The broad chemical steps in DNA and RNA synthesis are quite similar, in that both processes represent reading of a DNA strand as the template. However, while both strands of DNA have to be copied, transcription is polar because only one strand is normally copied into RNA whose sequence is identical to the other strand (except for replacement of thymidine by uridine). This is achieved by the presence of discrete start and stop signals bracketing “transcription units” corresponding to each gene containing unique sequences, called promoters; their sequences provide the recognition motif for RNA polymerase to bind and start RNA synthesis unidirectionally. Similarly, the stop sequences are recognition motifs for the transcription machinery to stop and fall off the DNA template.
As mentioned before, the two strands of a DNA double helix are of opposite polarity, i.e., one strand is in the 5´→3´ orientation and its complementary strand in the 3´→5´ orientation. Furthermore, the fact that all nucleic acid polymerases can polymerize nucleotide monomers only in the 5´→3´ direction as guided by base pairing with a template does not pose a problem for RNA synthesis because only the 3´→5´ strand of the DNA template is copied. However, DNA replication, where both strands have to be copied in the same 5´→3´ direction of the duplex template, introduces a complication situation (Figs. 2 and 5). The 3´→5´ strand is copied like RNA, while the 5´→3´ strand has to be copied in the opposite direction. It has been observed in all cases that simultaneous replication of both strands is accomplished by continuous copying of the 3´→5´ strand, also called the leading strand, while the 5´→3´ strand is copied after a brief delay when separation of the strands occur, so this nascent strand is called the lagging strand (Fig. 2). The leading strand can be synthesized continuously without interruption, while the lagging strand is synthesized discontinuously after the leading strand is synthesized. The discontinuous fragments are also called Okazaki fragments, named after its discoverer.
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