Question

If there are two fragments of RNA say strand 1 and strand 2 to be "stitched" together (both sequence 1 and 2 going in 5' to 3' direction),

for example, strand 1 is 5' AAUGACCAC 3' and strand 2 is 5' AAGCUCGCGGCCGUACAUCUU 3', would the stitching be done as

strand 1+strand 2 - 5' AAUGACCACAAGCUCGCGGCCGUACAUCUU 3'

or

strand 2+strand 1? - 5' AAGCUCGCGGCCGUACAUCUUAAUGACCAC 3'

I understand RNA is always made in 5' to 3' direction but both seem to be a valid 5' to 3' growth. The question asks to stitch the first 9 nucleotides of a sequence (strand 1) to sequence 2.

Please explain as which of the two is the right way to stitch and why.

Answer 1

According to the information, stitching or sealing of the two DNA strands is required to be done. Here, it must be carefully noted that whatever is the order of stitching the strands, the RNA strand containing an AUG codin earliest towards the 5' side must be taken as the reference. Thisbis because post-transcription, the RNA would be translated and the translational machinery identifies the RNA strand carrying a start codon or AUG as thr primary site.

Since the sequence 1 contains this start codon earlier than the sequence 2, the order of stitching must be 1+2, so that appropriate translation might take place.