The Effect of Monovalent Cation Binding on DNA Hairpin Stability

University Of Iowa, Iowa City IA

Investigators

Abstract

In this research supported by the Analytical and Surface Chemistry Program, Professor Stellwagen and her group will study the binding of monovalent cations to DNA hairpins, and the effect of monovalent cation binding on hairpin stability, using capillary electrophoresis. The current structure-prediction algorithms do not reliably predict DNA hairpin stability, indicating that the interactions leading to hairpin formation are not properly included in the folding routines. Since hairpin structures in single-stranded DNA oligomers are only marginally stable, they are difficult to study by conventional methods such as ultraviolet absorption or differential scanning calorimetry. By contrast, free solution capillary electrophoresis can detect hairpin formation and cation binding directly, because electrophoretic mobility depends on both the shape and the effective charge of the analyte. Broader impact of the proposed research: An important aspect of the project is its contribution to the training of undergraduate students and recent graduates in the biochemical and/or biophysical sciences. There are also scientific and technological broader impacts. Unexpected hairpin formation in single-stranded DNA oligomers can interfere with the hybridization of DNA oligomers to their target DNA or RNA sequences, creating difficulties in the design of multiplex PCR reactions and the interpretation of microarray experiments. Hairpin formation can also interfere with the effectiveness of DNA oligonucleotides used as antisense gene therapy agents. Hence, it is important to be able to predict hairpin formation in DNA oligomers and to understand the factors contributing to hairpin stability. The capillary electrophoresis methods that we have developed to measure monovalent cation binding to DNA are of general utility and can be used to measure the binding of other ligands to other analytes. .