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Confused on how to do this 2. Two bases in the region indicated by oval A in the above figure are colored yellow. The bases

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2. Two bases in the region indicated by oval A in the above figure are colored yellow. The bases are part of the protospacer adjacent motif (PAM) which is important for Cas 9 recognition of the target DNA. Shown below are two views of the PAM with interacting amino acids. Note: the right panel excludes some residues for clarity. A) In the right panel, identify the nucleotides (bases) and the amino acids (i.e. name the nucleotide(s) and amino acid(s)). Indicate with a dotted line any potential H-bond or ionic interactions between them. (4 pts.) B) What element of nucleic acid secondary structure do you expect this interaction to occur in? Be as specific as possible. (2 pts.) C) In the left panel a number of forces likely stabilize the residues (nucleotides and amino acids) shown. Briefly describe what forces may stabilize this region and between what specific elements? (2 pts.) 2. Two bases in the region indicated by oval A in the above figure are colored yellow. The bases are part of the protospacer adjacent motif (PAM) which is important for Cas 9 recognition of the target DNA. Shown below are two views of the PAM with interacting amino acids. Note: the right panel excludes some residues for clarity. A) In the right panel, identify the nucleotides (bases) and the amino acids (i.e. name the nucleotide(s) and amino acid(s)). Indicate with a dotted line any potential H-bond or ionic interactions between them. (4 pts.) B) What element of nucleic acid secondary structure do you expect this interaction to occur in? Be as specific as possible. (2 pts.) C) In the left panel a number of forces likely stabilize the residues (nucleotides and amino acids) shown. Briefly describe what forces may stabilize this region and between what specific elements? (2 pts.)

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