Quantification of Fewer Than Ten Copies of a DNA Biomarker without Amplification or Labeling

Yoonhee Lee, Youngkyu Kim, Donggyu Lee, Dhruvajyoti Roy, and Joon Won Park

Polymerase chain reaction (PCR) is a highly sensitive diagnosis technique for detection of nucleic acids and for monitoring residual disease; however, PCR can be unreliable for samples containing very few target molecules. Here, we describe a quantification method, using force–distance (FD) curve based atomic force microscopy (AFM) to detect a target DNA bound to small (1.4–1.9 μm diameter) probe DNA spots, allowing mapping of entire spots to nanometer resolution. Using a synthetic BCR-ABL fusion gene sequence target, we examined samples containing between one and 10 target copies. A high degree of correlation (r² = 0.994) between numbers of target copies and detected probe clusters was observed, and the approach could detect the BCR-ABL biomarker when only a single copy was present, although multiple screens were required. Our results clearly demonstrate that FD curve-based imaging is suitable for quantitative analysis of fewer than 10 copies of DNA biomarkers without amplification, modification, or labeling.