I am interested in information contained within DNA sequences. I am presently working with DNA curvature and chromatin structure, and in periodicity information within genomic DNA sequences. I am looking for a few good students who would be interested in helping me to continue with this line of research in these three areas.

Project # 1 - cloning & sequencing an intrinsically curved DNA fragment.

 This project would provide experience in the following techniques:

 1.) purifying DNA

 2.) running "high resolution" acrylamide and agarose gels

 3.) designing and cloning a DNA fragment

 4.) sequencing (and naming) of all the new clones you create!

 I have found that most DNA sequences contain at least a small amount of curvature, and that the degree of curvature detected strongly depends on environmental conditions - in particular temperature and salt. Presently I am using this data, in conjunction with results recently published from other labs, to refine the wedge angles used to predict curvature of a given piece of DNA. The next step will then be to focus on delineating DNA flexibility from intrinsic curvature, by designing specific oligomers (probably 21 nucleotides long), and synthesising them and running ligation ladders on acrylamide gels. This would be a good project for a student to start work on. After the initial characterisation of curvature, small fragments of the ligated oligomer (say about 126 bp) could be cloned into a plasmid vector (like pBluescript) and then large amounts of DNA grown up and used for future experiments, including the measurement of protein affinity to the various types of curves. I have done (am doing) these types of experiments myself, and of course the amount of independence I give to the student would depend on their motivation and present level of understanding.

Project # 2 - purification of chromatin proteins.

 This project would provide experience in the following techniques:

 1.) purifying protein

 2.) running "high resolution" acrylamide and agarose "protein" gels

 3.) running of "bandshift gels" to charactarise DNA/Protein binding

 4.) possibly sequencing of any new proteins you might find!

The second area of research is chromatin-associated proteins, and would be ideally suited for a student interested in learning a bit about protein purification and DNA binding proteins. In particular I am interested in bacterial chromatin-associated proteins isolated from enteric bacteria, and the ability of these proteins to constrain supercoils and to bind (and bend) preferentially curved DNA sequences. This would be similar to a set of experiments I have worked on at the Institute of Molecular Medicine, in Oxford. (These experiments have resulted in two papers so far.)

Project # 3 - comparative analysis of completely sequenced genomes

 This project would provide experience in the use of computers for:

 1.) "BLAST" search for similar DNA sequences in GenBank

 2.) Alignment of DNA/protein sequences

 3.) Construction of "logo plots" for aligned sequences

4.) Structural analysis of various DNA/RNA/protein sequences

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