[Nescafe]

So in the CYQUANT technique I read that they use a dye by the name of Cyquant GR Dye to stain the nucleic acids. I could not find the exact structure of this dye but I know it is a green fluorescent dye so I will assume it has a structure similar to 5-FAM. Under physiological conditions nucleic acids bare a negative charge, I am having a hard time visioning how exactly a dye binds to the rather negatively charged nucleic acids.

Anyone familiar with this technique and what PH do they usually do such an experiment under?

Nescafe.

[Arkcon]

The similar colors doesn't mean that they have similar structures.  Many of the DNA binding dyes work by intercalating with the purine bases.  Basically that is pi-bond stacking, but the secret is for the dye molecule to be just the right size to fit inside the DNA double helix without disrupting it too much.

[Nescafe]

The similar colors doesn't mean that they have similar structures.  Many of the DNA binding dyes work by intercalating with the purine bases.  Basically that is pi-bond stacking, but the secret is for the dye molecule to be just the right size to fit inside the DNA double helix without disrupting it too much.

Hi I get that it does not mean they have similar structures, it is just that I could not find one for the Cyquant GR dye they keep mentioning so I used FAM as an example. So pi-bond stacking, well that makes sense, what about the PH? if it is protonated or deprotonated how does that effect absorption/emission?

[fledarmus]

From reading the sales brochures, it appears that the CyQuant stains are unsymmetrical cyanine dyes. Since they are patented compounds that went to InVitrogen through Molecular Probes, it is possible that they are related to this family of compounds - http://www.freepatentsonline.com/6664047.pdf. The references in the text should get you reasonably close to finding out how they work.

If there is any patent number included in your packaging, it might help you zero in on a possible structure and mechanism.

[DrCMS]

I could not find the exact structure of this dye but I know it is a green fluorescent dye so I will assume it has a structure similar to 5-FAM.

Do you use red paint if you can't find any tomato ketchup?

[fledarmus]

I could not find the exact structure of this dye but I know it is a green fluorescent dye so I will assume it has a structure similar to 5-FAM.

Do you use red paint if you can't find any tomato ketchup?

Sorry, I had to laugh out loud at this one - my wife likes milk in her coffee, but refers to the powdered non-dairy creamers as "white paint". And no, white paint is not an adequate substitution for milk in her coffee, no matter what color it makes the coffee look!

[Nescafe]

I could not find the exact structure of this dye but I know it is a green fluorescent dye so I will assume it has a structure similar to 5-FAM.

Do you use red paint if you can't find any tomato ketchup?

Bit of a douche comment if you ask me