This piece is based on my Ph.D. thesis “Repair of Oxidative DNA Damage by E. coli Endonuclease IV” [Curator's note: I shortened it to RODDE IV, as the full title did not fit in the box!]. This enzyme is a key part of the response to DNA damage caused by free radicals/gamma radiation/oxidation. The piece is dedicated to Bruce Demple, my Ph.D. advisor.

The DNA helix is represented by the circle of fifths. One strand is played by the right hand piano and the other strand by the left hand. The two strands are separated by a tritone (i.e. a minor fifth), which exactly splits the octave. The strands are also offset by half a beat, to better represent the true structure of the double helix.
This theme, representing the double-stranded helix of DNA, repeats several times for the first 30 seconds or so of the piece. Then the upper strand of DNA is damaged by the oxidative effects of free radicals (represented by staccato and dotted notes, note that this is similar to representation of the free radical with a dot, i.e. .OH as hydroxyl radical).

If a DNA base is damaged, the repair reaction is initiated by a glycosylase (represented by a descending chromatic scale, or sort of a glissando—glissando/glycosylase). If the sugar phosphate backbone is damaged, the endonuclease IV enzyme comes in and fixes it. Endo IV also fixes the apurinic/apyrimidinic site left by action of the glycosylase. Endo IV is represented by a series of “fourths”, followed by the quick removal of the damage (a quickly ascending series of notes). Finally, DNA polymerase I comes in and adds back the missing nucleotides, and the DNA strand is repaired.

For more details on this enzyme, search PubMed for “Levin” and “Demple” and you will find four papers (in Journal of Biological Chemistry and Nucleic Acids Research) that Bruce Demple and I published on this enzyme between 1988 and 1996.

DISCLAIMER: In my current day job, I am a regulatory scientist with the U.S. Food and Drug Administration. The opinions expressed on this post, as well as my activities on this site, are solely mine as a private citizen and should not be taken as agency policy or be a reflection on my employer (i.e. the U.S. taxpayer).

DNA Repair by Endonuclease IV (3).mp3 (1 MB)

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