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Help. Real- time against nested - I need to run a real time experiment (Mar/09/2006 )

Hello everybody!
Here the problem. I'm inserting a mutation (4 different nucleotides) in a cell line. The mutant cells are expected at a frequency 2 to 4 every 10 to the fifth cells. Actually the protocol says that I should diluite the cells in 96 wells plates at 5000 cells per well and check every well with a nested PCR (external one and one PCR allele specific). I'm trying to optimize everything in one Real time PCR step with molecular beacons. I made my plasmids with wt and mutant sequence and I can still detect my plasmid with the mutant sequence at 10 to the minus tenth (1 copy) which has a Ct away for Wt plamid at 10 to the minus third of about 1.8 Ct. Do you think I can detect even 1 copy of this gene or should I stay sticky to the nested PCR protocol? Who know if the real time is more sensitive?

Thanks
Micky

-micky_74-

QUOTE (micky_74 @ Mar 9 2006, 09:21 PM)
Hello everybody!
Here the problem. I'm inserting a mutation (4 different nucleotides) in a cell line. The mutant cells are expected at a frequency 2 to 4 every 10 to the fifth cells. Actually the protocol says that I should diluite the cells in 96 wells plates at 5000 cells per well and check every well with a nested PCR (external one and one PCR allele specific). I'm trying to optimize everything in one Real time PCR step with molecular beacons. I made my plasmids with wt and mutant sequence and I can still detect my plasmid with the mutant sequence at 10 to the minus tenth (1 copy) which has a Ct away for Wt plamid at 10 to the minus third of about 1.8 Ct. Do you think I can detect even 1 copy of this gene or should I stay sticky to the nested PCR protocol? Who know if the real time is more sensitive?

Thanks
Micky



Real time can not be more SENSITIVE than agarose stained by SYBR GOLD and detected
by CCD using DarkReader smile.gif)) 25 picogram per band smile.gif
because it is ClosedTube chemystry with extremely poor "Signal to Noise Ratio" and NOISE in
realtime is extremely high smile.gif Nested is not nessesary- standard is enough smile.gif)

Early protocols worked with 1 microgramm of "background" genomic DNA smile.gif Shurelly - NOT FOR REAL TIME smile.gif

-artem-