Porins are beta-barrel proteins that cross the cell membranes that result in a hole. Some porins even allow full length DNA to pass through them. Regulation of these porins is important to allow passage of the right substances and exclusion of all others. Analyze the X-Ray structure of porin-regulator OmpR with DNA (PDB=6LXN) and answer the following questions.

(NOTE: I BELIEVE YOU NEED TO LOAD THE STRUCTURE INTO A MOLECULAR VISUALIZATION SOFTWARE TO ANSWER THE PARTS FOR THIS ONE QUESTION)

a. Give the nucleotide sequence for both strands. b. Describe whether the DNA strand is in the A-, B-, or Z-DNA conformation and briefly explain how you determined this. c. Determine the P-P distance across the major groove. d. Determine the P-P distance across the minor groove. e. Draw the chemical structure (level of atoms and bonds) of the hydrogen bonding interactions of one pair of nucleobases of the DNA segment. Identify which residues you chose. f. Use Wallaces rule to calculate the expected Tm of the oligonucleotide. g. Sketch a melting curve for the oligonucleotide based on part f. h. Include on your curve in part (g) what would happen to the melting curve if the nucleotide was lengthened. i. Include on your curve in part (g) what would happen to the melting curve if the nucleotide contained a single base-pair mismatch. j. Identify the amino acid residues on OmpR that interact with the oligonucleotide via electrostatic interactions (a.k.a. salt bridges). [Note: Provide both the amino acid and #.] k. Identify the amino acid residues on OmpR that interact with the oligonucleotide via other non- covalent interactions. [Note: Provide the amino acid, #, and type of interaction.] l. How many possible nucleotides of the same length as the one in 6LXN are possible with the number of types of nucleotides common in living organisms on this planet?