title: Extending the language of DNA molecular recognition by polyamides: unexpected influence of imidazole and pyrrole arrangement on binding affinity and specificity.
abstract: Pyrrole (Py) and imidazole (Im) polyamides can be designed to target specific DNA sequences. The effect that the pyrrole and imidazole arrangement, plus DNA sequence, have on sequence specificity and binding affinity has been investigated using DNA melting (DeltaT(M)), circular dichroism (CD), and surface plasmon resonance (SPR) studies. SPR results obtained from a complete set of triheterocyclic polyamides show a dramatic difference in the affinity of f-ImPyIm for its cognate DNA (K(eq) = 1.9 x 10(8) M(-1)) and f-PyPyIm for its cognate DNA (K(eq) = 5.9 x 10(5) M(-1)), which could not have been anticipated prior to characterization of these compounds. Moreover, f-ImPyIm has a 10-fold greater affinity for CGCG than distamycin A has for its cognate, AATT. To understand this difference, the triamide dimers are divided into two structural groupings: central and terminal pairings. The four possible central pairings show decreasing selectivity and affinity for their respective cognate sequences: -ImPy > -PyPy- >> -PyIm- approximately -ImIm-. These results extend the language of current design motifs for polyamide sequence recognition to include the use of "words" for recognizing two adjacent base pairs, rather than "letters" for binding to single base pairs. Thus, polyamides designed to target Watson-Crick base pairs should utilize the strength of -ImPy- and -PyPy- central pairings. The f/Im and f/Py terminal groups yielded no advantage for their respective C/G or T/A base pairs. The exception is with the -ImPy- central pairing, for which f/Im has a 10-fold greater affinity for C/G than f/Py has for T/A.
authors.affiliation: Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
authors.forename: Karen L
authors.initials: KL
authors.lastname: Buchmueller
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Staples
authors.forename: Cameron M
authors.initials: CM
authors.lastname: Howard
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Horick
authors.forename: Peter B
authors.initials: PB
authors.lastname: Uthe
authors.forename: N Minh
authors.initials: NM
authors.lastname: Le
authors.forename: Kari K
authors.initials: KK
authors.lastname: Cox
authors.forename: Binh
authors.initials: B
authors.lastname: Nguyen
authors.forename: Kimberly A O
authors.initials: KA
authors.lastname: Pacheco
authors.forename: W David
authors.initials: WD
authors.lastname: Wilson
authors.forename: Moses
authors.initials: M
authors.lastname: Lee
mesh_terms: D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D007093:Imidazoles / Q000737:chemistry* / Q000378:metabolism; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009757:Nylons / Q000737:chemistry* / Q000378:metabolism; D011758:Pyrroles / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity; D020349:Surface Plasmon Resonance
chemical_list: D007093:Imidazoles; C487889:N-(2-(dimethylamino)ethyl)-1-methyl-4-(1-methyl-4-(4-formamido-1-methylimidazole-2-carboxamide)imidazole-2- carboxamido)imidazole-2-carboxamide; D009757:Nylons; D011758:Pyrroles; D004247:DNA