SYNTHESIS, DYNAMICS AND DRUG INTERACTIONS OF MODEL OLIGONUCLEOTIDES (THERMODYNAMICS, BINDING)

IVONNE MARITZA LASSALLE, Purdue University

Abstract

Several oligodeoxyribonucleotides were synthesized in large scale using liquid phase phosphotriester methodologies. Although special difficulties were encountered during the synthesis of the guanosine rich strand SS(,4) (attributable to the low solubility and side reactions of the guanosine residues) the remaining strands were synthesized in high to satisfactory yields. Thermal optical studies were conducted on several duplexes and the melting curve data were analyzed using a modified two state model for the helix to coil transition. Thermodynamic parameters were derived from melting curves by three different methods in order to get information about the nature of the transition and the factors influencing the derived parameters. Two of the methods assumed that the thermodynamic parameters derived were independent of temperature. A third method examined the temperature dependence of the thermodynamic parameters. This temperature dependence allowed the estimation of the difference in heat capacity between products and reactants and the correction of the parameters derived under the assumption of temperature independence. The largest deviations from two-state behavior (helix (--->) coils) were obtained for duplexes with the greatest structural and sequence diversity, factors which will give rise to multiple double helical states. The (DELTA)(DELTA)G(DEGREES) associated with the introduction of an extra, bulged-out thymidine base was estimated. Binding parameters for the interaction of several 9-amino-acridine derivatives to the model sequences were derived by the Scatchard method. Nonspecific binding of intercalators to single-stranded and double-stranded regions appears to be determined by the stability of such regions. The binding of more specific intercalators to single stranded regions appears to be determined by the favorable induced drug-DNA interactions in the complex rather than the stability of the oligomer. The binding of the drugs to single stranded regions was found to correlate with the mutagenicity of the drugs in the Ames' test. It is postulated that binding to single strands rather than to duplexes might play an important role in mutagenesis. From these studies, the sequence specificity for the binding of several acridines to the model sequences was determined.

Degree

Ph.D.

Subject Area

Biology

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