Determination of reaction mechanism and specificity in nucleotide sequence recognition

In this project we will address the fundamental question of how the genetic information in DNA codes for rates of binding and unbinding, by using p53 - DNA binding as a model system.

To answer this question, we will use and  develop new technology to measure association and dissociation rates to millions of DNA sequences simultaneously on a sequencing chip. The research will be performed in the Greenleaf lab at Stanford University.

The first year of the project will be used to do sample preparation of fluorescent p53, and high-throughput kinetic measurements with p53 constructs.

The second year will be used to analyse data, and to fit models to the data, to extract the microscopic parameters and mechanism of the binding.

The third year will be used to model and predict binding patterns for DNA binding sites that are not present in the training dataset.

In general and overarching terms, the research is important because it will allow us to determine how the genetic information codes for binding of regulatory elements.

When we can quantitatively predict the binding patterns of transcription factors to promoters from the DNA sequence information, this will revolutionize systems biology. Determining the kinetic mechanism of binding of p53 to DNA would have important impacts for medicinal research.