DNA barcodes for rapid, whole genome, single-molecule analyses

ABSTRACT We report an approach for visualizing DNA sequence and using these ‘DNA barcodes’ to search complex mixtures of genomic material for DNA molecules of interest. We demonstrate three applications of this methodology; by identifying specific molecules of interest from a dataset containing gigabasepairs of genome; by straightforward strain-typing of bacteria from such a dataset and, finally, by locating infecting virus molecules in a background of human genomic material. DNA barcodes enable quantitative understanding of complex genome mixtures, on a large scale. As a result of the dense fluorescent labelling of the DNA, individual barcodes of the order 40 kilobase pairs in length can be reliably identified. This means DNA can be prepared for imaging using standard handling and purification techniques. The recorded dataset provides stable physical and electronic records of the total genomic content of a sample that can be readily searched for a molecule or region of interest.