Transcription: DNA copied into RNA

Transcription is the process through which a DNA sequence is enzymaticaly copied by an RNA polymerase to produce a complementary RNA. In other words, it is the transfer of genetic information from DNA into RNA. In the case of protein-encoding DNA, transcription is the beginning of the process that ultimately leads to the translation of the genetic code (via the mRNAintermediate) into a functional peptide or protein. Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for DNA; therefore, transcription has a lower copying fidelity than DNA replication. Like DNA replication, transcription proceeds in the 5' to 3' direction (see DNA Backbone) - in other words the old polymer is read in the 3' to 5' direction and the new, complementary fragments are generated in the 5' to 3' direction. Prokaryotic transcription is divided into 3 stages; initiation, elongation, and termination.

Initiation -
RNA polymerase (RNAP) recognizes and specifically binds to the promoter region on DNA. At this stage, the DNA is double-stranded ("closed"). This RNAP/wound-DNA structure is referred to as the closed complex. The DNA is unwound and becomes single-stranded ("open") in the vicinity of the initiation site (defined as +1). This RNAP/unwound-DNA structure is called the open complex. The RNA polymerase transcribes the DNA, but produces about 10 abortive (short, non-productive) transcripts which are unable to leave the RNA polymerase because the exit channel is blocked by the sigma factor.

The sigma factor eventually dissociates from the holoenzyme and elongation proceeds. Promoters can differ in "strength," or how actively they promote transcription of their adjacent DNA sequence. Promoter strength is in many (but not all) cases, a matter of how tightly RNA polymerase and its associated accessory proteins bind to their respective DNA sequences. The more similar the sequences are to a consensus sequence, the stronger the binding is.

Most transcripts originate using adenosine-5'-triphosphate (ATP) and, to a lesser extent, guanosine-5'-triphosphate (GTP) (purine nucleoside triphosphates) at the +1 site. Uridine-5'-triphosphate (UTP) and cytidine-5'-triphosphate (CTP) (pyrimidine nucleoside triphosphates) are disfavored at the initiation site.

Termination -
Two termination mechanisms are well known: Intrinsic termination (also called Rho-independent termination) involves terminator sequences within the RNA that signal the RNA polymerase to stop. The terminator sequence is usually a palindrome sequence (reads the same forward as backward) that forms a stem-loop hairpin structure that leads to the dissociation of the RNAP from the DNA template. One such common termination motif is the palindrome sequence 'GCCGCCG'. The RNA polymerase fails to proceed beyond this point and consequently, the nascent DNA-RNA hybrid dissociates. The RNA polymerase then proceeds to look for a new initiation-region from which to start the initiation process again.

Rho-dependent termination uses a termination factor called rho-factor to stop RNA synthesis at specific sites. This protein binds and runs along the mRNA towards the RNAP. When rho-factor reaches the RNAP, it causes RNAP to dissociate from the DNA, terminating transcription.

Other termination mechanisms include where RNAP comes across a region with repetitious thymidine residues in the DNA template, or where a GC-rich inverted repeat followed by 4 A residues. The inverted repeat forms a stable stem loop structure in the RNA, which causes the RNA to dissociate from the DNA template.

The -35 region and the -10 ("Pribnow box") region comprise the basic prokaryotic promoter, and |T| stands for the terminator. The DNA on the template strand between the +1 site and the terminator is transcribed into RNA, which is then translated into protein. (from Prokaryotic Transcription at Wikipedia)