A transcription bubble is a molecular structure that occurs during the transcription of DNA when a limited portion of the DNA double strand is unwound and is about 11bp of DNA. RNA polymerase may then bind to the exposed DNA and begin synthesizing a new strand of RNA. As RNA polymerase progresses down the DNA template strand in the 3' to 5' direction (the DNA coding strand in the 5' to 3' direction), more of the double stranded DNA is unwound upstream of the polymerase (towards the 3' end of the template strand or 5' end of the coding strand) while DNA downstream of the polymerase (towards the 5' end of the template strand or 3' end of the coding strand) re-anneals. Moving of the transcription bubble in the process may be seen with specialized staining techniques, spectroscopy or microscopy.
- George Plopper. Principles of Cell Biology. Jones & Bartlett Publishers, Jan 17, 2012 pg .258