|Title||Linearization and Labeling of Single-Stranded DNA for Optical Sequence Analysis|
|Author(s)||Basak, Rajib; Liu, Fan; Qureshi, Sarfraz; Gupta, Neelima; Zhang, Ce; Vries, Renko de; Kan, Jeroen A. van; Dheen, S.T.; Maarel, Johan R.C. van der|
|Source||Journal of Physical Chemistry Letters 10 (2019)3. - ISSN 1948-7185 - p. 316 - 321.|
Physical Chemistry and Soft Matter
|Publication type||Refereed Article in a scientific journal|
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.