title: Base pair recognition of the stereochemically alpha-substituted gamma-turn of pyrrole/imidazole hairpin polyamides.
abstract: Recognition of the sequences 5'-NGCACA-3' (N = T, A, C, G) by pyrrole/imidazole polyamides with (R/S)-alpha-hydroxyl/alpha-amino-substituted gamma-aminobutyric acid as a gamma-turn was investigated. Four novel polyamides, 2, 3, 4, and 5, including (R)-alpha-hydroxyl-gamma-aminobutyric acid (gammaRO), (S)-alpha-hydroxyl-gamma-aminobutyric acid (gammaSO), (R)-alpha,gamma-diaminobutyric acid (gammaRN), and (S)-alpha,gamma-diaminobutyric acid (gammaSN) residues, respectively, were synthesized, and their binding affinity to T.A, A.T, G.C, and C.G base pairs at turn position was studied by the surface plasmon resonance (SPR) technique. SPR data revealed that polyamide 3, AcImbetaImPy-gammaSO-ImPybetaPy-beta-Dp, with a gammaSO turn, possesses a marked binding preference for T.A over A.T with a 25-fold increase in specificity, despite low binding affinity relative to 2, with a gammaRO turn. Similarly, AcImbetaImPy-gammaSN-ImPybetaPy-beta-Dp (5), with a gammaSN-turn, gives rise to a 8.7-fold increase in specificity for T.A over A.T. Computer-assisted molecular modeling suggests that 3 binds more deeply in the minor groove of the T.A base pair relative to the A.T base pair, allowing hydrogen bonding to O2 of the thymine at the turn position, which explains the SPR results. These results suggest that gammaSO and gammaSN may function as T-recognition units at the turn position, as well as a gamma-turn in the discrimination of polyamides.
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
authors.forename: Wen
authors.initials: W
authors.lastname: Zhang
authors.forename: Masafumi
authors.initials: M
authors.lastname: Minoshima
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sugiyama
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D007093:Imidazoles / Q000737:chemistry*; D008958:Models, Molecular; D009757:Nylons / Q000737:chemistry*; D011758:Pyrroles / Q000737:chemistry*; D013237:Stereoisomerism; D020349:Surface Plasmon Resonance
chemical_list: D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles