GC-rich segments

Two symmetrical GC-rich segments in the transcript have the potential to form a stem-loop structure... 

RNA Polymerase slows down, or pauses, when it reaches the first GC-rich segment, because the stability of G-C base pairs makes the template hard to unwind. In vitro, RNA polymerase does pause for several minutes at a GC-rich segment. 

The pausing gives time for the complementary GC-rich parts of the nascent transcript to base-pair with one another. In the process, the downstream GC-rich segment of the transcript is displaced from its template (or from that part of the enzyme molecule to which it is bound see Figure 26.8b). Hence, the ternary complex of RNA polymerase,... 

In the Z-conformation (3), which can occur within GC-rich regions of B-DNA, the organization of the nucleotides is completely different. In this case, the helix is left-handed, and the backbone adopts a characteristic zig-zag conformation (hence Z-DNA ). The Z double helix has a smaller pitch than B-DNA. DNA segments in the Z conformation probably have physiological significance, but details are not yet known. 

The termination that is not dependent on p, is controlled by the specific sequence in DNA termed termination sites (terminators). The terminators that signal the termination and release of RNA transcript, code for GC-rich inverted repeats punctuated by a nonrepeating segment between them just preceding the 3 polyU (U(j-g)-end of the transcript. Therefore a G C-rich stem/loop structure (hairpin) is formed between the inverted repeats preceding the 3 -polyU end of the transcript. The stem/loop structure causes a pause in the RNA polymerase and resulting dissociation of the RNA transcript form the DNA template. 

One of the first, historically, is the modelling of the denaturation of DNA. When a solution of DNA is heated, the double stranded molecules denature into single strands. In this process, looping out of AT rich regions of the DNA segments first occurs, followed eventually by separation of the two strands as the paired GC segments denature. This denaturation process corresponds to a phase transition [69]. 

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