Fuming nitric acid

Perylene-3,4,9,10-tetracarboxylic dianhydride 97% (PTCDA), 2-ethyl-1-hexylamine 98%, bromine ≥99.99%), fuming nitric acid >90%, 4-styryl boronic acid ≥95%, phenyl boronic acid ≥97%, magnesium sulphate anhydrous >99.5% (MgSO₄), sodium sulphite >98% Na₂SO₃ were purchased from Merck (Darmstadt, 64293, Germany). Tetrahydrofuran was purchased also from Merck and was freshly distilled with benzophenone and metallic sodium (THF (dry)). All other solvents and reagents were purchased from Aldrich or Alfa Aesar and were used without further purification unless otherwise stated. 4-(2-tetrahydropyranyloxy) phenylboronic acid [41 (link)], 6-Bromo phenyl-(2-perfluorophenyl)-4-phenyl-quinoline (Br5FQ) [32 (link)], 6-phenyl-(2-perfluorophenyl)-4-phenyl-quinoline (Ph-5FQ) [33 (link)] 6-bromo-(2-pyridinyl)-4-phenyl-quinoline (Br-QPy) [35 (link)] and the catalyst palladium (II) tetrakis triphenyl2phosphine [Pd (PPh₃)₄] [47 ] were synthesized according to published procedures.

The gold pads were cleaned by immersing them stepwise for 20 s into 100% fuming nitric acid (Merck) and 1 min into a neutralization solution [hydrogen peroxide (30 wt % in water; Merck), ammonia solution (25 wt % in water; Merck) and ddH₂O in the ratio 1:1:5] and rinsed with ddH₂O. Then, such a glass slide was placed in an inverted optical microscope (Axiovert 200M, Carl Zeiss MicroImaging) equipped with a 100×/1.45 numerical aperture oil immersion objective and appropriate fluorescence filter sets. A PDMS ring was sealed with silicon oil on the glass substrate in between the electrodes and contact pads. In addition, the microscope was equipped with micromanipulators (Suess MICROTec PH100) that were used to place tungsten needles (SIGNATONE SE-T) on the contact pads, and thus, connect the electrodes with the function generator (Textonix AFG 320; Sony). The DNA nanostructures were stained with YOYO^®-1 (Life Technologies) in a ratio of 1:10 and diluted with ddH₂O to a final concentration of 45 pM 6HBs and 1.5 mM Mg²⁺. 15 µL of this solution was pipetted into the PDMS ring and an (ac) field applied. Images were taken in the green channel with a frame-transfer intensified CCD camera (Cascade 512:B, Roper Scientific) using the MetaMorph software (Molecular Devices).