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Answer by Surfbanana. Confidence votes 22. Helicase and RNA polymerase separate DNA strands by breaking the hydrogen bonds between complementary bases. Helicase parts the strands of DNA during DNA replication, and RNA polymerase parts them during transcription. The enzyme that separates DNA in called DNA helicases. There are two of them that work away from the origin of replication, creating in bubble in the DNA molecule.
Quick Answer. The powerful enzyme DNA helicase unwinds the double strands of DNA by breaking the bonds between each of the complementary bases. These bases are held together by strong hydrogen bonds, but in breaking these, DNA helicase creates two single-stranded DNA molecules.