Dna oligonucleotides

All reactions were performed in salt 20 mM Tris-HCl pH 8, 150 mM NaCl with added 20 mM MgCl₂. DNA oligonucleotides (Biomers, Germany) were used at 200 nM concentration per strand in reactions containing a fixed-sequence subset of eight strands (e.g. 0/ ${\displaystyle \overline{0}}$ only) and 100 nM per strand in reactions containing all 16 different strands.
Thermal cycling was done in a standard PCR cycler (Bio-Rad C1000). Reaction kinetics were obtained by running each reaction for different run times or numbers of cycles in parallel. The products were analyzed using native PAGE. The time between thermal cycling and PAGE analysis was minimized to exclude artifacts from storage on ice.
Template sequences were prepared using a two-step protocol. Annealing from 95°C to 70°C within 1 hr, followed by incubation at 70 °C for 30 min. Afterwards, samples were cooled to 2 °C and stored on ice. When assembling complexes containing paired information domains (Figure 2), samples were slowly cooled down from 70 to 25 °C within 90 min before being transferred onto ice. DNA double hairpins were quenched into monomolecular state by heating to 95 °C and subsequent fast transfer into ice water.

Phosphate buffered saline (PBS, 10 mM phosphate, 138 mM NaCl, 2.7 mM KCl, pH 7.4), PBS-Tween (10 mM phosphate, 138 mM NaCl, 2.7 mM KCl, 0.05% v/v Tween 20, pH 7.4), 1-ethyl-3-(dimethylaminopropyl) carboiimide (EDC), N-hydroxysuccinimide (NHS), and all other reagents were purchased from Sigma (Barcelona, Spain). Magnesium chloride, sodium chloride, sodium hydroxide and hydrochloric acid were purchased from Scharlau Chemie S.A. (Barcelona, Spain). Pierce^TM maleimide activated plates, 8-well strip, were from Pierce (Madrid, Spain) and DNA oligonucleotides were purchased from BIOMERS (Ulm, Germany). All primers and probe sequences can be found in Table 3.

DNA oligonucleotides were purchased from Biomers. The oligonucleotide concentration was determined by measuring the absorbance at 260 nm and 90 °C, using the appropriate molar extinction coefficients. c_ex-NDI was synthesised and purified as previously described [34 (link)]. The c_ex-NDI stock solution was prepared by dissolving the solid compound in aqueous solution at 100 mM KCl, 20 mM potassium phosphate buffer (pH 7), 90%/10% H₂O/D₂O, at 20 mM concentration of the ligand.