Antisense oligos (was: none)

Wolfgang Schechinger wgschech at med.uni-tuebingen.de
Sat Apr 4 07:18:38 EST 1998


Dear Chen, 

There is probably no guarantee that a sequence will work. 

I had good experiences with full phosphorothioates (PTOs, nice if you 
have your own synthesizer, if not, have at least four or five 
phosphorothioates at the ends). PTOs are more stable than "normal" 
DNAs, commercial snthesis is expensive though, because the thioation 
step is time consuming.
 Another point of consideration might be that your target sequence is 
accessible for the oligo and for RNAse H. Look at secondary structure 
plots of the mRNA sequence and pick out regions that are in loops, 
not in stems. Binding to stems might enhance stability of mRNA by 
triplex formation. (These ideas are open for discussion!). 
 Leave the trityl protecting group on the molecule, it will make it 
easier for the oligo to enter the cells. Intracellularily, it will be 
cleaved off.
 General considerations for PCR primers might be applicable to 
antisense oligos, too. Having (GCs) at the ends might stabilize 
complexes more than (ATs).  There's a good (my opinion) journal on 
that topic: Antisense Research and Development

Wolfgang


> Hi, all,
> 
> Is there any principal about designing antisense sequence against
> its complementary sequence(mRNA or DNA) in vivo?
> 
> thanks
> 
> Chen Linan
> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
> _/                                              _/
> _/      _/_/_/_/_/  _/            _/        _/  _/            
> _/    _/           _/            _/_/      _/   _/  
> _/   _/           _/            _/  _/    _/    _/  
> _/  _/           _/            _/    _/  _/     _/  
> _/ _/           _/            _/      _/_/      _/       
> _/ _/_/_/_/_/  _/_/_/_/_/_/  _/        _/       _/ 
> _/                                              _/
> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
> 
> Chen Linan               
> Dept. Anatomy
> Beijing Medical University
> Beijing
> P.R.China
> Tel:86-10-63051481
> Email:chenln at public.bta.net.cn 
> HTTP://www.freeyellow.com/members2/chenln/
> 
> 
> 
> 
> 
-----
This message is RNAse free - please don't touch!
-----                              
Wolfgang Schechinger         
University of Tuebingen
email: wgschech at med.uni-tuebingen.de
http://www.medizin.uni-tuebingen.de/~wgschech/start.htm
-------
!Junk mail is *not* appreciated!
SPAMs will be answered automatically by sending my 128MByte virtual memory file.
This is *NO* joke.
------
usual disclaimers apply
------



More information about the Methods mailing list