Open complex- closed complex is converted into open complex by melting short region of DNA (-10bp). RNA polymerase bind at promoter region and unwind it and it covers (-55 to +1) 55 bp, and start initiation here one template strand available for incoming nucleotide for base pairing and synthesis of RNA occurs. -10 region of template is essential for recognition, the promoter region are double stranded in closed complex and single stranded in open complex. RNA polymerase has two binding sites for nucleotides: 1) initiation sites 2) elongation sites. Initiation site binds to first nucleotide within open promoter complex at +1 position which is usually a purine-A or G. It means first nucleotide will be ATP or GTP. Elongation site bind with second incoming nucleotide base pairing at +2 positions. Two nucleotides are joined together then the first base is released from the initiation site, and the initiation is complete.
2) Chain elongation: Chain elongation occurs in 5’-3’ direction.RNA synthesis is carried out by transcription bubble which form due to transient separation of double stranded DNA into a single stranded DNA; and transcription takes place at template DNA strand, whichis given below in Figure 28.6.
Figure 28.6 : Elongation of Transcription
RNA chain synthesis occur basically at 5’ end to 3’ end direction by adding nucleotide at 3’ end .The 3’ OH group of last nucleotide is combined to the incoming 5’ ϒ phosphate nucleotide; α and β phosphate groups are removed and only ϒ phosphate is used in the formation of phosphodiester bond. Likewise other nucleotide added which are complementary to template DNA and thus RNA chain strand translocation occurs. In bacteria transcription rate is nearly 40 to 50 nucleotide per second at 370C which is nearly same as the translation in prokaryotes (50 amino acid per second). RNA polymerase bind to promoter and create a transcription bubble .RNA polymerase moves along with DNA and RNA chain grows continuously. The length of transcription bubble is approximately. 12 to 14 bp. Length of DNA RNA hybrid is about 8 to 9 bp. As the RNA polymerase moves, the duplex reforms again. RNA hangs as free polynucleotide chain. Transcription bubble moves continuously by disrupting the DNA structure. Nucleotides are added covalently to 3’ end of the chain of RNA. β and ϒ phosphates are removed from incoming nucleotides and hydroxyl group is removed from 3’ carbon nucleotide presents at end of chain.