In order for proper gene expression to occur, transcription must stop at specific sites. Two termination mechanisms are well known:
*Intrinsic termination (also called Rho-independent termination): Specific DNA nucleotide sequences signal the RNA polymerase to stop. The sequence is commonly a palindromic sequence that causes the strand to loop which stalls the RNA polymerase. Generally, this type of termination follows the same standard procedure. A pause will occur due to a polyuridine sequence that allows the formation of a hairpin loop. This hairpin loop will aid in forming a trapped complex, which will ultimately cause the dissociation of RNA polymerase from the template DNA strand and halt transcription.
*Rho-dependent termination: ρ factor (rho factor) is a terminator protein that attaches to the RNA strand and follows behind the polymerase during elongation. Once the polymerase nears the end of the gene it is transcribing, it encounters a series of G nucleotides which causes it to stall. This stalling allows the rho factor to catch up to the RNA polymerase. The rho protein then pulls the RNA transcript from the DNA template and the newly synthesized mRNA is released, ending transcription. Rho factor is a protein complex that also displays helicase activities (is able to unwind the nucleic acid strands). It will bind to the DNA in cytosine rich regions and when RNA polymerase encounters it, a trapped complex will form causing the dissociation of all molecules involved and end transcription.
The termination of DNA transcription in bacteria may be stopped by certain mechanisms wherein the RNA polymerase will ignore the terminator sequence until the next one is reached. This phenomenon is known as antitermination and is utilized by certain bacteriophages.