title: Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides.
abstract: Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, -ImPy- and -PyPy-. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and DeltaT (M) experiments. The f/Py pairing, when placed next to the -ImPy- or -PyPy- central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With -ImPy- central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson-Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the -PyPy- central pairings.
authors.affiliation: Department of Chemistry, Furman University, Greenville, SC 29613, USA.
authors.forename: Karen L
authors.initials: KL
authors.lastname: Buchmueller
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Staples
authors.forename: Peter B
authors.initials: PB
authors.lastname: Uthe
authors.forename: Cameron M
authors.initials: CM
authors.lastname: Howard
authors.forename: Kimberly A O
authors.initials: KA
authors.lastname: Pacheco
authors.forename: Kari K
authors.initials: KK
authors.lastname: Cox
authors.forename: James A
authors.initials: JA
authors.lastname: Henry
authors.forename: Suzanna L
authors.initials: SL
authors.lastname: Bailey
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Horick
authors.forename: Binh
authors.initials: B
authors.lastname: Nguyen
authors.forename: W David
authors.initials: WD
authors.lastname: Wilson
authors.forename: Moses
authors.initials: M
authors.lastname: Lee
mesh_terms: D020029:Base Pairing; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D007093:Imidazoles / Q000737:chemistry*; D009691:Nucleic Acid Denaturation; D009757:Nylons / Q000737:chemistry*; D011758:Pyrroles / Q000737:chemistry*; D020349:Surface Plasmon Resonance
chemical_list: D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; D004247:DNA