Gravies site about

2014-05-11 Update: This is a very old post and seems like a long time ago now!

About the gravies files

This site exists mostly for my benefit to enable me to tinker with html. It will therefore lack content but bristle with mistakes and failed attempts to use fancy html / javascript / other things. It is under construction and will remain unfinished indefinitely. For my own benefit, so that I can keep track of how much time I waste on the internet and to coax others into falling into the same trap, I will be maintaining a links section with a high emphasis on sites that offer no use other than to keep you amused and distracted from the important things you should be thinking about. You may want to stop reading this crap and jump to these right now. I’ll also keep up section on links that are useful for molecular biologists and the like… again entirely for my own benefit because I am a selfish bar’s tard.

This site is called the Gravies files for no particular reason other than the fact that I have a very limited imagination. Gravies is a name I was given by Bob / Emma / Justin when I lived in Dowry Road Bristol. An odd nickname formed from the G in Graham and the ravies in Davies (like you needed me to explain that). In addition, at the time there was a tendency of “student-types” (as we were) to call each other by the surname prefaced by the term “The Boy”. It works better with some names… eg. “The Boy Dillingham” (aka Mark).

about distractions

about my Ph.D.

Choose your section below based on your desire to know:

Not interested I worked on a protein that runs along DNA and cuts it up.

“Interested” I worked on an protein that is found in E. coli (nothing to do with the pathogenic E. coli 0157) and other bacteria (aka germs, ie. not animals / humans / goats or amoebae) that protects the bacteria from infection by viruses (bacterial viruses not like HIV / hepatitis - only infect bacteria). The protein is like a tiny machine that recognises the viral DNA and cuts it up. In doing this it runs along the DNA and snips it up when it meets a blockage. I was interested in how it cut the DNA and how it moved.

Very bored Molecular Biologist I worked on a type I restriction enzyme. Very different from the type II restriction enzymes that you use in the lab because it does not cut at a specific point near the recognition sequence but at great distances instead. The enzyme has translocates DNA in both directions having bound an unmethylated recognition sequence and eventually cleaves both strands of the duplex when it collides with another enzyme or another block to translocation.

Type I RM person Probably simpler if you just read the following and email me with queries.

EcoKI with an amino acid substitution in any one of seven DEAD-box motifs has impaired ATPase and endonuclease activities
Graham P. Davies, Lynn M. Powell, Julie L. Webb, Laurie P. Cooper, Noreen E. Murray
(1998) Nucleic Acids Research, 26, pp. 4828-4836
Abstract   Full-text HTML (95 KB)   Full-text PDF   Full-text PostScript (614 KB)

On the structure and operation of type I DNA restriction enzymes
Graham P. Davies, Ina Martin, Shane S. Sturrock, Andrew Cronshaw, Noreen E. Murray, and David T.F. Dryden
(1999) Journal of Molecular Biology, 290, pp.565-579

The assembly of the EcoKI type I DNA restriction/modification enzyme and its interaction with DNA
D.T.F. Dryden, G.P.Davies, I. Martin, L.M. Powell, N.E. Murray, D.J. Ellis, T. Berge, J.M. Edwardson, and R.M. Henderson.
(1999) Biochemical Society Trasactions, 27, pp.691-696.

The DNA translocation and ATPase activities of Restriction-deficient mutants of EcoKI
Graham P. Davies, Priscilla Kemp, Ian J. Molineux, and Noreen E. Murray
(1999) Journal of Molecular Biology, 292, pp.787-796

Amino acids motifs necessary for DNA translocation and DNA cleavage by EcoKI.
Ph.D. thesis Edinburgh University… available online if you really are desperate.

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