Statistical Mechanics Approach to DNA Promoter Prediction

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The objective of this project is the development of an efficient method for the prediction of the location of promoter regions in any given DNA sequence. Promoters are regulatory regions of DNA providing a control point for gene transcription, and in eukaryotes, they are very diverse and difficult to characterize. It has been demonstrated that their location is associated with regions along the DNA sequence where there is high probability for the hydrogen bonds to be stretched. Among the problems that will be addressed in this project is the extension of the currently used models of the DNA double helix to account for the heterogeneity and other relevant structural properties of DNA sequences, and the study of the spectrum of integral operators involved in the calculation of the thermodynamical properties of such sequences.The proposed course of study has as ultimate goal the development of a methodology that will allow the fast and reliable analysis of very long DNA sequences. This is crucial, because, on one hand, there is evidence that many diseases, e.g., asthma, are associated with promoter elements and on the other hand, the controlled regulation of genes represents a powerful therapeutic approach. Once such a method has been tested on already studied sequences, it will be possible to make it available to scientists in the biological disciplines, and to use it in the design of experiments.