One can use FRET to follow the hybridization of two complimentary strands of DNA

Question

One can use FRET to follow the hybridization of two complimentary strands of DNA. When the two strands bind to form a double helix, FRET can occur from the donor to the acceptor allowing one to monitor the kinetics of helix formation . You are designing an experiment using a FRET pair with R_0 = 59.6 . For B-form DNA the length of the helix increases 3.46 per residue. If you can accurately measure FRET efficiency down to 0.10, how many residues is the longest piece of DNA that you can study using this FRET pair?

Explanation / Answer

R is the distance between the donor and acceptor, R0 is the distance where the energy transfer is half efficient. R0 is also called as Forster radius.

Efficiency of FRET, E = (R0/R) ^6 / 1+ (R0/R) ^6

= 59.6 ^ 6/ R ^6 / 1+ 59.6 ^ 6/ R ^6

0.1 = 44820588898.717696 / 44820588898.717696 + R^6

0.1 (44820588898.717696 + R^6) = 44820588898.717696

0.1 * R^6 = 44820588898.717696 - 4482058889.8717696

0.1 * R^6 = 44372383009.73051904

R^6 = 443723830097.3051904

R = 10205648092238 ^ (1/6) / 23 ^ (1/6)

= 147.2 / 1.685

R = 87.36 A0

Length of each residue is 3.46 A0.

Number of residues that can be studied using FRET in the problem are 87.36/3.46 = 25.25 residues.

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