title: Hx-amides: DNA sequence recognition by the fluorescent Hx (p-anisylbenzimidazole)•pyrrole and Hx•imidazole pairings.
abstract: Hx-amides are fluorescent hybrids of imidazole (I)- 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 ΔTM 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.
authors: Division of Natural & Applied Sciences and Department of Chemistry, Hope College, Holland, MI 49423, USA.
authors: Vijay
authors: V
authors: Satam
authors: Pravin
authors: P
authors: Patil
authors: Balaji
authors: B
authors: Babu
authors: Matthew
authors: M
authors: Gregory
authors: Michael
authors: M
authors: Bowerman
authors: Mia
authors: M
authors: Savagian
authors: Megan
authors: M
authors: Lee
authors: Samuel
authors: S
authors: Tzou
authors: Kevin
authors: K
authors: Olson
authors: Yang
authors: Y
authors: Liu
authors: Joseph
authors: J
authors: Ramos
authors: W David
authors: WD
authors: Wilson
authors: John P
authors: JP
authors: Bingham
authors: Kostantinos
authors: K
authors: Kiakos
authors: John A
authors: JA
authors: Hartley
authors: Moses
authors: M
authors: Lee
mesh_terms: D000577:Amides / Q000737:chemistry*; D000840:Anisoles / Q000737:chemistry*; D020029:Base Pairing; D001562:Benzimidazoles / Q000737:chemistry*; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D005456:Fluorescent Dyes / Q000737:chemistry; D007093:Imidazoles / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D011758:Pyrroles / Q000737:chemistry*
chemical_list: D000577:Amides; D000840:Anisoles; D001562:Benzimidazoles; D005456:Fluorescent Dyes; D007093:Imidazoles; D011758:Pyrroles; C029899:imidazole; D004247:DNA; C031000:benzimidazole