DNA Sequencing
Materials for each student/pair:
 Paper copy of a DNA Sequencing gel
 Instructions
 4 template strands
 1 set of paper clips
Instructions:
Part 1
1. You will come up with a DNA sequence from the paper copy of a DNA sequencing gel. Write this on your own
paper.
Part 2
2. Each of you will be doing one of the four reactions, A, T, G, or C.
3. Each color of paper clips represents one of the four bases: blue (C), green (T), red/pink (G), purple (A)
4. The stars (***) mean that this is the reaction that contains dideoxynucleotides, the special nucleotides that
terminate the elongation of the DNA sequence. Dideoxynucleotides are represented by white/silver paper clips.
5. Begin to synthesize your DNA. You will add new nucleotides from the 3’ end of the primer. Remember that DNA
replication always goes from the 5’3’. F(ive) is before T(here) in the alphabet.
For Example:
The first nucleotide of the template strand after the primer is an A (it is marked with a #1). You will connect a
green paper clip to the primer. A goes with T, which is represented by a green paper clip.
6. Repeat this process with all four of your template strands. Link your paper clips together as you go.
7. If you pull out a dideoxynucleotide (ddA, ddT, ddC, ddG) your strand ends. Continue with your other strands
until you pull out a ddDNA.
Question: If a cell culture were “fed” some dideoxynucleotides in media, what cellular process, if any,
would be most affected?
All of the other strands continue being elongated.
Notice the white paper clip! This
is a ddT and it terminates the
DNA elongation.
8. When you have completed all of your four strands you will create single stranded DNA.
Question: Would the long template molecule show up in the sequencing gel?
9. As a class we will “run a sequencing gel”.
10. Draw the class gel on your own paper.
11. Now you will come up with a sequence based on this gel.
Part 3.
Now you will read the article “Chain Terminators as Antiviral Drugs”. Answer the following questions:
Questions:
1. How can DNA terminators be useful in fighting AIDS or Herpes?
2. Why are AIDS and Herpes particularly good candidates for using terminators?
3. Why is reverse transcriptase a good candidate for using DNA terminators?
4. Why are only non-phosphorolated dideoxynucleotides used as drugs?
5. How do AZT and ddC work to fight AIDS?
6. How do AZT and ddC affect normal somatic (body) cells?
7. Why is Zovirax not toxic to most somatic cell?
8. How does Zovirax work?