Effect of DNA Local Conformation on the Affinity and Binding Specificity of bis-Netropsins to DNA

The interaction of short nucleotide duplexes with bis-netropsins, in which netropsin fragments are linked tail-to-tail via cis-diammineplatinum group ([arrow left]Nt-Pt(NH^sub 3^ )-Nt[arrow right]) or aliphatic pentamethylene chain ([arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right]), has been studied. Both bis-netropsins have been shown to bind to DNA oligomer 5"-CCTATATCC-3" (I) as a hairpin with parallel orientation of netropsin fragments in 1:1 stoichiometry. Monodentate binding has been detected upon binding of bis-netropsins to other duplexes of sequences 5"-CCXCC-3" [where X = TTATT (II), TTAÐnT (III), TTTTT (IV), and AATTT (V)] along with the binding of bis-netropsins as a hairpin. The formation of dimeric antiparallel motif between the halves of two bound bis-netropsin molecules has been observed in the complexes of [arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right] with DNA oligomers IV and V. The ratio of binding constant of bis-netropsin as a hairpin (Ðs^sub 2^) to monodentate binding constant (Ðs^sub 1^) has been shown to correlate with the width and/or conformational lability of DNA in the binding site. The share of bis-netropsin bound as a hairpin decreases in the order: TATAT > TTATT > TTAAT > TTTTT > AATTT, whereas the contribution of monodentate binding rises. The minimal strong binding site for [arrow left]Nt-Pt(NH^sub 3^ )-Nt[arrow right] and [arrow left]Nt-(CH^sub 2^ )^sub 5^ -Nt[arrow right] binding as a hairpin has been found to be DNA duplex 5"-CGTATACG-3".[PUBLICATION ABSTRACT]