Intrinsic, or rho-independent termination, is a process in prokaryotes to signal the end of transcription and release the newly constructed RNA molecule. In prokaryotes such as E. coli, transcription is terminated either by a rho-dependent process or rho-independent process. In the Rho-dependent process, the rho-protein locates and binds the signal sequence in the mRNA and signals for cleavage. Contrarily, intrinsic termination does not require a special protein to signal for termination and is controlled by the specific sequences of RNA. When the termination process begins, the transcribed mRNA forms a stable secondary structure hairpin loop, also known as a Stem-loop. This RNA hairpin is followed by multiple uracil nucleotides. The bonds between uracil and adenine are very weak. A protein bound to RNA polymerase (nusA) binds to the stem-loop structure tightly enough to cause the polymerase to temporarily stall. This pausing of the polymerase coincides with transcription of the poly-uracil sequence. The weak adenine-uracil bonds lower the energy of destabilization for the RNA-DNA duplex, allowing it to unwind and dissociate from the RNA polymerase. Overall, the modified RNA structure is what terminates transcription. Stem-loop structures that are not followed by a poly-uracil sequence cause the RNA polymerase to pause, but it will typically continue transcription after a brief time because the duplex is too stable to unwind far enough to cause termination. Rho-independent transcription termination is a frequent mechanism underlying the activity of cis-acting RNA regulatory elements, such as riboswitches. Function The purpose function of intrinsic termination is to signal for the dissociation of the ternary elongation complex (TEC), signaling the end of a transcript in prokaryotes. Intrinsic termination independent of the protein Rho, as opposed to Rho-dependent termination, where the prokaryotic Rho protein comes in and acts on the RNA polymerase, causing it to dissociate. Here, there is no extra protein and the transcript forms its own loop structure. Intrinsic termination thus regulates the level of transcription as well, determining how many Polymerase can transcribe a gene over a given period of time, and can help prevent interactions with neighboring chromosomes. Regulation of Intrinsic Termination The process itself is regulated through both positive and negative termination factors, usually through modification of the hairpin structure. This is accomplished through interactions with single stranded RNA that corresponds to the upstream area of the loop, resulting in disruption of the termination process. Furthermore, there is some implication that the nut site may