The first step is the conversion of the information into messenger RNA (mRNA).
Transcription is carried out by RNA polymerase. As with DNA synthesis, the RNA strand is made in the 5′ to 3′ direction.
Firstly, only a comparatively short molecule is produced, and secondly, only one of the DNA strands is transcribed. Since only a single strand is made, it can be produced continuously using a single enzyme; there is no need for lagging strand synthesis.
In addition the production of relatively short single-stranded RNA causes fewer topological problems: the enzyme and the RNA product can essentially rotate around the helix, so there is no need for the helicases and topoisomerases that are essential for replication.
Furthermore, RNA polymerase can start synthesis from scratch – no primer is needed. Transcription is therefore considerably simpler than replication.
In E. coli, depending on growth conditions, 2000–5000 copies of RNA polymerase may be engaged on mRNA synthesis at any time.
The transcription reaction can be divided into the three stages: initiation, in which the promoter is recognized, a bubble is created, and RNA synthesis begins; elongation, in which the bubble moves along the DNA as the RNA transcript is synthesized; and termination, in which the RNA transcript is released and the bubble closes.
Initiation itself can be divided into multiple steps.
Template recognition begins with the binding of RNA polymerase to the double-stranded DNA at a DNA sequence called the promoter. The enzyme first forms a closed complex in which the DNA remains double-stranded. Next the enzyme locally unwinds the section of promoter DNA that includes the transcription start site to form the open complex.
Separation of the DNA double strands makes the template strand available for base pairing with incoming ribonucleotides and synthesis of the first nucleotide bonds in RNA. The initiation phase can be protracted by the occurrence of abortive events, in which the enzyme makes short transcripts, typically shorter than around 10 nucleotides (nt), while still bound at the promoter. The enzyme often makes successive rounds of abortive transcripts by releasing them and starting RNA synthesis again. The initiation phase ends when the enzyme finally succeeds in extending the chain and clearing the promoter.
Elongation involves processive movement of the enzyme by disruption of base pairing in double-stranded DNA, exposing the template strand for nucleotide addition and translocation of the transcription bubble downstream. As the enzyme moves, the template strand of the transiently unwound region is paired with the nascent RNA at the point of growth. Nucleotides are added covalently to the 3 ‘ end of the growing RNA chain, forming an RNA-DNA hybrid within the unwound region . Behind the unwound region, the DNA template strand pairs with its original partner to reform the double helix, and the growing strand of RNA emerges from the enzyme.
The traditional view of elongation as a monotonic process, in which the enzyme moves forward along the DNA at a steady pace corresponding to nucleotide addition, has been revised in recent years. RNA polymerase pauses or even arrests at certain sequences. Displacement of the 3 ‘ end of the RNA from the active site can cause the polymerase to “backtrack” and remove a few nucleotides from the growing RNA chain before restarting. Pausing can also be programmed to occur by the use of a coded RNA hairpin structure or sequence context-caused misalignment of the incoming nucleotide with its complementary base.
Termination involves recognition of sequences that signal the enzyme to halt further nucleotide addition to the RNA chain. In addition, long pauses can lead to termination. The transcription bubble collapses as the RNA-DNA hybrid is disrupted and the DNA reforms a duplex, phosphodiester bond formation ceases, and the transcription complex dissociates into its component parts: RNA polymerase, DNA, and RNA transcript. The sequence of DNA that directs the end of transcription is called the terminator.