The DNA sequence below is a segment of a protein coding gene. It includes the promoter region and the beginning of the sequence to be transcribed. The transcription start site is indicated by the +1. To begin, drag and drop the appropriate icons onto the DNA to establish the -35 and -10 promoter sequences.
Bacterial RNA polymerase cannot associate with DNA on its own; it requires an additional factor to help it recognize specific regulatory sequences. Locate this factor in the palette and bring it to the RNA polymerase.
The RNA polymerase complex is now ready to go! Drag and drop the complex onto the region of DNA that it recognizes. [Note: The RNA polymerase complex shown here is not drawn to scale—in reality it spans approximately 100 bp of DNA.]
Once the σ70-RNA polymerase complex binds to the promoter region of DNA, spontaneous isomerization converts the complex from a closed state to an open state, where a bubble of the duplex DNA is separated in preparation for transcription.
Congratulations, you’ve formed the open complex and are ready to begin RNA synthesis! Your next task is to synthesize RNA. The floating green letters represent RNA nucleotides. Using one DNA strand as a template, drag and drop the RNA nucleotides to the template, to initiate formation of the RNA transcript.
The polymerase, after abortive initiation, has reset to the transcription start site and RNA synthesis is attempted again. Your task is to drag and drop RNA nucleotides (floating green letters) to the template to reinitiate formation of the RNA transcript.
Transcription initiation was successful! The polymerase complex has stabilized. Transcription has entered the elongation phase, and will continue along the DNA until the polymerase reaches a termination signal. For clarity, the RNA transcript simulated here is short. Actual bacterial transcripts are many hundreds of bases.
Simulating RNA transcription elongation....the simulation will stop when the sequence that signifies the termination type is visible. When this happens, it is your task to drag-and-drop the correct symbol for the termination type onto the signature sequence.
The RNA polymerase has transcribed a termination sequence, and transcription has paused. Examine the RNA transcript to determine the type of termination that will occur. From the palette, identify the factor required for this type of termination and bring it to the appropriate sequence in the RNA transcript.
Great job! You you correctly identified the termination type as ρ-dependent. The hexameric ρ-helicase uses ATP to move along the RNA transcript toward the RNA polymerase, which results in release of the RNA transcript from the DNA template and the polymerase.
Great job! You correctly identified the termination type as ρ-independent. Formation of the hairpin in the RNA transcript disrupts interactions between the RNA, DNA template, and RNA polymerase, leading to release of the RNA transcript.
RNA transcript is released from the DNA and polymerase. The resulting RNA transcript contains the transcription of the gene and the termination sequence.
Congratulations! You have successfully transcribed the bacterial protein-coding gene. Your score shows you have a solid understanding of bacterial transcription. Click the button below to begin the Tutorial Comprehension Quiz.
Congratulations! You have successfully transcribed the bacterial protein-coding gene. However, your score indicates you have some uncertainty with bacterial transcription. Consider reviewing your text, and then try the exercise again before taking the Tutorial Comprehension Quiz.
Abortive initiation has occurred! In the initial stages of transcription, the association between the RNA, template, and polymerase complex is tenuous. The polymerase often releases the nascent transcript without extending it further. The polymerase resets to the transcription start site and RNA synthesis is attempted again.

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Prerequisite skills needed:

  • DNA/RNA Structure and Base Pairing
  • Relevant book section: pages 1036-1042

By completing this simulation, you will:

  • Understand the chemical reactions underlying transcription in bacteria
  • Understand how the different components of transcription come together to transcribe DNA into RNA
  • Distinguish between two possible modes of transcription termination
ρ-Helicase -35 Promoter Sequence RNA Polymerase -10 Promoter Sequence RNA Hairpin σ70
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