DNA fluorocode: A single molecule, optical map of DNA with nanometre resolution

Abstract

We present a new method for single-molecule optical DNA mapping using an exceptionally dense, yet sequence-specific coverage of DNA with a fluorescent probe. The method employs a DNA methyltransferase enzyme to direct the DNA labelling, followed by molecular combing of the DNA onto a polymer-coated surface and subsequent sub-diffraction limit localization of the fluorophores. The result is a ‘DNA fluorocode’; a simple description of the DNA sequence, with a maximum achievable resolution of less than 20 bases, which can be read and analyzed like a barcode. We demonstrate the generation of a fluorocode for genomic DNA from the lambda bacteriophage using a DNA methyltransferase, M.HhaI, to direct fluorescent labels to four-base sequences reading 5′-GCGC-3′. A consensus fluorocode that allows the study of the DNA sequence at the level of an individual labelling site can be generated from a handful of molecules.