Q on Antisense-Oligo Design
u7k0201 at sunmail.lrz-muenchen.de
Thu Jul 13 06:09:05 EST 1995
Hi. I would like to hear your opinion.
I`m using fully thioated 17-mers as antisense-oligos with the final trityl group left at the
molecule for better uptake int my cultured mesangial (i.e. SMC-like) cells.
I want to design a control sequence for demonstrating that the measured effects are basing on
the antisense-effect, but not on chemical or biological toxicity of the substance.
I`m favoring a really scrambled control, i.e. the same Formula [A(n), T(m), C(o), G (p), but
statistically messed up, because I think, it wille be important to maintain the same chemical
composition of monomeric nucleotides. But the problem is - as the technician says, that the
ABI-synthesizer couldn't be programmed for doing that - I would have to prepare a solution mix
of all activated bases in the correct ratio. Is that true?
My professor preferes a mixed up oligo that has the same length, but the chance o a certain
nucleotide is 0.25 for appearing at a certain place (The summary formula would be
A(4.25), T(4.25), C(4.25) G(4.25) for the 17mer). Thus, the chemical composition is different.
A colleague of mine prposed a unique sequence (but the same summary formula) derived from the
antisense-sequence in that he exchanged the bases pairwise at different places for several
times resulting in an antisense-oligo with a lowered melting temperature.
Another idea would be constucing the sense oligo, but I cannot see any advantage in that.
What do you think?
I appreciate ANY comment.
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