PCR on cDNA and SGamplification???
Posted 29 February 2012 - 05:50 AM
I've attached a pic of my most recently failed attempt at SGamplifications and one that worked in the past but the sequences from the amplicons seen were not clean.
I ran a bulk amplification reaction in parallel with the most recent SGamplifications. The bulk amplification has worked in the past, under the same conditions and with the same reagents and concentrations. But this time, it also did not give me a result and I can see this band in my well.
I use the Qiagen RNA extraction kit to get the RNA from the virus Invitrogen Superscript III for cDNA synthesis. My RNA and cDNA yields respectively after each step for this particular sample are 63.6ng/ul and 60ng/ul (by Nanodrop)
Above are failed PCRS
Above are 2 supposed single genome amplicons that gave dirty sequences after analysis. You can also see the bnds in the wells of the negative reactions (which I think is the source of contamination wrt my sequences)
My PCR conditions for both 1st round and nested PCRs
Phusion HIFI buffer 5ul
dNTPs (10mM) 0.5ul
primer 1 (50uM) 0.25ul
primer 2 (50uM) 0.25ul
Phusion Taq pol 0.5ul
94oC for 3 mins
94oC for 30secs
optimized annealing temp for 30 secs
72oC for 4 mins
72oC for 10 mins
Posted 06 March 2012 - 10:07 AM
That thing in wells look like genomic DNA yes. But I find unlikely that this high-weight DNA would come from amplification (what is the size of your longest band in marker?). You ca try to make a reaction and run it on gel without amplification to see if it was there beforehand. Anyway it looks like there is so much of it in reaction, other thing you can try is to lower the amount of template like 10x or 100x.
Other option is that it's not long DNA at all, but something having a big difficulty passing through gel and binding EtBr. Maybe some protein-DNA complex - wild guess.
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