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Hi, everyone here!
Now I confuse about the exact position which reverse transcriptase stop at in SHAPE (Selective 2′-hydroxyl acylation analyzed by primer extension) reaction. Is the nucleotide modified by MDS (may be some times 1M7 or NAI-N3) or the nucleotide before the modified one? Is the last base of RT product corresponding to the modified nucleotide （5‘-3’）? If you are interested in the topic and know the answer, please tell me.
Many thanks!
Now I confuse about the exact position which reverse transcriptase stop at in SHAPE (Selective 2′-hydroxyl acylation analyzed by primer extension) reaction. Is the nucleotide modified by MDS (may be some times 1M7 or NAI-N3) or the nucleotide before the modified one? Is the last base of RT product corresponding to the modified nucleotide （5‘-3’）? If you are interested in the topic and know the answer, please tell me.
Many thanks!