Stopping transcription. What can you do with RNA?

How does the RNA polymerase know when to stop transcribing a gene? In E. coli, RNA polymerase will stop transcribing a DNA sequence in one of three ways:

- The RNA polymerase ‘slips off’ the DNA: If you look back to Chapter 1, where you learned about the structure of double-stranded DNA and the zippering that occurs between complementary nucleotides, you’ll notice in Figure 1-17 that there are a different number of bonds (dashed lines) between a G-C pair compared to an A-T pair. A ‘G-C’ complement has three bonds that hold the complementary nucleotides together. An ‘A-T’ pair, has only two bonds. More bonds mean stronger interactions, which means that the bonding strength between A-T is weaker than G-C.

When RNA polymerase is riding along transcribing DNA, it uses the bonds between the transcribed RNA and the DNA (-) template strand to hold itself connected to the DNA. A long stretch of repeat T’s in the DNA’s (+) leading strand (which correspond to A’s in the (-) template strand) results in a string of U’s in RNA (U-U-U-U-U...), each of which also only has two bonds. This results in weak interactions between the RNA polymerase and the DNA, and often the RNA polymerase simply slips off. You will often find stretches of T’s in DNA (U’s in RNA) at the end of a gene. These are placed to cause the RNA polymerase to fall off of the DNA and stop transcription.

- The RNA strand folds up, causing RNA polymerase to fall off - a ‘terminator’: What would happen if ribonucleotides of an RNA string were able to interact with other ribonucleotides in the same string? You’ve seen that two different strands of DNA can come together to form a double helix. Can something similar happen with RNA? Yes!

Because RNA transcripts are quite flexible, they can flip and flop around, allowing nucleotides of the RNA strand to come into contact with one another. A string of RNA can interact with itself, and similar rules apply: A binds to U, G binds to C.

When this happens, a ‘hairpin structure’ can form. In the example in Figure 4-30, you’ll see what is called the bacteriophage 82 late gene terminator. Two regions of the RNA transcript complement well enough to form what is called a stem and loop. The overall structure is called a hairpin, and the formation of the hairpin structure creates physical stress between the RNA transcript in the RNA polymerase. This causes the RNA polymerase to fall off of the DNA. In most cases, there is also a poly-uridine, also called poly-U, segment (U-U-U-U-U...) immediately following the stem. This results in the RNA polymerase slipping off of the DNA, as you saw in the first example.

Figure 4-30. A hairpin is a structure where RNA folds upon itself to create a structure that causes the RNA polymerase to get jammed up and detach from the DNA. Another name for this is a ‘terminator’

- Another protein chases RNA polymerase off the strand: Rho is a protein that has the function of actively stopping transcription from happening. The way Rho works is really cool. As RNA polymerase continues to move downstream and transcribe RNA from DNA, Rho is able to bind near the 5’ end of the new RNA transcript and move downstream on the strand toward the 3’ end as if it is chasing the RNA polymerase (Figure 4-31). The Rho protein eventually catches up to the RNA polymerase and is thought to tug the RNA strand out of the RNA polymerase, resulting in the termination of that transcript.

Figure 4-31. A protein called Rho is able to bind to RNA transcripts. As RNA polymerase is transcribing, Rho will glide up the transcript. When it reaches the RNA polymerase, it can ‘tug’ the RNA out of the polymerase, which stops transcription

What can you do with RNA? You’ve now learned what it takes to start, do, and stop transcription! So, what can you do with RNA?

RNA has many known functions, and many more will be discovered in the coming decades. The most understood use of RNA is the subject of Chapter 5, where we will look at how RNA is read by cellular machinery and translated into proteins. Proteins make up the vast majority of cellular machinery that catalyze chemical reactions or form cell structures.

RNA itself can also cause chemical reactions. ‘Ribo- zymes’ are short strands of RNA that fold in the right way so they can cause chemical reactions to happen. Maybe you have heard of CRISPR-Cas9? An integral part of the CRISPR system working includes using RNA to guide a protein to a specific DNA sequence.

There are many more functions and uses for RNA, and you are now well-equipped to explore further! This is a topic of great interest amongst genetic engineers and you will undoubtedly be able to discover many resources by exploring the web.