Nonpolar Fluorophore

[Beam, Brooke M - (bbeam)]

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I know this is not a specific confocal question, but I have a student in my facility working on a nonpolar system.  She is looking for a fluorophore that is readily soluble in very nonpolar solvents such as chloroform or THF, with a high molar extinction coefficient (>40,000 1/Mcm).  The laser lines that she has available for use are 405, 488, 514, and 561.

She tried calling the Life Technologies technical assistance line, but didn't receive much help because they couldn't tell her the solubility/extinction coefficients of any of the dyes in nonpolar solvents.

I am looking for any suggestions/references that you may have!
Thanks,
Brooke


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Brooke Beam, Ph.D.
W.M. Keck Center for Surface and Interface Imaging
University of Arizona Chemistry & Biochemistry
1306 E. University Blvd.
Tucson, AZ 85721
website: www.chem.arizona.edu/rss/keck/keck.html<http://www.chem.arizona.edu/rss/keck/keck.html>
email: [hidden email]<mailto:[hidden email]>
Ph: [phone]
Fax: [phone]

[Mark Cannell-2]

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Tell them they have an idiot working for them. The data you need is here:

http://www.invitrogen.com/site/us/en/home/References/Molecular-Probes-The-Handbook/Probes-for-Lipids-and-Membranes/Other-Nonpolar-and-Amphiphilic-Probes.html#datatable

HTH

On 11/06/2013, at 10:24 PM, "Beam, Brooke M - (bbeam)" <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I know this is not a specific confocal question, but I have a student in my facility working on a nonpolar system.  She is looking for a fluorophore that is readily soluble in very nonpolar solvents such as chloroform or THF, with a high molar extinction coefficient (>40,000 1/Mcm).  The laser lines that she has available for use are 405, 488, 514, and 561.
>
> She tried calling the Life Technologies technical assistance line, but didn't receive much help because they couldn't tell her the solubility/extinction coefficients of any of the dyes in nonpolar solvents.
>
> I am looking for any suggestions/references that you may have!
> Thanks,
> Brooke
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Brooke Beam, Ph.D.
> W.M. Keck Center for Surface and Interface Imaging
> University of Arizona Chemistry & Biochemistry
> 1306 E. University Blvd.
> Tucson, AZ 85721
> website: www.chem.arizona.edu/rss/keck/keck.html<http://www.chem.arizona.edu/rss/keck/keck.html>
> email: [hidden email]<mailto:[hidden email]>
> Ph: [phone]
> Fax: [phone]

Mark  B. Cannell Ph.D. FRSNZ
Professor of Cardiac Cell Biology
School of Physiology &  Pharmacology
Medical Sciences Building
University of Bristol
Bristol
BS8 1TD UK

[hidden email]

[Unruh, Jay]

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I've  never tried chloroform, but the cyanine dyes are quite nonpolar, especially the long chain ones (DiI-C18 and DiO-C18).  Given their similarity to non-polar lipids, I would be shocked if they are not soluble in chloroform.  They all have extinction coefficients above 100,000.

Jay

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Beam, Brooke M - (bbeam)
Sent: Tuesday, June 11, 2013 4:24 PM
To: [hidden email]
Subject: Nonpolar Fluorophore

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I know this is not a specific confocal question, but I have a student in my facility working on a nonpolar system.  She is looking for a fluorophore that is readily soluble in very nonpolar solvents such as chloroform or THF, with a high molar extinction coefficient (>40,000 1/Mcm).  The laser lines that she has available for use are 405, 488, 514, and 561.

She tried calling the Life Technologies technical assistance line, but didn't receive much help because they couldn't tell her the solubility/extinction coefficients of any of the dyes in nonpolar solvents.

I am looking for any suggestions/references that you may have!
Thanks,
Brooke


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Brooke Beam, Ph.D.
W.M. Keck Center for Surface and Interface Imaging University of Arizona Chemistry & Biochemistry
1306 E. University Blvd.
Tucson, AZ 85721
website: www.chem.arizona.edu/rss/keck/keck.html<http://www.chem.arizona.edu/rss/keck/keck.html>
email: [hidden email]<mailto:[hidden email]>
Ph: [phone]
Fax: [phone]

[John Oreopoulos]

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I can confirm that the dyes Jay mentions will dissolve in chloroform. I used to prepare fluorescent liposomes all the time from stock solutions of lipid and dye in this solvent.

John Oreopoulos

On 2013-06-11, at 5:57 PM, "Unruh, Jay" <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I've  never tried chloroform, but the cyanine dyes are quite nonpolar, especially the long chain ones (DiI-C18 and DiO-C18).  Given their similarity to non-polar lipids, I would be shocked if they are not soluble in chloroform.  They all have extinction coefficients above 100,000.
>
> Jay
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Beam, Brooke M - (bbeam)
> Sent: Tuesday, June 11, 2013 4:24 PM
> To: [hidden email]
> Subject: Nonpolar Fluorophore
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I know this is not a specific confocal question, but I have a student in my facility working on a nonpolar system.  She is looking for a fluorophore that is readily soluble in very nonpolar solvents such as chloroform or THF, with a high molar extinction coefficient (>40,000 1/Mcm).  The laser lines that she has available for use are 405, 488, 514, and 561.
>
> She tried calling the Life Technologies technical assistance line, but didn't receive much help because they couldn't tell her the solubility/extinction coefficients of any of the dyes in nonpolar solvents.
>
> I am looking for any suggestions/references that you may have!
> Thanks,
> Brooke
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Brooke Beam, Ph.D.
> W.M. Keck Center for Surface and Interface Imaging University of Arizona Chemistry & Biochemistry
> 1306 E. University Blvd.
> Tucson, AZ 85721
> website: www.chem.arizona.edu/rss/keck/keck.html<http://www.chem.arizona.edu/rss/keck/keck.html>
> email: [hidden email]<mailto:[hidden email]>
> Ph: [phone]
> Fax: [phone]

[Iain Johnson]

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If you are just looking for something that is fluorescent and nonpolar and
nothing else (i.e. no reactive groups for functionalization) then the best
dyes are the ones called BODIPY (by Life Technologies).  The dye
pentamethyl BODIPY (aka BODIPY 493/503) is the most nonpolar of all the
ones sold by Life Technologies.  It has an extinction coefficient of 80,000
M-1 cm-1 at 493 nm.  As with most dyes, the extinction coefficient does not
vary by more than 10% in any solvent you choose (as long as full solubility
is attained).

You can buy exactly the same dye under the name pyrromethene 546 from
Exciton Chemical Co (Dayton, OH; www.exciton.com).  This has two
advantages. (1) It is much cheaper.  Because Exciton sells it as a laser
dye, a gram from them is probably about the same price as 10 mg from Life
Technologies.  (2) Because for dye laser applications one has to routinely
make very concentrated stock solutions, Exciton provides quantitative
solubility data in a bunch of solvents on their spec sheet (which you can
download from their website).  Both the Life Technologies BODIPY family and
the Exciton pyrromethene family have longer-wavelength analogs if want to
use another laser line (though neither pyrromethene or BODIPY goes down to
405 nm; you would need to use one of the Exciton Coumarin laser dyes for
that).

If you have to use chloroform, be careful to not expose the stock solution
to light (will result in photosensitized generation of chlorine radicals,
which will react with dye).  I prefer things like toluene for dissolving
aromatics.  You will easily get a 10 mM solution of BODIPY 493/503 in
toluene.  Also, don't use DMF or any other solvent that may contain trace
contamination of free amines for making stock solutions of
BODIPY/pyrromethene dyes.

Iain

Iain Johnson Consulting
Eugene, OR




On Tue, Jun 11, 2013 at 2:24 PM, Beam, Brooke M - (bbeam) <
[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I know this is not a specific confocal question, but I have a student in
> my facility working on a nonpolar system.  She is looking for a fluorophore
> that is readily soluble in very nonpolar solvents such as chloroform or
> THF, with a high molar extinction coefficient (>40,000 1/Mcm).  The laser
> lines that she has available for use are 405, 488, 514, and 561.
>
> She tried calling the Life Technologies technical assistance line, but
> didn't receive much help because they couldn't tell her the
> solubility/extinction coefficients of any of the dyes in nonpolar solvents.
>
> I am looking for any suggestions/references that you may have!
> Thanks,
> Brooke
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Brooke Beam, Ph.D.
> W.M. Keck Center for Surface and Interface Imaging
> University of Arizona Chemistry & Biochemistry
> 1306 E. University Blvd.
> Tucson, AZ 85721
> website: www.chem.arizona.edu/rss/keck/keck.html<
> http://www.chem.arizona.edu/rss/keck/keck.html>
> email: [hidden email]<mailto:[hidden email]>
> Ph: [phone]
> Fax: [phone]
>

[pdetombe]

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On the same same topic, but slightly different …

We have been doing experiments with Bodipy-FL-ATP to follow ATP turnover in a muscle cell .. the idea is to chase Bodipy-FL-ATP with "cold" ATP and measure the decay of fluorescence .. now, a critical parameter in this experiment is the passive diffusion of unbound bodily-FL-ATP from the tissue -- to measure this, we are searching for a water soluble bodily (or equivalent) dye that will not react with anything in the permeabilized muscle (i.e. only a collection of cytoskeletal proteins) so we can measure the rate of washout in the absence of binding of the probe (pure diffusion) … any recommendation for fluorescent dye to pick for this, preferably with the 488 excitation line, but not an absolute requirement (we could switch to other excitation wavelengths) .. help much appreciated …

Pieter de Tombe
Loyola University Chicago; Physiology Dept.

On Jun 12, 2013, at 1:28 AM, Iain Johnson <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> If you are just looking for something that is fluorescent and nonpolar and
> nothing else (i.e. no reactive groups for functionalization) then the best
> dyes are the ones called BODIPY (by Life Technologies).  The dye
> pentamethyl BODIPY (aka BODIPY 493/503) is the most nonpolar of all the
> ones sold by Life Technologies.  It has an extinction coefficient of 80,000
> M-1 cm-1 at 493 nm.  As with most dyes, the extinction coefficient does not
> vary by more than 10% in any solvent you choose (as long as full solubility
> is attained).
>
> You can buy exactly the same dye under the name pyrromethene 546 from
> Exciton Chemical Co (Dayton, OH; www.exciton.com).  This has two
> advantages. (1) It is much cheaper.  Because Exciton sells it as a laser
> dye, a gram from them is probably about the same price as 10 mg from Life
> Technologies.  (2) Because for dye laser applications one has to routinely
> make very concentrated stock solutions, Exciton provides quantitative
> solubility data in a bunch of solvents on their spec sheet (which you can
> download from their website).  Both the Life Technologies BODIPY family and
> the Exciton pyrromethene family have longer-wavelength analogs if want to
> use another laser line (though neither pyrromethene or BODIPY goes down to
> 405 nm; you would need to use one of the Exciton Coumarin laser dyes for
> that).
>
> If you have to use chloroform, be careful to not expose the stock solution
> to light (will result in photosensitized generation of chlorine radicals,
> which will react with dye).  I prefer things like toluene for dissolving
> aromatics.  You will easily get a 10 mM solution of BODIPY 493/503 in
> toluene.  Also, don't use DMF or any other solvent that may contain trace
> contamination of free amines for making stock solutions of
> BODIPY/pyrromethene dyes.
>
> Iain
>
> Iain Johnson Consulting
> Eugene, OR
>
>
>
>
> On Tue, Jun 11, 2013 at 2:24 PM, Beam, Brooke M - (bbeam) <
> [hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> I know this is not a specific confocal question, but I have a student in
>> my facility working on a nonpolar system.  She is looking for a fluorophore
>> that is readily soluble in very nonpolar solvents such as chloroform or
>> THF, with a high molar extinction coefficient (>40,000 1/Mcm).  The laser
>> lines that she has available for use are 405, 488, 514, and 561.
>>
>> She tried calling the Life Technologies technical assistance line, but
>> didn't receive much help because they couldn't tell her the
>> solubility/extinction coefficients of any of the dyes in nonpolar solvents.
>>
>> I am looking for any suggestions/references that you may have!
>> Thanks,
>> Brooke
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Brooke Beam, Ph.D.
>> W.M. Keck Center for Surface and Interface Imaging
>> University of Arizona Chemistry & Biochemistry
>> 1306 E. University Blvd.
>> Tucson, AZ 85721
>> website: www.chem.arizona.edu/rss/keck/keck.html<
>> http://www.chem.arizona.edu/rss/keck/keck.html>
>> email: [hidden email]<mailto:[hidden email]>
>> Ph: [phone]
>> Fax: [phone]
>>