A polynucleotide CD probe: interactions with oligomers of a polycationic amine that exhibit positive extrinsic bands at greater than 300 nm.

Abstract

AbstractA set of large positive extrinsic CD bands ([θ]333 = 2.6 X 104 deg‐cm2/decimole phosphate) in the > 300 nm region as well as diminution of the intrinsic signals (θ275) have been observed in the CD spectra of various nucleic acids complexed with the achiral compound, N‐poly{α‐[N‐(4‐pyridylethylene‐4‐pyridyl‐N′‐)α′‐p‐xylyl]dibromide}‐4‐pyridylethylene‐4‐pyridinium bromide, (polymer X).1,2,5 The signal changes are attributed to the binding of polymer X chromophores isogeometrically to the DNA helix in an ordered chiral arrangement. Fractionation of polymer X gives 10 well‐separated oligomers. The oligomers were characterized by nmr. Their interactions with DNA have been investigated with respect to r(r = ratio of equivalents of polymer X charge/g‐atoms DNA phosphorus) and n (oligomer chain length). In all cases where n ≥ 1, [θ]333 increases linearly with increasing r between 0 and 0.32, and is accompanied by a corresponding decrease in [θ]275, which becomes negative as r approaches .32. Extrinsic band intensities reveal a dependence on n up to n = 5, above which increases in nonspecific binding result in a reduction in normalized band intensities. Polymer X shows a strong preference for B‐form nucleic acids and induces maximum extrinsic CD signal intensities with A‐T homopolymers. Alterations in helix hydration are believed to accompany complex formation. Inversions in [θ]275 of the octamer X‐poly(dA‐dT) complex have been attributed to the “alternating B” conformation of poly(dA‐dT).3 Similar inversions are not observed in other nucleic acid‐octamer X complexes. Visible and CD spectrometry data from competition studies in the presence of the antibiotics actinomycin D (AMD), daunomycin (DM), and distamycin A (DST) are consistent with “nonclassical” intercalation as the mode of binding, and these data place the potential binding site in or near the hydrophobic region of the minor groove. Reductions in [θ]333 with increasing urea further implicate the involvement of hydrophobic interactions in the formation of an asymmetric complex. Stabilization of the helix results in all cases as evidenced by alterations in Tm; corresponding changes, however, in cooperativity are not clearly discernable. Viscosity and light‐scattering data indicate no changes in molecular weight due to aggregation, and as such are not consistent with a transition to the ψ‐DNA upon complex formation.