Ated DNA). Polymerase chain reaction reagents for each 50 microliter reaction volume included: 1 unit of Taq polymerase (New England BioLabs), 5 ml of 10x PCR buffer (New England BioLabs), 10 pmol of the forward primer and 10 pmol of reverse primer, 5 ml of 2 mM dNTPs (Fermentas), and 50 ng of the plasmid DNA. The PCR profile was as follows: 1 min at 94uC, 30 cycles of 30 s at 94uC, 60 s at 52uC and 3 min at 72uC, finally followed by 10 min at 72uC and a 4uC soak.Expression and purification of Maltose Binding Protein (MBP)Two repeats of the sequence encoding the ST 11967625 (tST) were introduced with PCR at the C-terminus of MBP sequence using plasmid pNN226 as a template. The inserts were ligated with HindIII/NdeI restriction sites to the pET3 vector to generate the expression plasmid. The correctness of the newly made vector was confirmed by double-strand DNA sequencing. Escherichia coli strain BL21.1 was used to express the MBP construct. The cells were grown at 37uC in LB medium P7C3 custom synthesis containing 100 mg/ml ampicillin to OD600,0.6?.7. After induction with 0.5 mM IPTG the cells were further incubated O/N at room temperature and harvested by centrifugation at 5000 rpm, 4uC for 30 min. The cells were resuspended in cold MBP buffer (20 mM Tris-HCl (pH 7.4), 200 mM NaCl, 1 mM EDTA, 10 mM DTT) with 1x protease inhibitor. PD 168393 Lysozyme (Sigma Aldrich) was added to a final concentration of 1 mg/ml and the mixture was kept on ice for 20 min. The cells were lysed by tandem freezing (in liquid nitrogen until fully frozen) and thawing (at 37uC). A little-spatula tip of DNAase I was added to lysate and the mixture was kept on ice for 20 min. Freezing and thawing were repeated until the cloudy suspension became translucent. The extract was clarified by centrifugation (at 15000 rpm, 4uC for 20 min). The tST-MBP hybrid was purified from the crude cell extract using amylose resin affinity chromatography (New England BioLabs). The clarified extract (10 ml) was transferred to fresh amylose resin column (1 ml bead volume) and rocked gently at 4uC for 2 hr. Unbound material then were removed by centrifugation (at 2000 rpm, 4uCOptical Tweezers Study of 1655472 Protein-DNA Hybridsfor 1 min). The resin was washed 3x with cold MBP buffer. The protein was eluted from resin by 2.5 ml elution buffer (MBP buffer, 10 mM matose).Gel analysisDNA samples were analyzed by gel electrophoresis (Figure 1b, 1e and 1f) in non-denaturing 1 agarose gels in 0.5xTBE buffer at 80 V/cm. Agarose gels were stained with ethidium bromide (EtBr). Protein samples were applied on an 8 SDS-PAGE gel in 1x running buffer (190 mM Glycine, 25 mM Tris-base and 0.1 SDS) at 180 V/cm. SDS-PAGE gels were stained with Coomassie InstantBlue (Expedeon Ltd.).The beads were trapped in a flow chamber consisting of three parallel streams in laminar flow: one containing STN-coated beads; one containing NTV-coated beads with the DNA construct and a central buffer channel in which the measurements were conducted. Structure of the resulting molecular tether is schematically depicted in Figure 2a.Results and Discussion Polypeptide-DNA hybridsTo construct DNA molecules linked to polypeptide (tST-DNA), we used a primer covalently linked to the polypeptide. The PCR conditions were optimized to efficiently amplify the DNA from the template plasmid. By using gradient PCR, and testing several polymerases (Taq Polymerase and Phusion) and different PCR conditions, we found that comparatively long annealing and extension time (1 and 3 min p.Ated DNA). Polymerase chain reaction reagents for each 50 microliter reaction volume included: 1 unit of Taq polymerase (New England BioLabs), 5 ml of 10x PCR buffer (New England BioLabs), 10 pmol of the forward primer and 10 pmol of reverse primer, 5 ml of 2 mM dNTPs (Fermentas), and 50 ng of the plasmid DNA. The PCR profile was as follows: 1 min at 94uC, 30 cycles of 30 s at 94uC, 60 s at 52uC and 3 min at 72uC, finally followed by 10 min at 72uC and a 4uC soak.Expression and purification of Maltose Binding Protein (MBP)Two repeats of the sequence encoding the ST 11967625 (tST) were introduced with PCR at the C-terminus of MBP sequence using plasmid pNN226 as a template. The inserts were ligated with HindIII/NdeI restriction sites to the pET3 vector to generate the expression plasmid. The correctness of the newly made vector was confirmed by double-strand DNA sequencing. Escherichia coli strain BL21.1 was used to express the MBP construct. The cells were grown at 37uC in LB medium containing 100 mg/ml ampicillin to OD600,0.6?.7. After induction with 0.5 mM IPTG the cells were further incubated O/N at room temperature and harvested by centrifugation at 5000 rpm, 4uC for 30 min. The cells were resuspended in cold MBP buffer (20 mM Tris-HCl (pH 7.4), 200 mM NaCl, 1 mM EDTA, 10 mM DTT) with 1x protease inhibitor. Lysozyme (Sigma Aldrich) was added to a final concentration of 1 mg/ml and the mixture was kept on ice for 20 min. The cells were lysed by tandem freezing (in liquid nitrogen until fully frozen) and thawing (at 37uC). A little-spatula tip of DNAase I was added to lysate and the mixture was kept on ice for 20 min. Freezing and thawing were repeated until the cloudy suspension became translucent. The extract was clarified by centrifugation (at 15000 rpm, 4uC for 20 min). The tST-MBP hybrid was purified from the crude cell extract using amylose resin affinity chromatography (New England BioLabs). The clarified extract (10 ml) was transferred to fresh amylose resin column (1 ml bead volume) and rocked gently at 4uC for 2 hr. Unbound material then were removed by centrifugation (at 2000 rpm, 4uCOptical Tweezers Study of 1655472 Protein-DNA Hybridsfor 1 min). The resin was washed 3x with cold MBP buffer. The protein was eluted from resin by 2.5 ml elution buffer (MBP buffer, 10 mM matose).Gel analysisDNA samples were analyzed by gel electrophoresis (Figure 1b, 1e and 1f) in non-denaturing 1 agarose gels in 0.5xTBE buffer at 80 V/cm. Agarose gels were stained with ethidium bromide (EtBr). Protein samples were applied on an 8 SDS-PAGE gel in 1x running buffer (190 mM Glycine, 25 mM Tris-base and 0.1 SDS) at 180 V/cm. SDS-PAGE gels were stained with Coomassie InstantBlue (Expedeon Ltd.).The beads were trapped in a flow chamber consisting of three parallel streams in laminar flow: one containing STN-coated beads; one containing NTV-coated beads with the DNA construct and a central buffer channel in which the measurements were conducted. Structure of the resulting molecular tether is schematically depicted in Figure 2a.Results and Discussion Polypeptide-DNA hybridsTo construct DNA molecules linked to polypeptide (tST-DNA), we used a primer covalently linked to the polypeptide. The PCR conditions were optimized to efficiently amplify the DNA from the template plasmid. By using gradient PCR, and testing several polymerases (Taq Polymerase and Phusion) and different PCR conditions, we found that comparatively long annealing and extension time (1 and 3 min p.
