Prokaryotic DNA Transcription Elongation and Termination
The elongation phase of transcription refers to the process through which nucleotides are added to the growing RNA chain. As the RNA polymerase moves down the DNA template strand, the open complex bubble moves also. The bubble is of a fixed number of nucleotides, meaning that at the leading end of the bubble the DNA helix is being unwound, while at its trailing end the single strands are being rejoined. Whereas separation of the DNA helix is permanent in replication, it is only temporary in transcription. depicts the beginning steps in transcription up to elongation and the relative positions of the bubble and the polymerase holoenzyme.
As the figure shows, within the open complex bubble the DNA and RNA form a hybrid or joint complex. The exact length of this region is unknown, but it is thought to be between 3 and 12 base pairs long and is found at the growing 3' end of the RNA. The figure also illustrates how the 5' tail end of the RNA chain is separate from, as opposed to base paired to, the DNA template strand. This is another difference between DNA replication and DNA transcription; in replication, the newly synthesized DNA strand remains bound in a helix to the strand with which it has base paired. After the initial stretch of approximately 8 base pairs has been synthesized, the sigma unit, which is responsible for recognition and binding to the promoter region, is released. The core enzyme is left to polymerize the growing RNA chain alone. This leads to the continuous extrusion of the 5' end of the RNA from the enzyme complex. At normal room temperature, the rate of transcription in prokaryotes is 40 nucleotides per second.
RNA synthesis will continue along the DNA template strand until the polymerase encounters a signal that tells it to stop, or terminate, transcription. In prokaryotes, this signal can take two forms, rho-independent and rho-dependent.
The rho-independent terminator is the more simple of the two systems and as a result is also called simple termination. The rho-independent signal is found on the DNA template strand and consists of a region that contains a section that is then repeated a few base pairs away in the inverted sequence.
As is shown in the figure, the patch is followed by a short string of adenines. When this stretch is transcribed into an RNA sequence, the RNA can fold back and base pair with itself forming a hairpin loop.
As you can see, the string of adenines in the DNA sequence are transcribed into uracils in the RNA sequence. Because the uracil bases will only pair weakly with the adenines, the RNA chain can easily be released from the DNA template, terminating transcription.
The rho-dependent terminator received its name because it is dependent on a specific protein called a rho factor. The rho factor is thought to bind to the end of the RNA chain and slide along the strand towards the open complex bubble. When the factor catches the polymerase, it causes the termination of transcription. The mechanism of this termination is unclear, but the rho factor could in some way pull the polymerase complex off of the DNA strand.