I have both my cDNA and matching mRNA sequence for the protein that I am eventually looking to synthesis and I cannot, for the life of me, figure out how to select said mRNA in the RT process ?
You'll need to design primers that flank your gene of interest. There are lots of good primer design programs. I use Primer3
http://bioinfo.ut.ee/primer3-0.4.0/
You can easily specify which areas your want to include or exclude, the product size, Tms, etc.
Or do you mean you don't know how to get rid of DNA from your nucleic acid prep? If that's the question, just add a DNase enzyme according to the manufacturer's instructions.
Hello
If you managed to design primers by a software, you may use only the reverse strand in the process of cDNA synthesis as a specific primer to yield more of your target region.
Your RT primer will just be a reverse primer, although for the RT you don't a very high Tm (the RT enzyme usually works at a low temperature). If it is mRNA, you can use an oligo dT primer (that will bind the polyA at the end of mRNAs) to make cDNA from all mRNAs in the cell, and then amplify your gene in the PCR reaction with primers that match the beginning and end of your gene.
If for some reason this doesn't work for you and you want to only/mainly produce cDNA of your protein, you can use a reverse primer that matches the end of your gene. Again, for the PCR you just amplify with primers matching the start and end of your gene using the cDNA as input.
If you want it for cloning, think about adding restriction sites into the primers (plus a few extra bases at the end to help the enzymes cut more efficiently) and maybe a kozak sequence.
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