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This is an mRNA strand of mouse meta-globin:

5'-ccccagauacggaauucgaau-3'

A) Which small RNA (below) is most likely to regulate expression of meta-globin?

  1. 5'-auucgaauuuucuaucugggg-3'
  2. 5'-ggggucuaucuuuuaagcuua-3'
  3. 5'-ccccagauacggaauucgaau-3'
  4. 5'-uaagcuuaaggcauagacccc-3'

B) This RNA most likely?

  1. acts as an siRNA
  2. inhibit meta-globin translation
  3. increase meta-globin translation
  4. help transport meta-globin mRNA back into the nucleus

My attempt:

I think A is 2 because the strand is complementary and will bind nicely to the mRNA strand. For B, I'm between 2 and 3, but cant decide.

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I'm going with 1) for A since you need the strand to be the reverse complement. –  bobthejoe Apr 23 '12 at 18:40
    
A) Is this a take-home exam question? 1) Yes, then I can't answer your questions for you. 2) No, well, I'll see if I have time tomorrow to get to it. –  Larry_Parnell Apr 23 '12 at 19:24
    
@Larry_Parnell this is a problem I found in an MCAT book. (I'm studying for the mcat) –  Kirby Apr 23 '12 at 19:32

1 Answer 1

There are always exceptions but you can consider some general rules.

A is 1 i.e the sequence that is perfectly complementary (2 is complementary but direction is parallel — cannot base-pair), then B would be 1 (siRNA). Reasons (some are just based on general rules of siRNA design):

  • siRNAs have to be perfectly complementary
  • The size is also perfect for a siRNA (21nt)
  • U/A (2-3 residues) at the 5' of the siRNA
  • U at 10th position
  • GC content 43% (ideal 30-50%)

See here for guidelines for siRNA design.

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