Q on Antisense-Oligo Design

Wolfgang Schechinger 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.
Please mail and post

Wolfgang Schechinger
Institute for Diabetes Research
Koelner Platz 1
80804 Muenchen (thats Munich)
Phone +49 (89) 30 79 31 24
Fax   +49 (89) 30 81 733
email u7k0201 at sunmail.lrz-muenchen.de

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