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What is the role of region 2 of the sigma factor in transcription initiation?
Region 2 of the sigma factor plays a crucial role in sequence-specific recognition of promoter elements by binding extensively to the phosphodiester backbone throughout the promoter region.
Describe the concurrent processes that occur during promoter sequence recognition and open complex formation.
Promoter sequence recognition and DNA melting occur concurrently, with base flipping initiating the melting process.
How does DNA footprinting reveal the binding sites of proteins on DNA?
In DNA footprinting, endonucleases digest the DNA, leaving behind protected regions where the protein binds. Missing bands on a gel indicate the binding sites of the protein, such as promoter sequences.
Explain the dynamic nature of DNA binding to the RNA polymerase holoenzyme during transcription initiation.
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Describe the modification-based method used to identify bases essential for protein-DNA contact.
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What is the significance of base flipping in the DNA melting process during transcription initiation?
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How does the sigma factor contribute to sequence-specific recognition of promoter elements?
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Explain the process of DNA footprinting and its application in identifying protein binding sites.
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How does the modification-based method differ from DNA footprinting in identifying protein-DNA interactions?
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Describe the dynamic nature of RNA polymerase binding during transcription initiation and its implications.
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