I. Molecular Recognition of Nucleic Acid by BMSP. II. Sequence Specific B → H → A Allosteric Transitions in DNA

Abstract

Chapter One Bis(methidium)spermine (BMSp), a dimer of two intercalating monomers of ethidium bromide (EB) connected by a spermine link has been synthesized and characterized. The results of these studies clearly demonstrate that both monomers of BMSp simultaneously intercalate nucleic acid, substantially enhancing both its binding affinity and specificity. Under physiological conditions both the binding affinity and specificity of BMSp are similar to DNA binding regulatory proteins. Thus BMSp represents one of the first rationally designed drugs which may selectively inhibit or alter gene expression. The binding affinity, binding cooperativity, binding site size, and visible spectrum of BMSp are found to vary with nucleic acid conformation. Both BMSp and EB are shown to bind H and A conformations of nucleic acid much more tightly than B conformations. As a result, both compounds induce sequence specific B → H → A allosteric transitions in DNA. Chapter Two A sensitive experimental technique which can accurately estimate equilibrium binding isotherms is described. Ligand-macromolecule interactions are monitored by classical indirect techniques over a broad ratio of LT/M, where LT is the total ligand concentration and M is the macromolecule concentration. When analyzed at constant X, where X is some physical property of ligand which is proportional to its concentration, the dependence of LT on M can be used to estimate the binding densities and free ligand concentrations characterizing the ligand-macromolecule interaction. In contrast to classical indirect and direct techniques, accurate binding isotherms can be estimated over a wide range of binding densities for tightly or weakly bound ligands. When the binding of ethidium bromide to polyd(C-G) and polydCdG is examined by this technique, previously undetected allosteric transitions are revealed. Chapter Three Evidence for a new conformational family of Watson-Crick DNA is presented. Termed H or hybrid DNA, such DNA is postulated to be an intermediate in the interfamily B → A transition. Hybrid DNA is characterized by a 2'-endo (3' → 5') 3'-endo alteration in sugar pucker every base pair and may also be an intermediate in DNA melting, DNA kinking, and drug intercalation. The ease with which DNA undergoes a B → H → A transition is found to vary greatly with its sequence. On the basis of these results, the equilibrium stability, rather than the structure of Watson-Crick DNA is postulated to vary greatly with base sequence.