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. Author manuscript; available in PMC: 2024 Sep 25.
Published in final edited form as: Angew Chem Int Ed Engl. 2023 Aug 18;62(39):e202308650. doi: 10.1002/anie.202308650

Figure 2.

Figure 2.

Analysis of dsDNA and dsRNA recognition by Max homodimer, a basic helix-loop-helix motif. (A) Max homodimer binds to fluorescein-labeled Ebox DNA hairpin sequence (5’-FAM-CAC CAC GTG GTT TTT ACC ACG TGG TG) with high affinity (Kd = 0.04 ± 0.02 μM) in a fluorescence polarization assay but shows no affinity for the analogous RNA hairpin sequence (5’-FAM-CAC CAC GUG GUU UUU ACC ACG UGG UG). (B) Comparison of dsDNA and dsRNA major groove interactions with α-helices. (i) Positioning of base pairs within major grooves. (ii-iv) Structural analysis of DNA in complex with Max homodimer (PDB code 1hlo) and RNA in complex with Rev peptide (PDB code 1etf) and TAV2b (PDB code 2zi0) reveals that the angles of entry of dimeric α-helical domains into dsDNA and dsRNA diverge. (C) Replacement of the leucine zipper region in Max homodimer with a flexible linker leads to CHF-Max (SI Appendix, Figs. S1 and S2). CHF-Max binding to Ebox DNA and RNA was evaluated in a fluorescence polarization assay. Kd(CHF-Max/RNA): 0.48 ± 0.22 μM; Kd(CHF-Max/DNA): 0.69 ± 0.21 μM. Error bars represent the standard deviation of three independent experiments.