RNA Polymerases

Transcription begins when RNA polymerase binds to the DNA double helix. This occurs at a site just "upstream" of the gene to be transcribed, called the promoter site. In eukaryotes, RNA polymerase is directed to the promoter site by transcription factors, proteins that bind to the DNA and provide a docking site for attachment of the polymerase enzyme. Once RNA polymerase binds to the DNA at the promoter, transcription can begin.

During transcription, the polymerase unwinds a portion of the double-stranded DNA, exposing the DNA template strand that will be copied into RNA. Individual RNA nucleotides enter the enzyme complex, and are paired with the DNA. C pairs with G, T (on DNA) pairs with A, and A (on DNA) pairs with U. Nine DNA-RNA nucleotide pairs exist within the polymerase molecule at any one time. After each new RNA nucleotide is paired, it is linked to the preceding RNA nucleotide, forming a growing strand of polymerized RNA called the primary transcript. This stage of transcription is called elongation.

Recent X-ray analysis of RNA polymerase has revealed important structural details that help explain the precise mechanism of transcription. Double-helical DNA enters a long cleft in the surface of the enzyme, and is held in place by a large flexible portion of the enzyme termed the "clamp." Within the cleft, the DNA is separated and RNA is paired to it. A magnesium ion, sitting at the critical point where RNA nucleotides are added to the primary transcript, is thought to help catalyze this reaction. An internal barrier forces a bend in the growing DNA-RNA duplex, exposing the RNA end for addition of the incoming nucleotide. A short protein extension, termed the "rudder," helps to separate the RNA from the DNA, and the two exit the polymerase along separate paths.

The average maximum rate of elongation in bacteria is 5 to 10 nucleotides per second. However, during transcription, the polymerase enzyme may pause for seconds to minutes. These pauses are thought to be part of a regulatory mechanism. Transcription continues until RNA polymerase reaches a special DNA sequence called the termination sequence, at which point it detaches from the DNA.