We purchased salmon protamine (P4005, 1.1 kDa, Sigma Aldrich) which contained 32 residues and had a +21 charge (21 arginine residues). We dissolved the protamine and stored aliquots at -20°C.
DNA of varying lengths [L = 25 nm (75 bp), 50 nm (150 bp), 105 nm (309 bp) and 217 nm (639 bp)] was made via Polymerase Chain Reaction (PCR) using standard protocols (29 (link),32–34 (link)), lambda phage DNA (New England Biolabs, N3011L) as a template, and LA Taq DNA polymerase (TaKaRa Bio, RR002). To biochemically tether the DNA to the surface of the cover slip and the streptavidin-coated polystyrene bead, one primer was labelled with a digoxigenin molecule, while the other was labelled with a biotin molecule (Integrated DNA Technologies). To purify the DNA, we performed gel electrophoresis using orange loading dye (B7022S, New England Biolabs) and standard protocols for short DNA molecules (35 ), then purified the DNA via gel extraction (QIAquick Gel Extraction Kit, Qiagen). We quantified the final concentration using a spectrophotometer (Nanodrop One, ThermoFisher Scientific).
DNA of varying lengths [L = 25 nm (75 bp), 50 nm (150 bp), 105 nm (309 bp) and 217 nm (639 bp)] was made via Polymerase Chain Reaction (PCR) using standard protocols (29 (link),32–34 (link)), lambda phage DNA (New England Biolabs, N3011L) as a template, and LA Taq DNA polymerase (TaKaRa Bio, RR002). To biochemically tether the DNA to the surface of the cover slip and the streptavidin-coated polystyrene bead, one primer was labelled with a digoxigenin molecule, while the other was labelled with a biotin molecule (Integrated DNA Technologies). To purify the DNA, we performed gel electrophoresis using orange loading dye (B7022S, New England Biolabs) and standard protocols for short DNA molecules (35 ), then purified the DNA via gel extraction (QIAquick Gel Extraction Kit, Qiagen). We quantified the final concentration using a spectrophotometer (Nanodrop One, ThermoFisher Scientific).
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