RNA polymerase catalyzes nucleoside monophosphate group transfer from a nucleoside triphosphate (NTP) to the 3'-end of the growing RNA chain (or the first nucleoside triphosphate) so that chain growth proceeds in a 5'→3'direction. The essential chemical characteristics of RNA synthesis are as follows:

    1. Phosphodiester bond formation takes place as the result of a nucleophilic attack of the 3'-hydroxyl group on the growing chain (or first nucleoside triphosphate) on the α phosphoryl group of the incoming NTP. This is the same type of reaction that takes place during DNA synthesis. Also, as with DNA synthesis, pyrophosphate hydrolysis drives the reaction to completion.

    2. The DNA template sequence determines the RNA sequence. Each base added to the growing 3'-end of the RNA chain is chosen by its ability to pair with a complementary base in the template strand. Thus, the bases C, T, G, and A in a DNA strand cause G, A, C, and U, respectively, to appear in the newly synthesized RNA molecule.

    3. All four ribonucleoside triphosphates (adenosine 5'-triphos-phate [ATP], guanosine 5'-triphosphate [GTP], cytidine 5'-triphosphate [CTP], and uridine 5'-triphosphate [UTP]) are required for RNA synthesis. When a single nucleotide is omitted RNA synthesis stops at the point where that nucleotide must be added.

    4. The RNA chain grows in the 5'→3'direction that is, nucleotides are added only to the 3'-OH end of the growing chain. This direction of chain growth is the same as that in DNA synthesis.

    5. RNA polymerases, in contrast with DNA polymerases, are able to initiate chain growth so that no primer is needed.

    6. 0nly ribonucleoside 5'-triphosphates participate in RNA synthesis. The first base to be laid down in the initiation event is a triphosphate. Its 3'-OH group is the point of attachment for the second nucleotide and its 5'-triphosphate group remains at the 5'-end throughout chain elongation.

    Only one of the two DNA strands in a given chromosome region acts as the template strand, dictating the sequence of the newly synthesized RNA molecule. The complementary DNA strand, the nontemplate strand, has the same base sequence as the RNA molecule (except that U replaces T) and is commonly referred to as the coding or sense strand. Sequence information is usually given for just the coding strand because this information also provides the sequence of the primary transcript (the newly synthesized RNA molecute before it is processed.) Template strand sequence is easily obtained from Watson-Crick base pairing rules.

    By convention, the nucleotide at the transcription start site on the coding strand is designated as position +1, the next nucleotide is at position +2, and so forth. The nucleotide that immediately precedes the transcription start site on the coding strand is at position -1, the nucleotide before that is at position -2, and so forth. Sequences that come after the transcription start site (on the 3'-side) are downstream while those that come be lore it (on the 5'-side) are upstream.