MAKING THE RNA
In bacteria, once the sigma subunit of RNA polymerase recognizes the –10 and –35 regions, the core enzyme forms a transcription bubble where the two DNA strands are separated from each other (Fig. 2.3). The strand used by RNA polymerase is called the template strand (aka noncoding or antisense) and is complementary to the resulting mRNA. The core enzyme adds RNA nucleotides in the 5′ to 3′ direction, based on the sequence of the template strand of DNA. The newly made RNA anneals to the template strand of the DNA via hydrogen bonds between base pairs. The opposite strand of DNA is called the coding strand (aka nontemplate or sense strand). Because this is complementary to the template strand, its sequence is identical to the RNA (except for the replacement of thymine with uracil in RNA).
RNA synthesis normally starts at a purine (normally an A) in the DNA that is flanked by two pyrimidines. The most typical start sequence is CAT, but sometimes the A is replaced with a G. The rate of elongation is about 40 nucleotides per second, which is much slower than replication (∼1000 bp/sec). RNA polymerase unwinds the DNA and creates positive supercoils as it travels down the DNA strand. Behind RNA polymerase, the DNA is partially unwound and has surplus negative supercoils. Just as during replication, DNA gyrase and topoisomerase I either insert or remove negative supercoils, respectively, returning the DNA back to its normal level of supercoiling.
RNA polymerase makes a copy of the gene using the noncoding or template strand of DNA. The RNA has uracils instead of thymines.