Chapter 13.5, Problem 1CS

Core Skill: Modeling The goal of this modeling challenge is to increase the complexity of the model shown in Figure 13.8d by including sequences in the crRNA and bacteriophage DNA that bind to each other.

Modeling Challenge: For simplicity, the structure of the crRNAs in Figure 13.8 is shown shorter than it really is. Let’s suppose that the part of a crRNA that recognizes the bacteriophage DNA is 20 nucleotides long with the following base sequence: 3'-GAUCCCAUACGGCUAAUCAA-5'. (Note: This is only part of the sequence of the crRNA; it does not include the part that binds to tracrRNA.) Suppose this crRNA is within a tracrRNA-crRNA-Cas9 complex, and draw a model that shows the binding of the complex to a bacteriophage. The general features of the model should be similar to those in Figure 13.8d, except you should include the sequences of the crRNA and the bacteriophage DNA that bind to each other. Label the 5' and 3' ends of the tracrRNA, crRNA and bacteriophage DNA.

Figure 13.8 The CRISPR-Cas system of genome defense in bacteria. The system shown here is a type II system, which is found in the chromosome of certain bacterial species but not in archaea. (a) Organization of the CRISPR-Cas system in a bacterial chromosome. This drawing shows a typical organization, but different species have variations. (b–d) A simplified mechanism of the CRISPR-Cas system. The defense occurs in three phases, called adaptation, expression, and interference.