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

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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