Characterization and mapping of DNA damage induced by reactive metabolites of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) at nucleotide resolution in human genomic DNA

J Mol Biol. 2001 Oct 26;313(3):539-57. doi: 10.1006/jmbi.2001.4997.


The nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is an important tobacco-specific carcinogen associated with lung cancer. Its complex enzymatic activation, leading to methyl and pyridyloxobutyl (POB)-modified DNA, makes DNA damage difficult to characterize and quantify. Therefore, we use the NNK analogue 4-[(acetoxymethyl)nitrosamino]-1-(3-pyridyl)-1-butanone (NNKOAc) to induce damage in genomic DNA, and to map the sites and frequency of adducts at nucleotide resolution using ligation-mediated polymerase chain reaction and terminal transferase-dependent polymerase chain reactions (LMPCR and TDPCR). NNKOAc induced single-strand breaks in a concentration-dependent manner. Post-alkylation treatments, including hot piperidine or digestion with the enzymes Escherichia coli 3-methyladenine-DNA glycosylase II, formamidopyrimidine-DNA glycosylase, Escherichia coli endonuclease III, or phage T4 UV endonuclease V did not increase the level of DNA breaks in NNKOAc-treated DNA. Detection of DNA damage using LMPCR was possible only when POB-DNA was 5'-phosphorylated prior to the LMPCR procedure. NNKOAc generated damage at all four bases with the decreasing order guanine>adenine>cytosine>thymine. In contrast to NNKOAc damage distribution patterns, those induced by N-nitroso(acetoxymethyl)methylamine, a methylating NNK analog, induced damage principally at G positions detectable by enzymatic means that did not require phosphorylation. Analysis of damage distribution patterns, reveals a high frequency of damage in the p53 gene in codons 241 and 245 and a lower frequency of damage in codon 248. We analyzed the 3' termini of the NNKOAc induced single-strand breaks using a (32)P-post-labeling assay or a nucleotide exchange reaction at the 3'-termini catalyzed by T4 DNA polymerase combined with endonuclease IV treatment. Both methods indicate that the 3' termini of the single-strand breaks are not hydroxyl groups and are blocked by an unknown chemical structure that is not recognized by endonuclease IV. These data are consistent with POB-phosphotriester hydrolysis leading to strand breaks in DNA. The POB-damage could be mutagenic because NNKOAc produces single-strand breaks with the products being a 5'-hydroxyl group and a 3'-blocking group and strand breaks. These results represent the first step in determining if NNK pyridyloxobutylates DNA with sequence specificity similar to those observed with other model compounds.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Alkylation
  • Base Sequence
  • Carcinogens / chemistry
  • Carcinogens / metabolism*
  • DNA Adducts / chemistry*
  • DNA Adducts / genetics
  • DNA Adducts / metabolism*
  • DNA Damage / genetics*
  • DNA Methylation
  • DNA Mutational Analysis
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / genetics
  • DNA, Single-Stranded / metabolism
  • Escherichia coli / enzymology
  • Exons / genetics
  • Genes, p53 / genetics
  • Genes, ras / genetics
  • Genome, Human*
  • Humans
  • Lung Neoplasms / genetics
  • Molecular Sequence Data
  • Mutagenesis / genetics
  • Nitrosamines / chemistry
  • Nitrosamines / metabolism*
  • Nucleotides / chemistry
  • Nucleotides / genetics
  • Nucleotides / metabolism*
  • Phosphodiesterase I
  • Phosphoric Diester Hydrolases / metabolism
  • Phosphorylation
  • Polymerase Chain Reaction
  • Smoking / adverse effects
  • Substrate Specificity


  • Carcinogens
  • DNA Adducts
  • DNA, Single-Stranded
  • Nitrosamines
  • Nucleotides
  • 4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone
  • Phosphoric Diester Hydrolases
  • Phosphodiesterase I