Matt Gethers/CRI, Thailand/Labwork/HmgR Binding Assay/Week of 7.13.08

7.15.08

To Do:

• Come up with shortlist of DNA fragments to use in gel shift assay.
  • Look for HmgR and GpxR boxes (putative boxes from Mayuree) at the HmgA/HmgR promoter (they're divergently transcribed, remember).
  • Maybe write a script to help me find the boxes.

Mayuree suggested a probe, but wants to look into using two different dyes. Want to avoid quenching or FRET - look at excitation and emission spectra.

Dye	Excitation	Emission	6-Fam Acceptor	6-Fam Donor
6-Fam	494	518	n/a	n/a
CY3	548	562	no	no
CY5	650	670-700	no	no
HEX	535	556	no	no
Iowa Black	/	/	Definitely a quencher of 6-fam
Joe	520	548	close, likely	no
ROX	585	605	no	no
TAMRA	565	580	no	no
TET	521	536	close, likely	no
Texas Red	589	615	no	no

sources: http://www.iss.com/resources/spectra.html

http://www.bdbiosciences.com/spectra/

https://www.omegafilters.com/curvo2/index.php?dyes=269