Linearization and Labeling of Single-Stranded DNA for Optical Sequence Analysis
Basak, Rajib Liu, Fan Qureshi, Sarfraz Gupta, Neelima Zhang, Ce de Vries, Renko van Kan, Jeroen A Dheen, S Thameem van der Maarel, Johan RC
Qureshi, Sarfraz
Zhang, Ce
de Vries, Renko
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Abstract
Copyright © 2019 American Chemical Society. Genetic profiling would benefit from linearization of ssDNA through the exposure of the unpaired bases to gene-targeting probes. This is compromised by ssDNA's high flexibility and tendency to form self-annealed structures. Here, we demonstrate that self-annealing can be avoided through controlled coating with a cationic-neutral diblock polypeptide copolymer. Coating does not preclude site-specific binding of fluorescence labeled oligonucleotides. Bottlebrush-coated ssDNA can be linearized by confinement inside a nanochannel or molecular combing. A stretch of 0.32 nm per nucleotide is achieved inside a channel with a cross-section of 100 nm and a 2-fold excess of polypeptide with respect to DNA charge. With combing, the complexes are stretched to a similar extent. Atomic force microscopy of dried complexes on silica revealed that the contour and persistence lengths are close to those of dsDNA in the B-form. Labeling is based on hybridization and not limited by restriction enzymes. Enzyme-free labeling offers new opportunities for the detection of specific sequences. ©
Keywords
Science & Technology, Physical Sciences, Technology, Chemistry, Physical, Nanoscience & Nanotechnology, Materials Science, Multidisciplinary, Physics, Atomic, Molecular & Chemical, Chemistry, Science & Technology - Other Topics, Materials Science, Physics, BINDING, MOLECULES, PLATFORM, POLYMER, LENGTH, YOYO, DYES
Source Title
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
Publisher
AMER CHEMICAL SOC
Series/Report No.
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Date
2019-02-07
DOI
10.1021/acs.jpclett.8b03465
Type
Article