IFN far red tandem conjugates & a question for Mario

Mario Roederer roederer at drmr.com
Thu Apr 29 14:16:07 EST 2004


What, and beg my 6th posting in 2 weeks?  I'm sure a collective groan 
will be heard around the world.

I guess the main reason for using the terminology Cy5PE as opposed to 
PECy5 is simply one of habit--we started with this terminology early. 
I can't honestly say if I picked it up from another source or not.  I 
looked up the original paper (Lansdorp et al), and found that they 
use PE/Cy5, so that would seem to settle any originality arguments.

The main reason that I prefer Cy5PE is that it puts the most 
important aspect of the fluorochrome out there first.  Thus, when you 
refer to TRPE, Cy5PE, Cy5.5PE, and Cy7PE, all of which we use 
simultaneously in our system, the first thing you see and hear is the 
molecule that is emitting, which, after all, is the important part of 
the system (and the part that distinguishes these four fluorochromes).

A very minor aspect is that I feel it is more readable, in that the 
digit naturally acts as a separator between the two moieties when 
written as Cy5PE... and anyone will automatically know how to say 
this abbreviation.  Someone not in the know, however, when confronted 
with PECy5, would never know to pronounce this as "P-E-Cy-5", rather 
than "P-E-C-y-5" (which some people use anyway), or "PEC-y-5", or the 
potentially interesting "pecky-five".

OK, that's a stupid reason, but I'm really grasping here.  Maybe I 
just like being different.  (Please, no need to confirm that, my 
email box will break).

mr

(PS, remember that PharMingen for a while tried their own names for 
these--PharRed (Cy7PE) and TruRed (Cy7APC), but it probably became 
difficult to keep coming up with new names for Cy5.5PE 
("virtuallyRed"), Cy5.5APC ("somewhatRedButNotAsRedAsTrueRed"), not 
to mention Cy5PE 
("NotVeryRedButADamnSightMoreRedThanTRPEWhichCoulterAlwaysConfusedUsByCallingItSomethingW
ierd"). 
Hey, we could have quite a bit of fun helping Quantum Dot, Inc., name 
all of their dots:  QD585 could be QuantumOrange, QD605 = QuantumRed, 
QD655 = QuantumRedder, QD705 = QuantumReddest.	QD745 would have to 
QuantumMFRed.

>Mario: A question I have always wanted to ask you. My instinct is to refer
>to a tandem with the excited dye noted first and the emitting dye noted
>second (e.g. PE/Cy5). I use this order because it is in the order in which
>the light energy interacts with the tandem (first excited, then emitted).
>Mario, you always use the opposite convention (e.g. Cy5/PE) and must have a
>good reason for doing so, what it it?




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