Modifications of genomic DNA may change gene expression and cause adverse health effects. Here we for the first time demonstrate a particle counting immunoassay for rapid and sensitive detection of DNA modifications using benzo[a]pyrenediol epoxide (BPDE)-DNA adducts as an example. The BPDE-adducted DNA is specifically captured by immunomagnetic particles and then isolated from unmodified DNA by applying an external magnetic field. By taking advantage of the fluorescence signal amplification through multiple labeling of captured DNA by OliGreen dye, the captured BPDE-DNA adducts can be quantified by particle counting from fluorescence imaging. This clearly demonstrates that the number of fluorescently countable particles is proportional to the modification content in genomic DNA. It is interesting to note that the background fluorescence signal caused by nonspecific adsorption of OliGreen dye can be more effectively quenched than that induced by the binding of OliGreen dye to ssDNA, allowing for significant reduction in the background fluorescence and further enhancing the detection sensitivity. The developed method can detect trace BPDE-DNA adducts as low as 180 fM in the presence of 1 billion times more normal nucleotides in genomic DNA and has a dynamic range over 4 orders of magnitude. By using anti-5-methylcytosine antibody, the method is extended to the detection of global DNA methylation. With high sensitivity and specificity, this rapid and easy-to-perform analytical method for DNA modifications shows a broad spectrum of potential applications in genotoxical and epigenetic analysis.Magnetic micro-and nanoparticles have wide applications in bioanalysis, including aptamer selection, proteomics research, and clinical diagnostics, due to their unique separation power endowed by their paramagnetic property. 1,2 When functionalized with specific recognition elements (e.g., affinity substrates, aptamers, DNA, and antibodies), magnetic particles can be used for specific capture of desired analytes from a complex biological matrix, 3,4 including environmental pollutants, 5 various nucleic acids, 6,7 aptamers, 8,9 phosphopeptides, 10-12 cancer marker proteins, [13][14][15] and pathogenic bacteria. [16][17][18] The captured targets can be detected using appropriately designed signal probes, such as quantum dots, 19 carbon nanotubes, 20 Au nanoparticles, 21 and liposomes encapsulated with fluorescent dye. 22 Although some of the designed signal probes may provide an amplified signal, it is still a challenge to quantitate targets simply by particle counting. Despite the complex design and versatile functions, routine flow cytometry based particle counting analysis cannot distinguish specific binding from nonspecific adsorption and is only suitable for particles with a size over micrometers.Here we for the first time demonstrate a particle counting immunoassay for rapid and sensitive detection of DNA modifica-* To whom correspondence should be addressed. Phone/fax: +86-10-62849600. E-mail: hlwang@rcees.ac.cn.(