position of HIV DNA in genome

giovanni maga maga at igbe.pv.cnr.it
Wed Jan 20 01:56:48 EST 1999


In article <77hbvv$6f1 at net.bio.net>, "Harry Banner" <harry at c1.com.au> wrote:

> I would appreciate a response to the following:
> 
> (a) does the retrovirus insert itself at a specific location within the
> genome or is it randomly recombined?
> 
> (b) as the DNA sequence of the virus is known why is it that we cannot
> synthesize an enzyme that will "look" for that particular sequence and then
> excise it from the genome?
> 
> Thanking you in advance.

(a) Random
(b) Well, let's say first that *synthesize* an enzyme is pretty much
difficult. There is a lower limit in the aminoacids required for a certain
catalytic function plus the required structural stability and substrate
recognition/binding functions. Current oligo synthesis capabilties are
well behind that limit. We could try to modify some known restriction
enzyme in order to give it the required sequence recognition ability but I
am pretty sure that it would be nearly impossible to come down to a
specificity such that the enzme will not cut anywhere else in the genome.
Even if we can do that, there is the problem to bring such enzyme in
contact with the target. That would mean transfecting specifically HIV-1
infected cells with an appropriate expression vector containing the coding
sequence for the enzyme...this is a sort of gene therapy and we are still
pretty much away from it. Anyway, just for the sake of speaking, the idea
per se is fine. I just wonder whether one could try to desing a ribozime
(catlytic RNA) with the required activity. A sort of *DNA splicing*
ribozime (forgive me for this) would also be able to catalyze the excision
and religation of the target sequence. Actually we do not need to excise
the entire genome (too long) but only some critical part of it, so that a
defective harmless provirus can be generated. Well, that's just for
talking guys, don't take me too seriously.
Regards.
G.Maga, PhD
IGBE-CNR, Pavia (Italy)




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