[DeanEdwards]

Question:
Molecular beacons have been used extensively for the detection of nucleic acids and are suitable for analyses in vivo. Recently, hospitalization of hundreds of people in the developing world has resulted from a waterborne viral infection known as the Coxsackievirus B6 (CVB6). A new molecular beacon has been proposed by Yeh et al. and uses a quantum dot - gold nanoparticle based FRET system to signal hybridisation of the molecular beacon to a CVB6 specific nucleic acid sequence. Yeh, H-S.; Yates, M.V.; Mulchandani, A.; Chen, W. Chem. Comm. 2010, 46, 3914-3916.

(a) In less than 250 of YOUR OWN words, explain how the designed sensing strategy functions. Point form answers are acceptable, feel free to use a diagram in your explanation.

(b) Using the reported FRET efficiency and a Förster distance of 4 nm, determine the
average separation distance between the quantum dot and an adjacent gold nanoparticle for the molecular beacon (in the absence of the target sequence).

(c) Given that the quantum dot PL increased by 20% after incubation with a pre-processed, 50 µL water sample from a local lake, determine the amount of CVB6 present in the sample if the concentration of quantum dots in the assay is 50 nM.

Once again, if someone can point me in the right direction, that would be much appreciated!

[Polytriazole]

For starters, explain to yourself what FRET (Forster or fluorescence resonance energy transfer) is and how it works.  Reading a little about photoluminescence and fluorescence may also help.  Then think about why you would want to use a gold nanoparticle in this process, especially in conjunction with a molecular beacon.  What does the beacon do?  How does FRET determine the behavior of the beacon when in the presence of the nanoparticles? 

The other questions can be answered by looking up more information on the FRET phenomenon and what equations are used to model its behavior.

I think it would also be helpful to look up and obtain a copy of the article in question.  You should be able to do so through your school's library website.  The article should have an explanation of how the technique is applied and their exact experimental process.

[DeanEdwards]

For starters, explain to yourself what FRET (Forster or fluorescence resonance energy transfer) is and how it works.  Reading a little about photoluminescence and fluorescence may also help.  Then think about why you would want to use a gold nanoparticle in this process, especially in conjunction with a molecular beacon.  What does the beacon do?  How does FRET determine the behavior of the beacon when in the presence of the nanoparticles? 

The other questions can be answered by looking up more information on the FRET phenomenon and what equations are used to model its behavior.

I think it would also be helpful to look up and obtain a copy of the article in question.  You should be able to do so through your school's library website.  The article should have an explanation of how the technique is applied and their exact experimental process.

My professor explained how it works in his lecture slides and we do have a recommended textbook, so I will probably have to read through it. I will update this thread with my answers... and you guys can feel free to rip me to shreds over them.