FRET spectral overlap integral

[Zdenek Svindrych-2]

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Dear microscopists,

I'm looking for a reliable source of the FRET spectral overlap integral
formula. I was unable to decipher it form the original Forster's paper
(http://onlinelibrary.wiley.com/doi/10.1002/andp.19484370105/epdf). Most
often I've encountered it in the form as on Wikipedia (https://en.wikipedia.
org/wiki/F%C3%B6rster_resonance_energy_transfer), that is in wavelength
units and lambda^4 factor. But in some papers (http://pubs.rsc.org/en/
content/articlepdf/2013/cp/c3cp50173f), formula (4), it's in the wavenumber
units and a nu^(-4) factor.

The problem is the two formulas are mathematically incompatible (I believe).
Given nu=1/lambda and the integral substitution rule (http://tutorial.math.
lamar.edu/Classes/CalcI/SubstitutionRuleIndefinite.aspx) there should be
another nu^(-2) "Jacobian", yielding nu^(-6). Or alternatively, if the "nu"-
formula is correct, then a lambda^(-2) factor would lead to lambda^2 in the
well know formula...

To sum up, I believe either one or the other part of the formula (5.5) here
(https://books.google.com/books?id=GXWAAQAAQBAJ&pg=PT117) is wrong. Btw, the
same should apply to formula (5.6) in the same book (if the link does not
work, it's "FRET - Förster Resonance Energy Transfer: From Theory to
Applications"), as the two ways to normalize the spectrum are very
different...

I found one experimental paper in favor of the "lambda"-version (http://www.
pnas.org/content/63/1/23.full.pdf), see fig 6. But can anyone point me
towards the origin of the formula?

Thanks, zdenek




-- 

Zdenek Svindrych, Ph.D.

W.M. Keck Center for Cellular Imaging (PLSB 003)

University of Virginia, Charlottesville, VA 

http://www.kcci.virginia.edu/

tel: [phone]

[George McNamara]

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Hi Zdenek,

http://works.bepress.com/gmcnamara/9/

McNamara 20071011 FRET Janos Szollosi Horvath Gabor FRET calculator -
added Cy3B-Cy5  Cy3-Cy5 and Cy2-Cy5.xls
be sure to extract the file before trying to open.

inside "more stuff' folder is a RET data

McNamara 2006 van der Meer 1994 RET book data tables.xls

from

B. Wieb Van Der Meer, George Coker, III, S.-Y. Simon Chen (1994)
Resonance Energy Transfer: Theory and Data, VCH Publishers, Inc., New
York, NY. ISBN 1-56081-643-0. 177 pages.

You can find several more spectra in the file

McNamara Boswell PubSpectra 20090427M (Excel 2007).xlsx

//
for any listservites who like any of: looking at spots, multiplexing
biosensors and/or rainbow of transcriptional (or translational)
reporters, I encourage skimming the tables and figures in the download at
http://works.bepress.com/gmcnamara/75

enjoy,

George



On 11/3/2015 3:07 PM, Zdenek Svindrych wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
>
> Dear microscopists,
>
> I'm looking for a reliable source of the FRET spectral overlap integral
> formula. I was unable to decipher it form the original Forster's paper
> (http://onlinelibrary.wiley.com/doi/10.1002/andp.19484370105/epdf). Most
> often I've encountered it in the form as on Wikipedia (https://en.wikipedia.
> org/wiki/F%C3%B6rster_resonance_energy_transfer), that is in wavelength
> units and lambda^4 factor. But in some papers (http://pubs.rsc.org/en/
> content/articlepdf/2013/cp/c3cp50173f), formula (4), it's in the wavenumber
> units and a nu^(-4) factor.
>
> The problem is the two formulas are mathematically incompatible (I believe).
> Given nu=1/lambda and the integral substitution rule (http://tutorial.math.
> lamar.edu/Classes/CalcI/SubstitutionRuleIndefinite.aspx) there should be
> another nu^(-2) "Jacobian", yielding nu^(-6). Or alternatively, if the "nu"-
> formula is correct, then a lambda^(-2) factor would lead to lambda^2 in the
> well know formula...
>
> To sum up, I believe either one or the other part of the formula (5.5) here
> (https://books.google.com/books?id=GXWAAQAAQBAJ&pg=PT117) is wrong. Btw, the
> same should apply to formula (5.6) in the same book (if the link does not
> work, it's "FRET - Förster Resonance Energy Transfer: From Theory to
> Applications"), as the two ways to normalize the spectrum are very
> different...
>
> I found one experimental paper in favor of the "lambda"-version (http://www.
> pnas.org/content/63/1/23.full.pdf), see fig 6. But can anyone point me
> towards the origin of the formula?
>
> Thanks, zdenek
>
>
>
>
> --
>
> Zdenek Svindrych, Ph.D.
>
> W.M. Keck Center for Cellular Imaging (PLSB 003)
>
> University of Virginia, Charlottesville, VA
>
> http://www.kcci.virginia.edu/
>
> tel: [phone]
>
>    

--



George McNamara, Ph.D.
Single Cells Analyst
L.J.N. Cooper Lab
University of Texas M.D. Anderson Cancer Center
Houston, TX 77054
Tattletales http://works.bepress.com/gmcnamara/42
http://works.bepress.com/gmcnamara/75
https://www.linkedin.com/in/georgemcnamara