Download Special enzymes, called restriction enzymes, can cut DNA fragments

Simulating Recombination in Snorks
Introduction
A transgenic, or genetically modified, organism is one that has been altered through
recombinant DNA technology, which involves either the combining of DNA from different genomes or
the insertion of foreign DNA into a genome. To mix and match genes in animals, often times a viral vector
is used to carry the desired gene into the target species. To do so, a piece of the viral DNA is cut out and
replaced with the foreign DNA. When the virus infects a cell of the target species, it injects its DNA into
the host cell, which is then incorporated into the host cell’s own DNA.
Special enzymes, called restriction enzymes, can cut DNA
fragments from almost any organism. Typically, restriction
enzymes are used to cut DNA molecules into individual
genes. There are many different restriction enzymes, each of
which recognizes one specific nucleotide sequence. Many
restriction enzymes work by finding palindrome sections of
DNA (regions where the order of nucleotides at one end is
the reverse of the sequence at the opposite end). This way a
restriction enzyme can cut tiny sticky ends of DNA that will
match and attach to sticky ends of any other DNA that has
been cut with the same enzyme. DNA ligase is an enzyme
that joins the matching sticky ends of the DNA pieces from
different sources that have been cut by the same restriction
enzyme.
Once a desired DNA fragment has been isolated and cut with
specific restriction enzymes, the sticky ends of both the
desired DNA fragment, and the vector’s DNA, which has
been cut by the same restriction enzyme, can be joined
together, forming recombinant DNA. This DNA then gets packaged into a protein coat to form the virus
that carries the gene to the target species.
In this exercise, you will simulate the process of forming recombinant DNA using paper models. You must
find appropriate restriction enzymes that can cut the gene of interest out of the Snike DNA and splice it
into the viral DNA using the matching sticky ends of DNA cut by the selected enzymes.
Snike Genes
Trait
Fur
Purple body
Short, curly tail
Horns
Wings
Amino Acid Sequence
Phe-Gln-Gly-Ala
Asn-His-Trp
Arg-Asn-Pro-Glu
Tyr-Leu-Cys
Lys-Ile-Ala-Ser-Pro
Correct Enzymes
2 and 3
9 and 6
8 and 9
9 and 7
3 and 8
Set Up
1. Cut out the Viral DNA Sequence strips along the dotted lines and tape them together into one long
strip so that the matching numbers on the ends of the strips overlap. The letters should all be in
the same direction. This is your Viral DNA.
2. Cut out the Snike DNA Base Sequence Strips along the dotted lines and tape them together in
numerical order. This is your Snike DNA, which contains all of the Snike genes listed on your
worksheet. The genes are in bold.
3. Decide which Snike trait you would like to add to the Snork genome. Your Snorks will exhibit all of
their existing traits plus this additional trait. Find the gene sequence in the Snike DNA and use a
highlighter or colored pencil to shade in the gene sequence.
4. Cut out the Restriction Enzyme Sequence Cards along the dotted lines. Each card shows a
sequence where a particular restriction enzyme cuts DNA.
Enzyme Selection
5. Compare the sequence of base pairs on an enzyme card with the sequences of the viral base pairs.
If you find the same sequence of pairs on both the enzyme card and the virus strip, mark the
location on the virus with a pencil, and write the enzyme number in the marked area. Repeat this
step for each enzyme card. Some enzyme sequences may not have a corresponding sequence on
the virus, and that some enzyme sequences may have more than one corresponding sequence on
the virus. In this step, you are simulating the process of choosing the correct restriction enzyme to
recombine your DNA. With hundreds of restriction enzymes available, scientists must determine
which one will work for the DNA they want to recombine. *Note: to make this step easier,
restriction sites are shaded.
6. Once you have identified all corresponding enzyme sequences on the virus, identify those
enzymes that cut the virus only once and discard the rest.
7. Next, compare the enzymes you chose in step 6 against the Snike DNA strip. Find any enzymes that
will make two cuts in the DNA, one above your desired Snike gene sequence (that you colored in
step 3) and one below the gene sequence. Mark the areas on the Snike DNA strip that each enzyme
will cut and make a note of which enzyme cuts in that spot.
8. Select two enzymes to use to make the cuts. The goal is to cut the Snike DNA strand as closely as
possible to the desired gene sequence without cutting into the gene sequence. Make cuts on both
the viral DNA and the Snike DNA strips. Make the cuts in the staggered fashion indicated by the
black line on the enzyme card.
Recombinant DNA Construction
9. Tape the sticky ends (the staggered ends) of the virus to the sticky ends of the Snike gene to create
their recombinant DNA. In the lab, DNA ligase is used to bind the strands together.
Congratulations! You have successfully created a virus that contains a Snike gene. This virus can be
used to infect Snork cells and insert the Snike gene into their genome.