Q on Antisense-Oligo Design

Jack M. Bernstein, M.D. bernstein at wsu-id.dayton.oh.us
Thu Jul 13 14:09:47 EST 1995

In article <3u2ush$o6b at sparcserver.lrz-muenchen.de> Wolfgang Schechinger <u7k0201 at sunmail.lrz-muenchen.de> writes:
>From: Wolfgang Schechinger <u7k0201 at sunmail.lrz-muenchen.de>
>Subject: Q on Antisense-Oligo Design
>Date: 13 Jul 1995 11:09:05 GMT

>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

Don't make a sense oligo. Others have reported both inhibition and 
augmentation with these.

I would favor just making a sequence with your bases scrambled but maintaining 
the same ATGC ratio. This should be simple enough and could be made on your 
synthesizer. If you are worried about the control not being representative, 
synthesize two controls.

Good luck.

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