Sybr safe

To assemble Pep-biotin-streptavidin-QD655, pentagonal pyramid wireframe DNA origami objects with a biotin domain at the inner center or outer edge were incubated with Streptavidin QD655 (molar ratio was 1:4) at room temperature for 2 h. The mixture (15 μL) was then combined with 3 μL of 6× loading buffer (NEB) and loaded to a 0.8% agarose gel with 1× TAE and 12 mM MgCl₂ and 1× SYBR Safe (Thermo Fisher Scientific, Waltham, MA). Each gel was run at 65 V for 2 h in 1× TAE with 12 mM MgCl₂ at 4 °C. Gels were then visualized under blue light. To assemble Pep-30 nt A*-QD630, pentagonal pyramid wireframe DNA origami objects with ps-backbone-based ssDNA wrapping domain at the inner center or outer edge were incubated with QD630 (molar ratio was 1:4 or 4:1) at room temperature overnight. The mixture (15 μL) was then combined with 3 μL of 6× loading buffer (NEB) and loaded to a 0.8% agarose gel with 1× TAE and 12 mM MgCl₂ and 1× SYBR Safe (Thermo Fisher Scientific, Waltham, MA). Each gel was run at 65 V for 1 h in 1× TAE with 12 mM MgCl₂ at 4 °C. Gels were then visualized under blue light. All DNA sequences are summarized in Supplementary Tables 6 and 8.

The 2D DNA brick shapes, 2D origami and 3D origami were analysed by electrophoresis in a native 1.5% agarose gel supplemented with 10 mM MgCl₂. Electrophoresis was performed at 90 V for 2 h in an ice-water bath. Gels were pre-stained with 1 × Sybr Safe (Life Technologies). The 3D DNA brick cuboid was analysed by electrophoresis in a native 1% agarose gel supplemented with 10 mM MgCl₂. Electrophoresis was performed at 80 V for 2 h in an ice-water bath. Gels were pre-stained with 1 × Sybr Safe (Life Technologies). Afterwards, gels were scanned with a Typhoon FLA 9000 (General Electric) using the Sybr Safe channel (excitation at 473 nm, emission ≥510 nm).
Gel bands were visualized using a Safe Imager 2.0 Blue-Light Transilluminator (Invitrogen) and excised from the gel using a fresh razor blade. The excised piece was then placed into a Freeze ‘N Squeeze column (Bio-Rad) and crushed using a plastic pestle (USA Scientific). For the 2D DNA brick shapes, 2D origami rectangle and the 3D origami cuboid, structures were eluted from the column by centrifugation at 400g for 3 min. For the 3D DNA brick cuboid, structures were eluted from the column by centrifugation at 1,200g for 3 min.

LAMP products were visually detected by two different methods: direct visual detection under UV light by staining DNA using SYBR^® Safe DNA intercalating dye and agarose gel electrophoresis.
Direct visual detection using SYBR^® Safe staining DNA: The SYBR^® Safe (10 000X concentrate in DMSO, Life Technology, Denmark) was diluted 1:10, and 1 μl of diluted dye was added to each tube after LAMP reaction. The tubes were observed under UV light from a portable DR22 blue LED transilluminator (Supplementary Figure S1) (Clare Chemical Research, Inc., United States).
Gel electrophoresis detection: After LAMP reactions, 5 μl of each amplified LAMP product were loaded on 2% agarose gel containing 1X of SYBR^® Safe DNA Gel Stain (Invitrogen, Life Technologies, United States). Gel electrophoresis was carried out at 100 volts for 60 min and the gel electrophoresis patterns were observed under Bio-Rad Gel Doc 2000 UV transilluminator (Bio-Rad Life Science, Denmark).