title: Expanding the recognition of the minor groove of DNA by incorporation of beta-alanine in hairpin polyamides.
abstract: In order to expand the recognition code by hairpin polyamides to include DNA sequences of the type 5'-CWWC-3' two polyamides, PyPyPyPy-(R)(H2N)gamma-ImPyPyIm-beta-Dp (1) and PyPyPyPy-(R)(H2N)gamma-ImPy-beta-Im-beta-Dp (2) were synthesized which have in common an Py/Im pair in the terminal position for targeting C x G but differ with respect to internal placement of a beta-alanine residue. The equilibrium association constants (Ka) were determined at four DNA sites which differ at a single common position, 5'-TNTACA-3' (N = T, A, G, C). Quantitative DNase I footprint titration experiments reveal that the eight-ring hairpin PyPyPyPy-(R)(H2N)gamma-ImPyPyIm-beta-Dp (1) binds the four binding sites with similar affinities, Ka = 1.3-1.9 x 10(10) M(-1) indicating that there is no preference for the position N. In contrast, a redesigned polyamide PyPyPyPy-(R)(H2N)gamma-ImPy-beta-Im-beta-Dp (2) that places an internal flexible aliphatic beta-alanine to the 5'-side of a key imidazole group bound the match site 5'-TCTACA-3' with high affinity and good sequence discrimination (Ka(match) = 4.9 x 10(10) M(-1) and the single base pair mismatch sites with 5- to 25-fold lower affinity). These results expand the repertoire of sequences targetable by hairpins and emphasize the importance of beta-alanine as a key element for minor groove recognition.
authors: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA.
authors: C C
authors: CC
authors: Wang
authors: U
authors: U
authors: Ellervik
authors: P B
authors: PB
authors: Dervan
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D018983:DNA Footprinting; D004268:DNA-Binding Proteins / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009757:Nylons / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D017433:Protein Structure, Secondary; D013329:Structure-Activity Relationship; D017186:Titrimetry; D015091:beta-Alanine / Q000737:chemistry
chemical_list: D004268:DNA-Binding Proteins; D009757:Nylons; D015091:beta-Alanine; D004247:DNA