DOM: Dual Optical Mapping Combining Sequence-specific Markers and A/T Frequency-dependent Profiles

Abstract We introduce Dual Optical Mapping (DOM), a method combining sequence-specific barcodes and AT frequency-dependent profiles. Conventional optical mapping primarily depends on barcodes generated by sequence-specific enzymes. There are also several AT frequency-dependent profiling methods. However, these methods often face challenges, including reduced confidence due to large distances between labels, the occurrence of false positives and negatives, and issues of single-molecule heterogeneity. Addressing these limitations, we devised DOM, which integrates sparse sequence-specific labeling with dense AT-specific staining, and developed an alignment program, DOM.py. Leveraging the experimental characterization of AT-specific staining, we generated an in silico reference map through computer simulation. As a demonstration of its efficacy, we applied DOM to the E. coli genome. Impressively, 178 out of 182 single-molecule DNA images were accurately mapped to the genome, yielding a 98% alignment rate. In conclusion, this study underscores the potential of DOM to confidently map single-molecule DNA images to genomes.