SV40 poly(A) signal works bidirectionally?

Alan KAY kay at
Wed Feb 5 11:27:51 EST 1997

In article <199702011239.VAA47036 at>, 
ohba at says...
>Dear Bionetters;
>Hello!  I am using pREP4 and pREP9 vectors from Invitrogen.  Looking at the
>vector sequences provided by the vendors, I found that the direction of
>SV40 poly(A) signal sequences of pREP vectors (405-6 of pREP4, 692-1090 of
>pREP9) are opposite to that of a pBK vector (750-469 of pBK-RSV) from
>Stratagene.  All the signal sequences are placed downstream to multiple
>cloning sites.  Does SV40 poly(A) signal work bidirectionally?
Dear Hiroyoshi,

Not really. In SV40, the early genes are transcribed off of one strand and 
the late genes off of the other. The two promoters are grouped near the 
origin of replication at position 1. Similarly, the two distinct 
polyadenylation signals are grouped roughly on the other side of the circular 
genome, and often in vectors the small SV40 DNA fragment that is used may 
contain both signals. You should also remember that polyadenylation requires 
normally not only the AATAAA signal but also the polyadenylation acceptor 
site (usually CA) 15-30 nucleotides downstream from the signal, which is 
often followed by a G/T rich region. I have one vector which uses the early 
SV40 polyadenylation signal and acceptor site. The late AATAAA signal is also 
in the fragment, but at the very end, so it no longer has its acceptor site. 
I have some evidence to back up the idea that this signal is not effective.


Alan KAY

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