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27 protocols using tnt sp6 quick coupled transcription translation system

1

Quantifying TOPBP1 and RAD9 Protein Levels

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IVTT reactions were performed using the SP6 TnT® Quick Coupled Transcription/Translation System (Promega #L2080) according to the manufacturer’s instructions. To determine the concentration of myc-TOPBP1 and MBP-TOPBP1 produced in a typical IVTT reaction the samples were probed with antibody HU142, which recognizes Xenopus TOPBP1 (Van Hatten et al., 2002 (link)), and the signal intensity was compared to a dilution series of Xenopus egg extract. The concentration of TOPBP1 in Xenopus egg extract is known (it is 37.4 nM, see Wühr et \al., 2014 (link)) and thus by matching Western blot signal intensities between egg extract and the IVTT reaction we could obtain a reliable estimation of the concentrations of IVTT-produced TOPBP1 derivatives. To estimate the concentration of myc-RAD9 we probed IVTT reactions with anti-myc antibody and compared the signal intensity to those obtained for myc-TOPBP1, whose concentration was known.
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2

Examining Mta2-Tipin Protein Interactions

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For pull down assays, recombinant His-Mta2 and His-Tipin were purified using Ni-NTA beads. Mta2 was also produced in vitro using the Sp6 TNT-quick coupled transcription/translation system (Promega). Binding reactions contained 2 μg his-tagged recombinant protein and 15 μl the in vitro translated protein in 1 ml binding buffer (20 mM TRIS-HCl pH 7.5 200 mM NaCl 0.5% NP40). The reactions were incubated for 3 h at 4 °C, followed by 5 washes in binding buffer. Complexes were resolved by SDS/PAGE and probed with the indicated antibodies or exposed to the phosphoimager for detection of the 35S signal. For the in vitro pull down shown in Figure S2C 2 µg recombinant His-Tipin protein were incubated for 1 h at 4 °C in binding buffer with either recombinant His-MTA2 (500 ng) or His-Geminin (1 µg) used as negative control. The mixture was then supplemented with 1 µg mouse anti-Tipin antibody or mouse IgG as control. One hour later, 15 µl protein A/G agarose beads (Santa Cruz) were added to reaction and left incubating for 1 h at 4 °C. Next, beads were washed 4 times with coupling buffer and once more with PBS before eluting proteins in Laemmli buffer. Samples were then resolved on a SDS-PAGE and analyzed by western blotting with anti-MTA2 antibody.
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3

IVTT Protein Production Protocol

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IVTT reactions were performed using the SP6 TnT Quick Coupled Transcription/Translation System (Promega #L2080) according to the manufacturer’s instructions. Proteins were not purified after their production by IVTT, rather, the entire IVTT reaction was used as the source of a given protein.
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4

In-vitro Transcription and Translation

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In-vitro transcription and translation (IVTT) reactions were performed using the SP6 TnT® Quick Coupled Transcription/Translation System (Promega #L2080) according to the manufacturer’s instructions. For Bug-Bunny binding assays we used 20μl of the IVTT reaction/sample.
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5

IVTT Protein Production Protocol

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IVTT reactions were performed using the SP6 TnT Quick Coupled Transcription/Translation System (Promega #L2080) according to the manufacturer’s instructions. Proteins were not purified after their production by IVTT, rather, the entire IVTT reaction was used as the source of a given protein.
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6

In vitro Sly1-SNARE Protein Interaction

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Sly1-HA3 was synthesized with the TNT SP6 Quick Coupled Transcription/Translation system (#L2080, Promega), according to the instructions of the manufacturer. The reaction was primed with 1 μg of pSP64::Sly1-HA3 cDNA. 10 μL of the resulting mix were combined with 15 µL of glutathione-Sepharose beads, previously loaded with SNARE-GST baits as described above, in 0.4 ml of pull-down binding buffer, using 0.8 ml Pierce columns that were rotated overnight at 4 °C before beads and flow-through were recovered after gentle centrifugation. Beads were washed three times for 10 min at 4 °C in pull-down binding buffer before eluting bound material with 30 µL of Laemmli loading buffer for 2 min at 90 °C. 20% of the elution sample volume was analyzed by western blotting with α-HA tag antibody (#3F10, Roche) for Sly1-HA immunodetection.
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7

Electrophoretic Mobility Shift Assay for Zebrafish NR2F1A

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EMSA was performed essentially as previously reported [77 (link)]. Oligonucleotides were designed containing the nr2f1a DR1 site (GTGTCAAAGTTCA), the nr2f1a DR1 site with a targeted mutation in the second half site of the DR1 abolishing the direct repeat (GTGTCAAAGTCAT), and a previously reported Cyp26a1 DR5 site [76 (link)]. A complementary oligonucleotide was designed with a 5’ LI-COR IRDye 700 (IDT). The oligonucleotides were annealed and the ends filled with Klenow (New England Biolabs). Zebrafish myc-rarab was in the pCS2+MT. Zebrafish RXRba was cloned into pCS2p+. Proteins for EMSA were made using the TnT SP6 Quick Coupled Transcription/Translation System (Promega). Protein samples were gently mixed with LI-COR tagged probes and incubated at room temperature for 20 minutes. 4% polyacrylamide gels were run for 2 hours at 150 V. Gels were imaged using an Odyssey CLx LI-COR imager.
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8

Electrophoretic Mobility Shift Assays with Zebrafish Transcription Factors

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EMSAs were performed as described previously [129 (link)]. Oligonucleotides were designed containing the ripply3 DR1 site (AGGTCAGAGGTCA), the ripply3 DR4 (AGTTCCTCAGGGGTCA) site, and a previously reported Cyp26a1 DR5 site [130 (link)]. A complementary oligonucleotide was designed with a 5’ LI-COR IRDye 700 (IDT). Sequences for oligos are listed in S1 Table. The oligonucleotides were annealed and the ends filled with Klenow (New England Biolabs). Zebrafish myc-rarab was cloned into pCS2+MT. Zebrafish RXRba was cloned into pCS2p+. Proteins for EMSA were made using the TnT SP6 Quick Coupled Transcription/Translation System (Promega). Protein samples were gently mixed with LI-COR tagged probes and incubated at room temperature for 20 minutes. 4% polyacrylamide gels were run for 2 hours at 150 V. Gels were imaged using an Odyssey CLx LI-COR imager.
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9

In Vitro Protein Synthesis Protocol

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Proteins were synthesized using TNT® SP6 Quick Coupled Transcription/Translation system (Promega #L2080) using the standard reaction mix (rabbit reticulocyte lysate plus amino acids) supplemented with 20 μM methionine. Reactions were primed with 1 μg of purified, circular pSP64 derivatives, which were purified using NucleoBond Xtra-Midi columns (Macherey Nagel, #740412).
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10

EMSA with Modified Oligonucleotides and Klenow

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EMSA was performed essentially as reported in [70 (link)], with the following modifications. Target oligonucleotides were designed with a 15 bp 3’ (ACATTCGCGCAGATC) extension. A common complementary oligonucleotide to the 15 bp extension was synthesized with a 5’ LI-COR IRDye 700 (IDT). The oligonucleotides were annealed and the ends filled with Klenow (New England Biolabs). Proteins for EMSA were made using the TnT SP6 Quick Coupled Transcription/Translation System (Promega). Gels were imaged using an Odyssey CLx LI-COR imager.
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