The correct way to punctuate the compound sentence is Dr. Burke wanted to trust her assistant with the secret formula, but she was afraid her assistant was a spy.
It should be noted that a compound sentence is most often punctuated with a comma as a result of the natural pause it creates in the sentence.
Therefore, the correct way to punctuate the compound sentence is that Dr. Burke wanted to trust her assistant with the secret formula, but she was afraid her assistant was a spy.
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