Interaction of amino acids and related compounds with neutral polyadenylic acid: a proton magnetic resonance study

Typescript.Thesis (Ph. D.)--University of Hawaii, 1971.Bibliography: leaves 157-164.xii, 164 l illusBy examining not only proton magnetic resonance (PMR) line separation but also actual chemical shifts of individual aromatic PMR lines of neutral-pH polyriboadenylic acid (poly A), it was established that poly A line separation reflects the degree of base stacking in the single-stranded polynucleotide under a variety of conditions. By monitoring the behavior of poly A in the presence of 19 amino acids and 10 derivatives, it was concluded that a number of aromatic and aliphatic compounds can interact with the polynucleotide via intercalation between adjacent bases, which thereby become destacked. The strength of binding depends primarily on the size, or hydrophobic character, as with the following amino acids: L-Trp>L-Phe>L-His L-Leu >L-Ile>L-Met >L-Vah~L-Pro >L-Ala>Gly but the binding can be aided (as with tryptamine, phenethylamine and histamine) or hindered (as with 3-indolepropionic, 3-phenylpropionic and dihydrourocanic acids) by an electrostatic interaction with the polynucleotide phosphates. It was shown that the PMR melting temperature (T) of 0.04M m - + poly A in 0.2M phosphate buffer, pH =7, was lowered 6±1°C upon addition of 0.15M L-Phe. Other amino acids caused a Tm depression m to an extent reflecting their binding strength. The binding of a number v of compounds was quantitated in terms of association constant K for a 1: 1 interactant: polynucleotide base complex, with the help of a computerized least-squares fit of PMR chemical shifts. Values ranged from K=5-10 M^-1 for L-Trp to KL-Phe> L-His. Negative results were obtained with neutral polycytidylic acid (poly C). The study represents a beginning attempt at understanding the molecular bases which underlie protein--polynucleotide interaction and specificity