SV40 late polyA signal orientation - (Mar/21/2006 )
I have a question regarding the orientation of the SV40 late polyA signal. Does anyone know if this polyA signal works in both directions? Let´s say in this context:
The SV40 polyA signal is in correct orientation to transcript1 and terminates transcription efficiently. But is transcription of transcipt 2 (an antisense transcript) terminated at all, or maybe with lower efficiency? Could transcript 2 provide an antisense RNA for transcript 1, leading to RNA interference?
Do you have any references for this problem, because I coudn´t find some?
i don't have currently time to check, but i think that poly a signal is for one strand only. first evidence is that the consensus AATAAA is in only one sense on that sequence.
By the features i have, the poly a SV40 signal starts at the "stop" codon.
and i think that's also necessary to have a good stop codon in the other sense.
here is the sequence i have for polyA:
1801 TCAATTCTCT AGAGCTCGCT GATCAGCCTC GACTGTGCCT TCTAGTTGCC
1851 AGCCATCTGT TGTTTGCCCC TCCCCCGTGC CTTCCTTGAC CCTGGAAGGT
1901 GCCACTCCCA CTGTCCTTTC CTAATAAAAT GAGGAAATTG CATCGCATTG
1951 TCTGAGTAGG TGTCATTCTA TTCTGGGGGG TGGGGTGGGG CAGGACAGCA
2001 AGGGGGAGGA TTGGGAAGAC AATAGCAGGC ATGCTGGGGA TGCGGTGGGC
2051 TCTATGGCTT CTGAGGCGGA AAGAACCAGC TGGG
As far as i recall the early and late polyA signal are very close together (few base pairs) but in oposite direction. So if you use the late poly A signal the early poly-A signal will be present in the oposite orientation and vice versa.
Thanks for your help.
I think I have to contact promega and ask them. In my special case I need to know if the polyA signal of the pGL3 vectors is bidirectional.