Transcription Bubble
A transcription bubble is a molecular structure that occurs during the transcription or replication of DNA when DNA helicase and DNA topoisomerase "unzip" the DNA double strand. DNA polymerase or RNA polymerase may then bind to the exposed DNA and begin synthesizing a new strand of DNA or RNA. As DNA and/or RNA polymerase progresses down the DNA strand in the 3' to 5' direction, more of the DNA double strand is unwound, creating a replication or transcription bubble in the process that may be seen with specialized staining techniques and microscopy.
During the elongation step in transcription, the transcription complex consisting of RNA polymerase plus various elongation factors moves along the double-stranded DNA copying the template strand to produce a single-stranded RNA. In the example shown below the RNA product is mRNA and the enzyme would be RNA polymerase II in eukaryotes.
The transcription bubble spans about 20 nucleotides of DNA. This corresponds to the opening of two turns of the double helix. During transcription, a transient DNA:RNA double helix forms and this is sufficient to form one turn of the hybrid helix. As the complex moves down the gene from left to right, ribonucleotides are added one at a time to the growing 3′ end of the RNA. This is positioned in the active site of RNA polymerase.