You digest DNA from the frog Xenopus laevis with the enzyme NotI that produces sticky DNA ends. You can ligate your DNA to (select all that apply)A) blunt AluI ends from Xenopus laevis.B) sticky NotI ends from Xenopus laevis.C) blunt AluI ends from bacteria.D) sticky NotI ends from bacteria.E) sticky EcoRI ends from Xenopus laevis.F) sticky EcoRI ends from bacteria.
What will be an ideal response?
B, D
Clarify Question
• What is the key concept addressed by the question?
o This question addresses restriction enzymes and cloning.
• What type of thinking is required?
o This question is asking you to take what you already know and apply it to this unfamiliar situation.
• What key words does the question contain and what do they mean?
o The frog Xenopus laevis is often used for cell biology research.
o Digesting DNA means to treat it with restriction enzymes.
o Sticky DNA ends are the result of cutting with most restriction enzymes-they have a staggered cut with one strand longer than the other.
Gather Content
• What do you already know about restriction enzymes?
e o Restriction enzymes recognize a specific DNA sequence, ranging from 4 bases to 12 bases, and cleave the DNA at a spcific base within this sequence.
o The recognition sites for most type II enzymes are palindromes. The palindromic DNA sequence reads the same from 5? to 3? on one strand as it does on the complementary strand.
o Given this kind of sequence, cutting the DNA at the same base on either strand produces staggered cuts that leaves sticky ends, or overhangs.
Consider Possibilities
• Consider the different answer options. Which can you rule out?
o Is your NotI-cut frog DNA going to ligate with blunt AluI ends from Xenopus laevis? No, sticky ends need to bind compatible sticky ends.
o Is your NotI-cut frog DNA going to ligate with blunt AluI ends from bacteria? No, sticky ends need to bind compatible sticky ends.
o Is your NotI-cut frog DNA going to ligate with sticky EcoRI ends from Xenopus laevis? No, the sticky ends need to have compatible overhangs.
o Is your NotI-cut frog DNA going to ligate with sticky EcoRI ends from bacteria? No, the sticky ends need to have compatible overhangs.
Choose Answer
• Given what you now know, what information and/or problem-solving approach is most likely to produce the correct answer?
o Is your NotI-cut frog DNA going to ligate with sticky NotI ends from Xenopus laevis? Yes, that should work fine.
o Is your NotI-cut frog DNA going to ligate with sticky NotI ends from bacteria? Yes, that should also work fine-as long as the sticky ends are the same, it doesn't matter where the DNA came from.
Reflect on Process
• Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?
o This question asked what types of DNA would be compatible.
o The question required you to take what you already know and apply it to this unfamiliar situation.
o Did you recognize that all that matters when cloning DNA is whether the pieces have compatible ends?
o Did you realize that frog DNA and bacterial DNA can ligate together if properly cut?
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