Computers Predicting the outcomes of cutting DNA :: Biology

The focus of this study is the interaction between DNA and I-Msol, an endonuclease. An endonuclease is a protein that cuts DNA at a certain sequence with a certain length; I-Msol cuts DNA at approximately 20-24 base pairs and is highly specific in what sequence it is designed to cut. The interaction between DNA and an endonuclease like I-Msol is difficult to determine just by looking at the amino acid sequence of the protein. The difficulty arises because of the many molecular interactions such as hydrogen bonding and electrostatic interactions are affected by how the protein specifically interacts with the DNA, 3-dimensionally. The best method of understanding these complexities is to create model that considers all these dynamics of the DNA/protein interaction. Thus, a I-Msol/DNA model was created in silico to study the areas of contact between the two macromolecules as well as what happened when changes were made to the base pairs of the DNA. In summary: * It is impossible to predict DNA and protein interaction by looking at the amino acid sequence * hydrogen-bonding and electrostatic interactions alter amino acid sequence * I-Msol is a endonuclease, which cuts DNA around 20-24 base pairs with high specificity * Preliminary testing resulted in determining many of areas of contact between I-Msol and the DNA molecule * The researches made base pair substitutions that affected the interaction of the protein with the DNA Results After the protein-DNA contacts were redesigned, then, in this complex, the amino acids that were likely to cause disruption were changed. These amino acids were categorized on affinity for the designed protein for the new site and the decrease in affinity for the original wild type I-Msol enzyme As from the table, the largest predicted change came from the -6C*G, + 6 C*G, because this automatically prevents direct hydrogen bonding. Different amino acids had different disruption predictions. Using a formula, the binding energies were calculated by using the value of the wild type and then subtracting the facilitate comparison. A difference map represented certain values such as electron density for the new amino acids. A gel electrophoretic shift was done to observe the binding specificity. As the experiment indicates the experimental changes in binding affinities differed from the predicted ones. The results indicate that the future looks very bright for medicine and biochemistry as the redesign of the of DNA complexes is predicted to allow us to make mass breakthroughs in the future.