Er cycle respectively) allowed efficient amplification, resulting in a final yield

Er cycle respectively) allowed efficient amplification, resulting in a final yield of about 500 ng. The resulting construct was then BTZ043 characterized by agarose gel electrophoresis (Figure 1b) and later tested with an optical tweezers assay (Figure 2a).Bead preparationCarboxylated polystyrene beads (4EGI-1 cost Polysciences Inc.) were covalently linked to protein (STN, NTV, STV and AntiDig) via Carbodiimide reaction (PolyLink Protein Coupling Kit, Polysciences Inc.). Briefly, 25 ml of 1 (w/v) 1.87 mm diameter carboxylated polystyrene microspheres were washed twice by pelleting at 13.2 rpm (for 10 min) in a microcentrifuge tube and resuspending in coupling buffer (400 ml in first wash and 170 ml in second washing) (PolyLink Protein Coupling Kit, Polysciences Inc.). Then 20 ml of the freshly prepared EDCA solution (20 mg/ ml; prepared by dissolving 1 mg EDCA in 50 ml coupling buffer) was added to the microparticle suspension and mixed gently endover-end. After that 20 mg of desired protein (STN, NTV, STV and AntiDig) was added and mixture was incubated for 1 hr at room temperature with gentle mixing. The mixture then washed two times in 400 mml storage buffer. Protein-coated beads were stored in 400 mml storage buffer at 4uC until use. DNA-coated microspheres were made by mixing ,70 ng of dsDNA molecules and 1 ml protein-coated beads in 10 ml HMK (50 mM Hepes, pH 7.6, 100 mM KCl, 5 mM MgCl2) buffer. After 30 minutes incubation on a rotary mixer (4uC), the beads 18325633 were diluted in 400 ml HMK buffer for use in optical tweezers experiments.Polypeptide-protein hybridsTo synthesize a protein-polypeptide hybrid, we chose Maltose Binding Protein (MBP) as our model protein. MBP is a protein with a variety of applications in biotechnology and biological research, widely used to prototype a variety of biosensing platforms [32]. It is also a model protein for folding and export studies and is commonly used as fusion partner in protein biochemistry [13,33]. The tST-MBP hybrid was constructed as described before. The hybrid was then tested with SDS-PAGE (Figure 1c), which showed a molecular weight between 37?0 kDa that corresponds well to the molecular weight of tST-MBP (,42.5 kDa).Protein-DNA hybridsHere we aimed to optimize the specific formation of a hybrid between MBP and DNA using ST-STN linkages (MBP-tST-STNtST-DNA). Tetrameric structure of STN provides four binding sites for STs which in principle could allow for the formation of MBP-DNA complexes with different stoichiometries. It has been shown that for STV family, a 1:1 stoichiometry can be successfully achieved by using excess amounts of ligand (e.g. biotin) or receptor (e.g. STV or AV) [34,35].Optical tweezers experimentsThe optical tweezers setup has been described elsewhere [13,31]. Detection of forces on the trapped beadwas performed using back focal plane interferometry. Forces were recorded at 50 Hz. Trap stiffness and sensitivity were determined to be169624 pN mm21 and 2.7460.24 V mm21 respectively. A piezo-nanopositioning stage (Physik Instrumente) was used to move the sample cell and micropipette at a speed of 50 nm s21.Figure 1. Hierarchical synthesis of protein-DNA hybrids. (a) Schematic drawing of the building blocks (b) 1 agarose gel demonstrating construction of tST-DNA-biotin hybrid at 2553 bps (c) SDS-PAGE analysis illustrating production of tST-MBP in Ecoli BL21.1 (d) SDS-PAGE characterization of STN-tST-MBP hybrid after amylose column purification. STN decomposes into monomers upon boilin.Er cycle respectively) allowed efficient amplification, resulting in a final yield of about 500 ng. The resulting construct was then characterized by agarose gel electrophoresis (Figure 1b) and later tested with an optical tweezers assay (Figure 2a).Bead preparationCarboxylated polystyrene beads (Polysciences Inc.) were covalently linked to protein (STN, NTV, STV and AntiDig) via Carbodiimide reaction (PolyLink Protein Coupling Kit, Polysciences Inc.). Briefly, 25 ml of 1 (w/v) 1.87 mm diameter carboxylated polystyrene microspheres were washed twice by pelleting at 13.2 rpm (for 10 min) in a microcentrifuge tube and resuspending in coupling buffer (400 ml in first wash and 170 ml in second washing) (PolyLink Protein Coupling Kit, Polysciences Inc.). Then 20 ml of the freshly prepared EDCA solution (20 mg/ ml; prepared by dissolving 1 mg EDCA in 50 ml coupling buffer) was added to the microparticle suspension and mixed gently endover-end. After that 20 mg of desired protein (STN, NTV, STV and AntiDig) was added and mixture was incubated for 1 hr at room temperature with gentle mixing. The mixture then washed two times in 400 mml storage buffer. Protein-coated beads were stored in 400 mml storage buffer at 4uC until use. DNA-coated microspheres were made by mixing ,70 ng of dsDNA molecules and 1 ml protein-coated beads in 10 ml HMK (50 mM Hepes, pH 7.6, 100 mM KCl, 5 mM MgCl2) buffer. After 30 minutes incubation on a rotary mixer (4uC), the beads 18325633 were diluted in 400 ml HMK buffer for use in optical tweezers experiments.Polypeptide-protein hybridsTo synthesize a protein-polypeptide hybrid, we chose Maltose Binding Protein (MBP) as our model protein. MBP is a protein with a variety of applications in biotechnology and biological research, widely used to prototype a variety of biosensing platforms [32]. It is also a model protein for folding and export studies and is commonly used as fusion partner in protein biochemistry [13,33]. The tST-MBP hybrid was constructed as described before. The hybrid was then tested with SDS-PAGE (Figure 1c), which showed a molecular weight between 37?0 kDa that corresponds well to the molecular weight of tST-MBP (,42.5 kDa).Protein-DNA hybridsHere we aimed to optimize the specific formation of a hybrid between MBP and DNA using ST-STN linkages (MBP-tST-STNtST-DNA). Tetrameric structure of STN provides four binding sites for STs which in principle could allow for the formation of MBP-DNA complexes with different stoichiometries. It has been shown that for STV family, a 1:1 stoichiometry can be successfully achieved by using excess amounts of ligand (e.g. biotin) or receptor (e.g. STV or AV) [34,35].Optical tweezers experimentsThe optical tweezers setup has been described elsewhere [13,31]. Detection of forces on the trapped beadwas performed using back focal plane interferometry. Forces were recorded at 50 Hz. Trap stiffness and sensitivity were determined to be169624 pN mm21 and 2.7460.24 V mm21 respectively. A piezo-nanopositioning stage (Physik Instrumente) was used to move the sample cell and micropipette at a speed of 50 nm s21.Figure 1. Hierarchical synthesis of protein-DNA hybrids. (a) Schematic drawing of the building blocks (b) 1 agarose gel demonstrating construction of tST-DNA-biotin hybrid at 2553 bps (c) SDS-PAGE analysis illustrating production of tST-MBP in Ecoli BL21.1 (d) SDS-PAGE characterization of STN-tST-MBP hybrid after amylose column purification. STN decomposes into monomers upon boilin.