Molecular recognition between oligopeptides and nucleic acids. DNA sequence specificity and binding properties of an acridine‐linked netropsin hybrid ligand

Abstract

The binding to DNA of a mixed function ligand (NETGA) is described, in which a potential intercalating group, an acridine moiety, is incorporated at the carboxyl terminus of the minor groove binding oligopeptide netropsin skeleton. Scatchard analysis of absorption data provided evidence of two modes of binding to DNA with K1 = 9.1 x 10(5) M-1 at low r values (0.003-0.1), and a binding site size n = 10, indicative of binding of both moeities. At high binding ratios (greater than 0.1), K2 = 0.9 x 10(5) M-1 and n = 5 corresponding to external binding. Complementary strand MPE footprinting on a pBR322 restriction fragment showed NETGA binds to 5'-AAAT like netropsin. It causes enhanced cleavage by MPE, particularly at G-C rich sequences and remote from the preferred binding sites. Viscometry measurements provided evidence for biphasic modes of the two binding portions of NETGA. Fluorescence polarization and linear dichroism measurements were in accord with distinct modes of interaction of the acridine (intercalation) and oligopeptide (minor groove binding) portions of NETGA. LD measurements on NETGA indicate that the oligopeptide moiety (netropsin-like) has an orientation typical of minor groove binders, whereas the degree of intercalation of the acridine group is decreased by association of the oligopeptide moiety.

Theoretical Design of a Bistetrapeptide Derivative of Mitoxantrone Targeted Towards the Double-Stranded Hexanucleotide Sequence d(GGCGCC)2

“…Design of intercalator-linked oligopeptides undertaken so far invariably targeted the oligopeptide in the minor groove (47)(48)(49)(50)(51). The present study and that of ref.…”

DNA Binding and Topoisomerase I Poisoning Activities of Novel Disaccharide Indolocarbazoles

“…Calf thymus DNA was deproteinized with sodium dodecyl sulfate (protein content Ͻ0.2%) and all nucleic acids were dialyzed against 1 mM sodium cacodylate buffered solution, pH 7.0. Details of the procedures used for electric linear dichroism (ELD) experiments were reported previously (Bailly et al, 1990;Colson et al, 1996). In the ionic strength conditions used for ELD measurements, chromatin (10-80 nucleosomes long) is mostly present as the 10-nm fiber.…”

Joint Molecular Modeling and Spectroscopic Studies of DNA Complexes of a Bis(arginyl) Conjugate of a Tricationic Porphyrin Designed to Target the Major Groove

“…In contrast, most antitumor drugs, whether intercalating (57,58) or nonintercalating (59,60), bind DNA in the minor groove. This is also the case for Virtually all synthetic sequence-specific oligopeptides, whether nonintercalating (61)(62)(63)(64) or covalently bound to an intercalator (65)(66)(67)(68)(69)(70). Yet the minor groove has, with respect to the major groove, a much more reduced potentiality for selective recognition, since its two principal electron-rich sites, N 3 of adenine and O 2 of thymine, not only occupy very similar positions in the B-DNA conformation, but have similar affinities for an incoming ligand as well, making them virtually indistinguishable (71).…”