Help: In situ oligo probe design

warda at vax.oxford.ac.uk warda at vax.oxford.ac.uk
Thu Nov 26 07:31:47 EST 1992


I'm about to start some non-radioactive (digoxigenin-labelled) in situ 
hybridisations on mouse embryos.  Is there any dogma on probe size using 
oligodeoxynucleotides?  There's a 37-bp sequence conserved between mouse 
human and rabbit that looks suitable for the probe - should I get the full
37-mer synthesized, or would a smaller probe be just as effective?  Also,
is secondary structure a consideration?  (The putative probe sequence can
potentially form a hairpin loop with 6 complementary base pairs and a
5-base loop). 

Thanks in advance for any help,

   Bill Bennett                           JANET: warda at uk.ac.oxford.vax    
   CRC Growth Factors Research Group   Internet: warda%vax.oxford.ac.uk  



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