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In the context of molecular biology, a chemical probe is a molecule that has a high affinitive for a well defined target region of a complex molecure, and an order of magnitude lower affinity for any non-target region.

In some experiments, a single strand of nucleotide bases is used as a probe because it will preferentially bind to a complementary sequence.

In the case of SHAPE chemistry for determining RNA structure, the probe is not a nucleic acid chain.  The criteria for a chemical to be a good SHAPE probe are that it

  1. reacts equally well with any base position of the RNA being probed, regardless of the base type (A, U, C or G),
  2. reacts differentially acording to whether, and/or how, a base is bound to other bases, and
  3. interacts with the RNA in such a way as to interrupt with reverse transcription of the RNA.

The last criteria is important because it is the key to determining the exact base at which each individual RNA molecule has been modified.