I want to synthesize a long oligo probe that may be approx 1 kb, is there any available methods on it? should I achieve it with overlap or sth?
Hi Jiaxin,
Might need a bit more information on your plans for it. But getting it synthesised as a single oligo using strings or G-block should be simple enough to get the entire 1kb oligo in one piece.
thank you! that's a ss oligo with multiple repeats and specific bases to enhance the affinity, and it is supposed to combine the interested sequence with one target mRNA. I know the long oligo can be synthesized but have no details on it, including which machine, and the protocol or other strategies, such as preparing several fragments of it and bridge them. could you give me more info on it? plz. thank you~
easiest would be to transcribe it using a T7 polymerase from a dsDNA template. if you need it synthesized you may need to ligate multiple shorter oligos together. we currently go up to about 120 bases for RNA on solid-phase synthesis and recommend purification beyond 40-50 bases. on the other hand its pretty easy and straight forward to design a dsDNA template from overlapping single stranded ssDNA oligomers, PCR them up to get one dsDNA template and then use that for in vitro transcription.
thanks Mario, but what I worried about is the RNA probe may degrade with normal situation, and I know the proper modification like LNA oligo can keep the probe with much higher affinity and stablity, comparing to the RNA probe. and T7 polymerase is indeed a common method but it is not what I want. and I tried what you said before, so that's what I wanna synthesize long oligo.
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