This proposal details our systematic approach to the design of new, sequence selective DNA minor groove binding compounds. Our approach differs from previous approaches in that we Wi"""""""" focus on the role of ligand shape, especially width, in molecular recognition of the minor groove of double-stranded DNA. We will address two specific questions: (a) What role does shape play in the interactions of small molecules with the minor groove? (b) How can we harness the role of ligand shape to rationally design ligands with predictable sequence and biochemical selectivities? Our focus on the role of shape in minor groove molecular recognition will specifically address the issues of the relative contribution of shape vis-a-vis hydrogen bonding and electrostatic contributions to molecular recognition, and the ability of the conformationally flexible minor groove of DNA to accommodate differently shaped ligands. As an application of this knowledge, we will specifically address the issues of sequence recognition and the ability of specific ligand/DNA complexes to effect DNA-processing enzymes that make contact with the minor groove, including Human Immunodeficiency Virus Type 1 (HIV-1) reverse transcriptase. Our long term goal is to have at hand a relatively small number of individual molecular building blocks, each of which possesses a well defined DNA binding specificity. These rigid molecular building blocks can then be assembled in a rational order to construct a DNA minor groove ligand that complements not only the electrostatic and hydrogen bonding environment of a particular sequence of DNA, but also its specific three-dimensional shape. We term such shape complementary DNA minor groove binding compounds morpholexins, because they read not only the lexis or """"""""words"""""""" of the genetic code but also the morph or """"""""shapes"""""""" of the regions in which these words reside.
Specific aims of this work include: 1. The design and synthesis of two new classes of morpholexin units. Structural features of the ligands that will be addressed are: the width, the conformational flexibility, and the hydrogen bonding and electrostatic functionality. 2. The design and synthesis of linked morpholexins. These compounds will be designed to probe two specific linking motifs: a head-to-tail amide bond linker and a head-to-head alkynyldiol linker. 3. The evaluation of the DNA binding of these morpholexins. Two specific binding characteristics will be investigated: the sequence selectivity, and the relationship between the minor groove width and flexibility, and binding site selectivity. 4. The evaluation of the effect of these morpholexins on the DNA- directed DNA polymerization reaction catalyzed by HIV-1 reverse transcriptase. Specific investigations will focus on the correlation of particular DNA binding sites with specific effects of the resulting ligand/DNA complex on the strand displacement DNA synthesis catalyzed by HIV-1 reverse transcriptase.
