I woke up at 6:30, without the help of the alarm. My internal clock must have finally been reset for the time zone we were in! Brennan woke up reporting that he had a headache as well as a back ache in addition to general fatigue. We were a little suspicious, given his recent difficulties with Sports Day, so we urged him to push himself and try to make it through the day at school. He continued to insist that he couldn’t make it, however, until we finally gave in and let him stay home. Due to our heated debate on Brennan’s health, I got in at 9:30 again, too late to attend Ana’s English journal club presentation. Instead, I went right to work on staining and scanning the gel I had run overnight.
The gel showed that I had finally come up with a ratio of histones to DNA that had worked: 1.75 parts of the former to each part of the latter. One thing that still distressed Kiyoe, however, was the amount of “glop” that had refused to run into the gel and which was stuck in the wells in which I had loaded my samples. She suspected that the glop was due to a non-specific binding of histones to DNA and could be prevented by the addition of additional DNA to my sample which would compete for this type of binding.
I spent the next several hours figuring out a way to produce this competitor DNA. Finally, I worked out a plan to cut a particular plasmid with two enzymes in order to produce DNA fragments that were too small to produce nucleosomes themselves but could serve to bind to histones in a non-specific fashion. By afternoon, I had set up the desired reaction as well as poured the gel which was required to run the digestion on. Unfortunately, I soon discovered that only one of the two enzymes had actually cut the DNA. Not knowing which of the two had failed, I set up two more enzyme reactions before I left for the day: one for each of the two enzymes separately instead of one reaction with the two together. I then left for home; arriving around 6 pm.
Trudy made pasta for dinner: gnocchi for the two of us, and penne for the kids, who actually preferred the latter. We spent the evening watching “Deep End of the Ocean”, a movie we had borrowed from Tsuneko about a family who has their 3-year old son kidnapped, only to have him return 9 years later.