Matt Gethers/CRI, Thailand/Labwork/HmgR Binding Assay/Week of 8.3.08

8.4.08

To Do:

• Photocopy the info for the HmgR Probe and the GpxR probe that arrived on Friday.
• Add the information to their profiles on the wiki
• Align second round of sequencing for pIs001.P1 to see if G insertion still remains when it arrives.

8.5.08

To Do:

• Photocopy the info for the HmgR Probe and the GpxR probe that arrived on Friday.
• Add the information to their profiles on the wiki
• Align second round of sequencing for pIs001.P1 to see if G insertion still remains when it arrives.

Summary:

Sequencing came in. I wrote a script, Sequencing_flags.m, to help me with cataloging disputed bases. Will finish tomorrow.

8.6.08

To Do:

• Photocopy the info for the HmgR Probe and the GpxR probe that arrived on Friday.
• Add the information to their profiles on the wiki
• Finish aligning second round of sequencing.

8.7.08

To Do:

• Run FA on GpxR today
  • Check the concentration of probe used in FA protocol
  • Reconstitute probe primers to 100 μM
  • Anneal 10 μl of each primer (add 80 μl water) - 100 degrees C for 5 minutes, then cool.
  • Get more GpxR from p'So
  • Get reaction buffer or protocol to make buffer from p'So.
  • Recheck concentration of GpxR aliquots with Bradford.
• Photocopy the info for the HmgR Probe and the GpxR probe that arrived on Friday.
• Add the information to their profiles on the wiki
• Finish aligning second round of sequencing.

Summary:

I completed my first run of the binding assay using GpxR and both Gpx1 and HmgA promoters. Results were not too promising. Tomorrow I will try the assay with the HmgR that I have.

8.8.08

Summary:

I did a second run of the binding assay using the "special" HmgR that I purified. Encouraging results - will place on wiki in morning.