1. Quiz#7 LC710 10/18/10 name___________
Q1 :I have a protein extract made from 1000 different mRNAs (I also have cDNAs for
them). I know this extract contains a single DNA binding protein. I decide to first figure out
what sequence that protein binds and then use this information to Identify the protein.
First, I set up a SELEX screening system with the following paradigm.
I have two outer sequences of 18 nucleotides, followed by two palindromic sequences and then
a degenerate core set of 6 nucleotides (1 strand is depicted) .
5’-CATTCAAATATGTATCCGAGCTAGCTNNNNNNAGCTAGCTGATAAATGCTTCAATAAT-3’
After multiple rounds of selection, I obtain the following sequencing results
5’-CATTCAAATATGTATCCGAGCTAGCTTAATTGAGCTAGCTGATAAATGCTTCAATAAT-3’
5’-ATTATTGAAGCATTTATCAGCTAGCTCAATTAAGCTAGCTCGGATACATATTTGAATG-3’
(1pt) What is the 6 nucleotide consensus sequence: _ _ _ _ _ _
(1pt) What is odd about your result?:____________________________________________
(1pt) What did you have to do in order to find the consensus? _______________________
(be specific)

2. Q2:
You set up the following one-hybrid screening system using the consensus sequence :
Draw an arrow as to where you would place your consensus sequence
In the plasmid below. Is there a benefit to putting more than 1 site (1pt)?
_____________________________________________________________
What does the red box represent in this experiment (1pt)?___________________________
(be specific)
Plasmid above has a minimal promoter (TATA box)
Q3:
Using the 1000 different cDNAs from Q1, please describe what you will fuse them to and why?(2pts)