How to measure Cy5-primer concentration ??

Duncan Clark blackhole at
Fri Oct 6 03:43:46 EST 2006

Historians believe that in newspost <qbhVg.1176$iP5.1045 at newsfe07.lga> 
on Fri, 6 Oct 2006, DK <dk at> penned the 
following literary masterpiece:
>Sure it does. What is there in Cy5 structure that indoles suddenly would
>stop absorbing ultraviolet? Nothing. Sorry, I don't believe it. Sure, you can
>say that it absorbs at ~ 280 stronger than at ~ 260 and that single Cy5
>contribution to the UV absorbance of the whole oligo is small - and I
>would agree.  But to say that it does not absorb at all and that it can
>always be neglected is an overkill.
>WRT the original question, quantifying based on Cy5 absorption is
>definitely more precise approach.

If one goes to IDT's web site and uses their calculator program, then a 
random 24mer with Cy5 at the 5' end gives about a 5% change between 
OD260 compared to same sequence without Cy5.

So yes it does make a difference by simply measuring OD260, but not a 
huge one. Depending upon one's application and usage of the label, that 
difference may or may not be acceptable.

I love deadlines. I especially like the whooshing noise they make as
they go flying by.

Duncan Clark
GeneSys Ltd.

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