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Primer stock confusion


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6 replies to this topic

#1 nbhu

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Posted 01 May 2009 - 08:34 AM

Hi guys,
I think i did something silly!
Basically i want to obtain a primer stock of 1ug/ul.
Instead of just adding the same volume as the ug amount, i blindly made up a 100pmol/ul stock by adding the volume the primer company recommended.
E.g.
Yield: (ug): 213
Vol for 100pmol/ul: 317ul
MW (g/mol): 6731

So i added the 317ul and have a 100pmol/ul .... how do i now go about diluting this to obtain a 1ug/ul stock?

Any help would be appreciated!!!

#2 tea-test

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Posted 01 May 2009 - 08:52 AM

without calculating it, but just from your description i would say it is not possible anymore.

you have 213g of primer. so, to get a 1g/l dilution you would have to add 213l, do you agree? but you have already added 317l....
tea-test: The artist formerly known as Ned Land

#3 Wolverena

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Posted 01 May 2009 - 09:15 AM

Hi guys,
I think i did something silly!
Basically i want to obtain a primer stock of 1ug/ul.
Instead of just adding the same volume as the ug amount, i blindly made up a 100pmol/ul stock by adding the volume the primer company recommended.
E.g.
Yield: (ug): 213
Vol for 100pmol/ul: 317ul
MW (g/mol): 6731

So i added the 317ul and have a 100pmol/ul .... how do i now go about diluting this to obtain a 1ug/ul stock?

Any help would be appreciated!!!


I think you have about 0.67ug/ul. Can you compensate by adding more ul for that primer when you do your PCR?
"You can give somebody a book on 'How to ride bike' and then test that person on that knowledge. Even if that person gets an "A", it doesn't mean that he or she can ride a bike."
---this is what I am telling myself when I get a bad grade....as long as you don't loose your passion, you'll be fine.....V

#4 wuxx0153

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Posted 01 May 2009 - 10:13 AM

without calculating it, but just from your description i would say it is not possible anymore.

you have 213g of primer. so, to get a 1g/l dilution you would have to add 213l, do you agree? but you have already added 317l....


As tea-test has said, no way you can back to 1 g/l.
However, your primer stock is now 100 M and as I understand, PCR primer final concentration (in most of my PCR reaction, 0.2 M) is the one important for the reaction.
You dilute your stock into working solution (in my case 5 M) and then add diluted primer to PCR master mix to reach final concentration.

Your primer concentration now is better than 1 g/l.
Why you have to get 1 g/l?

#5 nbhu

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Posted 01 May 2009 - 11:28 AM

without calculating it, but just from your description i would say it is not possible anymore.

you have 213g of primer. so, to get a 1g/l dilution you would have to add 213l, do you agree? but you have already added 317l....


As tea-test has said, no way you can back to 1 g/l.
However, your primer stock is now 100 M and as I understand, PCR primer final concentration (in most of my PCR reaction, 0.2 M) is the one important for the reaction.
You dilute your stock into working solution (in my case 5 M) and then add diluted primer to PCR master mix to reach final concentration.

Your primer concentration now is better than 1 g/l.
Why you have to get 1 g/l?


Well basically it is for a long range pcr, and it specifies 1ug/ul... i guess it will be easy enough compensating for it.
I would add 2ul to the reaction if it was a 1ug/ul stock, so how much do you think i should be adding now?

#6 nbhu

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Posted 01 May 2009 - 11:30 AM

without calculating it, but just from your description i would say it is not possible anymore.

you have 213g of primer. so, to get a 1g/l dilution you would have to add 213l, do you agree? but you have already added 317l....


As tea-test has said, no way you can back to 1 g/l.
However, your primer stock is now 100 M and as I understand, PCR primer final concentration (in most of my PCR reaction, 0.2 M) is the one important for the reaction.
You dilute your stock into working solution (in my case 5 M) and then add diluted primer to PCR master mix to reach final concentration.

Your primer concentration now is better than 1 g/l.
Why you have to get 1 g/l?


Well basically it is for a long range pcr, and it specifies 1ug/ul... i guess it will be easy enough compensating for it.
I would add 2ul to the reaction if it was a 1ug/ul stock, so how much do you think i should be adding now?


actually, sorry, i got that wrong... from the 1ug/ul, i dilute this to 60ng/ul and use 2ul....
its harder doing this when you are following someone elses protocols and the math just makes my head go all fuzzy :s

#7 almost a doctor

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Posted 04 May 2009 - 12:54 AM

without calculating it, but just from your description i would say it is not possible anymore.

you have 213g of primer. so, to get a 1g/l dilution you would have to add 213l, do you agree? but you have already added 317l....


As tea-test has said, no way you can back to 1 g/l.
However, your primer stock is now 100 M and as I understand, PCR primer final concentration (in most of my PCR reaction, 0.2 M) is the one important for the reaction.
You dilute your stock into working solution (in my case 5 M) and then add diluted primer to PCR master mix to reach final concentration.

Your primer concentration now is better than 1 g/l.
Why you have to get 1 g/l?


Well basically it is for a long range pcr, and it specifies 1ug/ul... i guess it will be easy enough compensating for it.
I would add 2ul to the reaction if it was a 1ug/ul stock, so how much do you think i should be adding now?


actually, sorry, i got that wrong... from the 1ug/ul, i dilute this to 60ng/ul and use 2ul....
its harder doing this when you are following someone elses protocols and the math just makes my head go all fuzzy :s


Hi, by adding 317l to your primer this is now at 0.672g/l, so is 10x more concentrated than you need it (60ng/l). You need to make a ~1:10 dilution of your stock to have the primer at 60ng/l (actually 1:10.3). This is, 8.9l of you stock into a final 100l volume. Then you can use 2l for your PCR reaction.




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