Is it possible to use a 5'-fluorophor labeled RNA dinucleotid (Alexa 647-GpG) as "Primer" for in vitro transcription with dsDNA template and standard T7-Promotor to directly transcribe fluorophor labeled RNA? GpG is incorporated by the inition complex in T7 transcription as first nucleotides but I'm not sure if the same accounts for the fluorophor labeled dinucleotide.
Found the answer. So there was a paper where they used 5'-labeled AMP for inition (The phi 2.5 T7 promotor is starting with AMP) unfortunately can't buy those as far as I know. IBA sells 5'- labeled ApG dinucleotides for transcription inition. After all I read about it, you probably need a 5x-10x excess of them in order to get a good yield of labeled RNA. They are very expensive though.
Thanks Andrei, they really have pretty good pricing per base. I found that sigma adlrich has comparable prices and 5' lableling is also very cheap. For some of the oligos synthesis is the best option.
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