Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy

Next generation sequencing (NGS) is revolutionizing all fields of biological research but it fails to extract the full range of information associated with genetic material. Optical mapping of DNA grants access to genetic and epigenetic information on individual DNA molecules up to ∼1 Mbp in length. Fluorescent labeling of specific sequence motifs, epigenetic marks and other genomic information on individual DNA molecules generates a high content optical barcode along the DNA. By stretching the DNA to a linear configuration this barcode may be directly visualized by fluorescence microscopy. We discuss the advances of these methods in light of recent developments in nano-fabrication and super-resolution optical imaging (nanoscopy) and review the latest achievements of optical mapping in the context of genomic analysis.

Graphical abstractFigure optionsDownload full-size imageDownload high-quality image (299 K)Download as PowerPoint slideHighlights► Individual DNA molecules hundreds of kbp long may be stretched and visualized by optical microscopy. ► An optical barcode is generated by fluorescent labeling of short sequence motifs along the stretched DNA. ► Optical maps complement DNA sequencing for gap closing, finishing, validation and de novo assembly of genomes. ► Genome structural variations not accessible to sequencing or DNA arrays may be directly visualized. ► Epigenetic marks such as DNA methylation and DNA binding proteins may also be mapped on single genomic fragments.