TaqMan probes vs Molecular Beacon probes - (May/12/2006 )

I teach molecular biology techniques. I have a question about the lengths of TaqMan probes vs Molecular Beacon probes. I found these recommendations for the size of these different probes:

TaqMan probes: 15-30 nt long
Molecar Beacon probes: 10-40 nt + 5-7 nt on each end for stem-formation

Now, what I don't get is the following: in TaqMan probes the quencher quenches the reporter signal; thios means that in probes of 30 nt (= the maximum TaqMan probe length) the reporter and quencher are still close enough for quencing to occur. But now the Molecular Beacon probes: the mininum length of a Molecular Beacon probe is 10 + 5 + 5 (10 for the target-specific part and 2 times 5 nt for the stem) = 20 nt. So, in a Molecular Beacon probe of 20 nt ling that is attached to its target, the reporter and the quencher apparently are far enough apart to result in a signal!

In short: how is it possible that in a TaqMan probe of 30 nt quenching can still occur, while in a Molecar Beacon probe of 20 nt that is annealing to its target there is no quenching???

Or even shorter: shouldn't molecular beacon probes always be longer than TaqMan probes??

I hope someone can help me, so I can clarify this to my students!

Help in this will be highly appreciated!

I teach molecular biology techniques. I have a question about the lengths of TaqMan probes vs Molecular Beacon probes. I found these recommendations for the size of these different probes:

TaqMan probes: 15-30 nt long
Molecar Beacon probes: 10-40 nt + 5-7 nt on each end for stem-formation

Now, what I don't get is the following: in TaqMan probes the quencher quenches the reporter signal; thios means that in probes of 30 nt (= the maximum TaqMan probe length) the reporter and quencher are still close enough for quencing to occur. But now the Molecular Beacon probes: the mininum length of a Molecular Beacon probe is 10 + 5 + 5 (10 for the target-specific part and 2 times 5 nt for the stem) = 20 nt. So, in a Molecular Beacon probe of 20 nt ling that is attached to its target, the reporter and the quencher apparently are far enough apart to result in a signal!

In short: how is it possible that in a TaqMan probe of 30 nt quenching can still occur, while in a Molecar Beacon probe of 20 nt that is annealing to its target there is no quenching???

You are looking just to the delta of fluorecence. The quenching effect is bigger when the quencher is closer to the florescence dye. If beacon aligns you have an increasement of florescence but you have still a quenching effect which is as high as in an TagMan Probe of the same length. The absolut florescence in the first cycle could be higher if you use TagMan Probes compared to Beacons or FRED. This dosn't automatically means beacons are better. Hope this answer your question a bit.
By the way were are you teaching qPCR?

Or even shorter: shouldn't molecular beacon probes always be longer than TaqMan probes??

I hope someone can help me, so I can clarify this to my students!

Help in this will be highly appreciated!