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Issue 4, 2017
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Optical DNA mapping in nanofluidic devices: principles and applications

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Abstract

Optical DNA mapping has over the last decade emerged as a very powerful tool for obtaining long range sequence information from single DNA molecules. In optical DNA mapping, intact large single DNA molecules are labeled, stretched out, and imaged using a fluorescence microscope. This means that sequence information ranging over hundreds of kilobasepairs (kbp) can be obtained in one single image. Nanochannels offer homogeneous and efficient stretching of DNA that is crucial to maximize the information that can be obtained from optical DNA maps. In this review, we highlight progress in the field of optical DNA mapping in nanochannels. We discuss the different protocols for sequence specific labeling and divide them into two main categories, enzymatic labeling and affinity-based labeling. Examples are highlighted where optical DNA mapping is used to gain information on length scales that would be inaccessible with traditional techniques. Enzymatic labeling has been commercialized and is mainly used in human genetics and assembly of complex genomes, while the affinity-based methods have primarily been applied in bacteriology, for example for rapid analysis of plasmids encoding antibiotic resistance. Next, we highlight how the design of nanofluidic channels can been altered in order to obtain the desired information and discuss how recent advances in the field make it possible to retrieve information beyond DNA sequence. In the outlook section, we discuss future directions of optical DNA mapping, such as fully integrated devices and portable microscopes.

Graphical abstract: Optical DNA mapping in nanofluidic devices: principles and applications

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Publication details

The article was received on 21 Nov 2016, accepted on 05 Jan 2017 and first published on 10 Jan 2017


Article type: Tutorial Review
DOI: 10.1039/C6LC01439A
Citation: Lab Chip, 2017,17, 579-590
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    Optical DNA mapping in nanofluidic devices: principles and applications

    V. Müller and F. Westerlund, Lab Chip, 2017, 17, 579
    DOI: 10.1039/C6LC01439A

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