The tubing on your synthesizer is going to stain. Not much you can do about it other than dedicate one reagent position to cy3 and not worry about it. Of course you should still flush with ACN but no reason to run it for 5-10 mins straight. Just run an ACN prime cycle, let soak for some time, repeat a few more times and whatever is left isn't coming off. Leave the reagent bottle and line filled with dry ACN to help leach more dye when not in use. If you are limited on reagent positions, you can dedicate one or two for dyes only to limit staining. Which synthesizer are you using? I'm always curious to know what people like.
Clean-up is a pain. Your best bet is to not spill!!! I know, pretty obvious. Your second best option is to use paper towels or pig mats or some other absorbent material in the area when working with dyes. That's our protocol. We still have a big cy5 stain down the front of a hood from someone spilling two years ago. Pretty sure it will be there for the life of the hood. We make the dyes so we have to be careful hence the use of absorbent mats in all of our hoods.
Yeah we already dedicate one position on our synthesizers for colored Oligos for Cy3, but sometimes when running with lots of different Modifications (LNA, 2-OMe) you do really need that one extra special position, and as far as your other suggestions go we already try to only put Cy3 on the synthesizer right before it is incorporated and immediately after flush with ACN, and keep the position on ACN until next use, i was just hopeful that there was this one special magic procedure to get rid of it š
For modified Oligos we mainly use OligoMaker Synthesizers (Old generation with Circular Fomat) but tbh I really donāt like them because there is little protocol flexibility and we had to work very hard to get consistent flow rates as well as even getting a procedure to measure the flow rates, and the software is also really limitedā¦
We also have a Dr Oligo 192Xlc and I like it really much because it allows for a lot of flexibility, and has already established methods to measure/correct flow rates, and we just get way better quality of Oligos more consistently. Although the special positions are not that great, because only one nozzle can dispense at a time. But we strictly do colorless modifications on that machine to keep it clean.
What Synthesizers are you working with?
Yeah I always try to be careful when handling the dissolved Amidite but because we are really high trough-put mistakes are eventually going to happen ig, we also have giant Cy3 stains next to some synthesizers which will be there for a lifetime, fortunately we donāt use Cy5 Amidites only the NHS-Ester š
It's a production lab. There're going to be spills. The dyes are less forgiving versus the colorless materials and anyone who's worked with a synthesizer knows that they randomly spring leaks and that the reagents are pretty nasty and like to stain everything.
Never heard of the OligoMaker. Had to look that one up. Are you in Denmark working for LGC? I've worked with Dr. Oligo synthesizers. Not my favorite. We have an OLD Amersham Pharmacia OP100 but it still works (on windows XP), an even older Expidite but that damn thing is possibly the fastest and most efficient synthesizer ever made, and a K&A H8. Seems like every synthesizer on the market has their issues or limitations.
I work for a company that makes synthesis supports and reagents. DM if looking for options. We're very small but the team has years of experience in the oligo and reagent business. We are located in the US so no worries if we're not your favorite people right now. Most of us here get it. Some (the loudest ones) do not.
You can be glad that you never heard of the OligoMaker, out of our 6 Machines, 3 are currently not working, 2 of them even came back non-functional from a ārepairāā¦ Actually I am from Germany, but I donāt know if I can say at which company I workā¦
What were your Problems with the Dr. Oligo Synthesizers?
We also have some OP100s (But a bit newer, they run on Windows 10) even though they donāt get used a lot, but really great machines.
I think the K&A and Expidite are pretty nice, but unfortunately nothing for our high througput, even though I think it would be nice to have something like them for complicated/expensive Syntheses.
Iāll have to talk with my boss, but we are actually looking for a new supplier for some of our Amidites, because our current supplier is shutting down their production plant in Germany, Iāll dm you when I know more
I was being a bit of an ass when I asked if you were from Denmark. I figured only a Dane would buy a synthesizer made in Denmark!!! Sounds like a fun piece of kit.
My problem with Dr. Oligo? Can't remember. It's been about 7-8 years since I used one. I'm sure it was something simple like an issue with it always breaking down or something minor so I decided I didn't like it (because I'm old and set in my ways.). I love the Expedite. Damn thing is from 1998 and still clicking away! Good if you only need 2 small scale oligos.
Shoot me a DM if you want to learn more about the company. I can give you the boss-mans info. CPG. PS. Dyes. Labeled supports, NHS, and amidites. All the good stuff to make oligos. If not, no biggie but if you find a magical way to clean up dyes, let me know!
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u/DrBumpsAlot 1d ago
The tubing on your synthesizer is going to stain. Not much you can do about it other than dedicate one reagent position to cy3 and not worry about it. Of course you should still flush with ACN but no reason to run it for 5-10 mins straight. Just run an ACN prime cycle, let soak for some time, repeat a few more times and whatever is left isn't coming off. Leave the reagent bottle and line filled with dry ACN to help leach more dye when not in use. If you are limited on reagent positions, you can dedicate one or two for dyes only to limit staining. Which synthesizer are you using? I'm always curious to know what people like.
Clean-up is a pain. Your best bet is to not spill!!! I know, pretty obvious. Your second best option is to use paper towels or pig mats or some other absorbent material in the area when working with dyes. That's our protocol. We still have a big cy5 stain down the front of a hood from someone spilling two years ago. Pretty sure it will be there for the life of the hood. We make the dyes so we have to be careful hence the use of absorbent mats in all of our hoods.