The SAM2® Biotin Capture Membranes can be used to study biotinylated molecules based on their affinity for streptavidin. The SAM2® Membranes linearly bind substrates and have low nonspecific binding. For DNA:protein binding studies, you have the option of using either biotin-labeled proteins with 32P-labeled oligos or 35S-labeled proteins with biotinylated oligos. DNA binding analysis is simple with the SAM2® Membranes. The in vitro translated protein and the appropriately labeled oligo are incubated and then an aliquot is spotted onto the Membrane. The Membrane is washed and each square is counted with a scintillation counter.
In Vitro Translation Reactions: Fifty-microliter reactions were assembled with either 500ng pSP64polyA-cjun plasmid or no DNA. Reactions were performed in the presence of no label, 2µl [35S]methionine or 1µl Transcend™ tRNA using either the TnT® SP6 Quick Coupled Transcription/Translation System (#TM045) or the TnT® Coupled Wheat Germ Extract System (#TB165).
DNA Probe Preparation: The AP1 Consensus Oligo (Cat.# E3201) was 5´-end labeled with [γ-32P]ATP and T4 Polynucleotide Kinase (Cat.# M4101) following the Gel Shift Assay System Technical Bulletin (#TB110). Biotin 5´-end labeled AP1 Oligos were prepared by annealing a labeled top strand oligo with the complementary bottom strand oligo then verifying the oligo was now double-stranded by polyacrylamide gel analysis (final concentration = 2 pmoles/µl).
SAM2® Membrane Analysis: Reactions were assembled in a final volume of 15µl and contained 1X Gel Shift Binding Buffer, 1µl labeled AP1 Oligo in the presence or absence of the AP1 protein (3–10µl in vitro translation reactions), cold AP1 oligo (1–3µl; 2pmol/µl), or 1µl cold SP1 oligo. The assembled reactions were incubated on ice for 20–30 minutes, spotted onto SAM2® Biotin Capture Membranes, washed 3 × 10 minutes in 1X Gel Shift Binding Buffer without poly(dI-dC)/poly(dI-dC), and each square was counted in a scintillation counter.
Figure 1 shows that Transcend™-labeled c-jun proteins expressed in the TnT® SP6 Quick Coupled Transcription/Translation System or the TnT® Coupled Wheat Germ Extract System bind to the 32P-labeled AP1 Consensus Oligo. The presence of unlabeled AP1 Oligo (100-fold excess) significantly reduced the binding of labeled AP1 Oligo to the c-jun protein.
To test the specificity of the binding, we performed reactions in the presence of an unlabeled specific competitor (AP1 Oligo) and an unlabeled nonspecific competitor (SP1 Oligo). Both competitors were in 300-fold excess. Figure 2 shows that unlabeled SP1 Oligo is an ineffective binding competitor when compared to unlabeled AP1, demonstrating the specificity of binding detection by the SAM2® Membranes. Proteins expressed with the TnT® SP6 Quick Coupled Transcription/Translation or the TnT® Coupled Wheat Germ Extract Systems had similar specificities.
Finally, we tested the interaction between a [35S]methionine-labeled in vitro expressed c-jun protein and a biotinylated AP1 Oligo captured on SAM2® Membranes (Figure 3). Protein expressed with both the TnT® SP6 Quick Coupled Transcription/Translation System and the TnT® Coupled Wheat Germ Extract System bound the AP1 Oligo. Due to volume constraints in the binding reaction, only a threefold excess of unlabeled AP1 Oligo was used and competition with the labeled AP1 Oligo was incomplete.
The detection of DNA binding does not require gel analysis. DNA:protein interactions can be measured using either a Transcend™-labeled protein and a 32P-labeled oligo or a 35S-labeled protein and a biotinylated oligo in conjunction with the SAM2® Membranes. SAM2® Membrane analysis is easier than gel analysis, especially if large numbers of samples will be analyzed.