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RNA quantification for Real Time RT-PCR - (Feb/21/2007 )

HI everyone:
I'm performing Real Time RT-PCR with SYBR GREEN and it's going really well but my problem is that, to do the standard curve to quantify, I'm using a field sample because my virus doesn't grow in any cell line. I don't want to clone the DNA in a TOPO vector so what I did was:

I measured in a spectophotometer my initial quantity of RNA in this field sample, I diluted it in serial ten fold dilutions and did with that the standard curve.
Now, my question is:
How could I know how many amplicons copies or virus copies did I have? I read in an article that they mesaured the PCR amplified DNA and deduced from its molarity and sequence the number of amplicons they had but they don't say the formula.
Someone can help me?
Thanks!!

-debokuki-

Thats very simple, actually. Since you know the sequence of your virus, you can calculate the molecular weight (MW) of the virus genome
(please be aware of online calculations - they often use the MWs of the bases and not of the nucleotides - here are the MWs of the DNA nucleotides:AMP = 347.2 TMP = 322,2 CMP = 323,2 GMP = 363.22 - calculate both strands separately - not just doubling of the first strand)
The MW is given in g/mol. Than, the MW is divided by the Avogadro's number, which is approximately 6.02214199 × 10^23 and given in mol^-1. Now you have the weight in g for one virus genome - you may convert it in µg or ng. Now you can recalculate your amount of DNA used in your standard curve in virus copy numbers!

QUOTE (debokuki @ Feb 21 2007, 11:13 AM)
HI everyone:
I'm performing Real Time RT-PCR with SYBR GREEN and it's going really well but my problem is that, to do the standard curve to quantify, I'm using a field sample because my virus doesn't grow in any cell line. I don't want to clone the DNA in a TOPO vector so what I did was:

I measured in a spectophotometer my initial quantity of RNA in this field sample, I diluted it in serial ten fold dilutions and did with that the standard curve.
Now, my question is:
How could I know how many amplicons copies or virus copies did I have? I read in an article that they mesaured the PCR amplified DNA and deduced from its molarity and sequence the number of amplicons they had but they don't say the formula.
Someone can help me?
Thanks!!

-humpback-whale-

HI:
Thanks for your reply! It's really easy and clear.
rolleyes.gif

-debokuki-