Challenge: Finding an RNA drug with no effect


p>In order to evaluate the biological effects of antisense oligonucleotides targeting RNA, it is nice to have a few oligos that are not supposed to bind to anything. Finding such oligos

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computationally is not trivial. Anybody able to do so will receive high praise. Here are the criteria to be met

  • The oligos should be 14 nucleotides in length.
  • They must not contain the dinculeotide cg (the more cg’s, the higher the chance of binding to Toll-like receptors thereby stimulating
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    the immune system).

  • No generic viagra online stretches of more than 3 identical nucleotides (e.g. AAAA, GGGGG, etc.).
  • There must be no perfect matches to the pre-mRNA transcriptomes of mouse, rat, or humans (the reverse complementary sequence of the oligonucleotide sequence must not generic cialis be found).
  • Similarly, and more restrictively, there must not cialis c20 be any matches where 1 mismatch is allowed, in the pre-mRNA transcriptomes of mouse, rat, or humans.
  • Ideally, but probably not possible, there must not be any matches where 2 mismatches are allowed either.

Are genericviagra-bestrxonline you clever enough sequence analysis-wise to find 14mers that meet all or most of these requirements?

Posted in Oligoinformatics

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