Hx-amides: DNA Sequence Recognition by the Fluorescent Hx (p-anisylbenzimidazole)•Pyrrole and Hx•Imidazole Pairings
Hx-amides are fluorescent hybrids of imidazole (1)- and pyrrole (P)-containing polyamides and Hoechst 33258, and they bind in the minor groove of specific DNA sequences. Synthesis and DNA binding studies of HxII (5) complete our studies on the first set of Hx-amides: Hx-I/P-I/P. HxPP (2), HxIP (3) and HxPI (4) were reported earlier. Results from DNase I footprinting, biosensor-SPR, CD and Delta T-M studies showed that Hx-amides interacted with DNA via the anti-parallel and stacked, side-by-side motif. Hx was found to mimic the DNA recognition properties of two consecutive pyrrole units (PP) in polyamides. Accordingly, the stacked Hx/PP pairing binds preferentially to two consecutive AT base pairs, A/T-A/T; Hx/IP prefers C-A/T; Hx/PI prefers A/T-C; and Hx/II prefers C-C. The results also showed that Hx-amides bound their cognate sequence at a higher affinity than their formamido-triamide counterparts. (C) 2013 Elsevier Ltd. All rights reserved.
Satam, Vijay, Pravin Patil, Balaji Babu, Matthew Gregory, Michael Bowerman, Mia Savagian, Megan Lee, Samuel Tzou, Kevin Olson, Yang Liu, Joseph Ramos, W. David Wilson, John P. Bingham, Kostantinos Kiakos, John A. Hartley and Moses Lee. "Hx-Amides: Dna Sequence Recognition by the Fluorescent Hx (P-Anisylbenzimidazole)•Pyrrole and Hx•Imidazole Pairings." Bioorganic & Medicinal Chemistry Letters 23, no. 6 (2013). http://dx.doi.org/10.1016/j.bmcl.2013.01.075