DPCs upon toxicant exposure would disrupt DNA− protein interactions that are part of normal cell physiology, they are extremely toxic.…”