I am working with 16s rRNA , my amplicon size is 390 bp with 315f-806r , however I have got 350 bp , is it normal? please , if any one know answer , replay to me
Stable secondary structure of rRNA may make the amplicon shorter than you expect due to revertase jumping (in RT-reaction) of some stable RNA-loops in the RNA secondary structure. In this case you should take "temperature resistant" revertases for RT-reaction (e.g. AMV or SuperScript (Invitrogene)) and carry out RT at a temperature of 50-55 С.
My expected band is 390 bp in microbial v4 16S rRNA gene , my working on normal pcr , so, I am looking to find in bacteia in biological fluid, , i do not know the species for these bacteria
How did you get the 30 size, etimation by gel elecrophoresis or sequencing? The sie stimation by gel is not as aqurate at that. If you obtained it by sequencing, did you sequence both strands or just one? If only one remeber that you do not obtain sequence from the primer use and also the firs nucleotides after are missing.