User:Cmatth/sandbox

=Rho Dependent Termination= Rho dependent termination is one of two prokaryotic transcription termination processes and is is responsible for terminating many types of RNA transcripts and allows genes to be transcribed that can't be terminated by intrinsic termination and may be constitutive or regulated. The trans-acting rho factor, a helicase, binds to the transcribed RNA and follows the RNA polymerase 5' to 3' while consuming ATP. The rho factor binds at an inverted repeat sequence, called the rho utilization (rut) site that has no specific consensus sequence, the rho factor's helicase action then follows the RNA Polymerase until it reaches the Polymerase and catalyzes the unwinding of the transcribed RNA from the DNA transcript. Other trans-acting factors, such as the elongation factor NusG that may connect the rho factor and RNA, help the rho factor bind and terminate transcription.

=Rho Utilization Site= The rut site is characterized by its high cytidine make up and forms a hairpin to help the rho factor properly bind to the RNA. The rho factor begins to stall at biotin-streptavidin roadblock pause sites after the rut site until it reaches the RNA DNA duplex. The rho factor binds to the rut site in two different states, binding to 57 or 85 nucleotides; RNA threads its way into the middle of the rho factor's hexamer shape to bind to it's secondary binding site, allowing it to hydrolyze ATP. The rho factors loop out transcript between the primary and secondary binding domains that grows as the rho factor chases the RNA Polymerase by a tethered tracking mechanism. Multiple rho factors are released from the rut site of transcripts and more are released the longer the transcript is. Rho factor binding has been shown with deletions to be dependent on the rut site and without it the transcript cannot undergo rho dependent transcription.

= External links =
 * Cooper, G. M. (2000) The Cell: A Molecular Approach. 2nd edition. Chapter 6 RNA Synthesis and Processing
 * Ciampi, M. S. (2006) Rho-dependent terminators and transcription termination

=References==