Bacteriophage strain typing by rapid single molecule analysis

Assaf Grunwald, Moran Dahan, Anna Giesbertz, Adam Nilsson, Lena K. Nyberg, Elmar Weinhold, Tobias Ambjörnsson, Fredrik Westerlund, Yuval Ebenstein*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a DNA methyltransferase. Due to the diffraction limit of light, the dense distribution of labels results in a continuous fluorescent signal along the DNA. The amplitude modulations (AM) of the fluorescence intensity along the stretched DNA molecules exhibit a unique molecular fingerprint that can be used for identification. We show that this labelling scheme is highly informative, allowing accurate genotyping. We demonstrate the method by labelling the genomes of λ and T7 bacteriophages, resulting in a consistent, unique AM profile for each genome. These profiles are also successfully used for identification of the phages from a background phage library. Our method may provide a facile route for screening and typing of various organisms and has potential applications in metagenomics studies of various ecosystems.

Original languageEnglish
Article numbere117
JournalNucleic Acids Research
Issue number18
StatePublished - 15 Oct 2015


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