Optical DNA mapping in nanofluidic devices: principles and applications
Artikel i vetenskaplig tidskrift, 2017

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.

saccharomyces-cerevisiae

single-molecule analysis

Biochemistry & Molecular Biology

nanochannel arrays

human genome

resistance plasmids

identification

Chemistry

quantification

structural variation analysis

sequence

technologies

Författare

Vilhelm Müller

Chalmers, Biologi och bioteknik, Kemisk biologi

Fredrik Westerlund

Chalmers, Biologi och bioteknik, Kemisk biologi

Lab on a Chip - Miniaturisation for Chemistry and Biology

1473-0197 (ISSN) 1473-0189 (eISSN)

Vol. 17 579-590

Ämneskategorier

Industriell bioteknik

Bioinformatik (beräkningsbiologi)

DOI

10.1039/c6lc01439a