DNA Scissors
An Introduction to Fragment Cutting
in Plasmid and Linear forms of DNA.
The picture below is a restriction map of a plasmid. Restriction sites, where enzymes cut at
specific base pairs, are shown on the map. The numbers after the enzyme names tell at what
base pair the enzyme cleaves the DNA. There is an EcoRI site at base pair 1. Your job is to
determine the length of the DNA fragments after the enzyme or enzymes are used to make
their cuts.
1. How long is the entire plasmid?__________________________________
2. Complete the following table for each restriction digest:
Restriction Digest of
Plasmid with:
EcoRI
# of fragments
Size of each fragment in base pairs
BamHI and HindIII
EcoRI,BAMHI and HindIII
10,000 base pairs total
BamHl 7,000
EcoRl 1/10,000
PlaPl
EcoRl 5,000
Hindlll 2,600
3. What is the relationship between the number of cut sites and the number of DNA
fragments for plasmid DNA?
The figure below is the map of the restriction enzyme sites of a plasmid named YIP5. This
plasmid contains 5,541 base pairs. The number after each enzyme name tells where the
enzyme cuts on the plasmid.
HindIII 32
EcoRI 1/5,541
PvuI 4916
EagI 942
YIP5
ApaI 2036
PvuII 3247
SmaI 2540
4. Complete the chart for each of the restriction digests listed below. Remember, to check
your work by making sure that the sum of the fragments is 5,541 for each question.
Restriction Digest of
Plasmid with:
EcoRl
EcoRl and Eagl
Hindlll and Apal
EcoRl, Eagl, and Pvull
Hindlll, Apal, and Pvul
Smal, Apal, and Pvull
# of fragments
Size of each fragment in base pairs
Linear DNA cuts can be determined in a similar way. Below are 3 linear pieces of the same
DNA. It is 5,000 base pairs long. Map the following cuts and complete the table below.
Restriction Digest of Linear DNA
with:
EcoRl cuts at 1,500 and 3,500
#of
fragments
Size of each fragment in base pairs
BamHl cuts at 2300, 3,900 and
4,500
Both EcoRl and BamHl
1
5000
1
5000
1
5000
EcoRl
BamHl
EcoRl &
BamHl
What is the relationship between the number of cut sites and the number of DNA
fragments for linear DNA?
The plasmid below has the restriction
sites as listed. Total length of the
plasmid is 20,000 base pairs.
Draw the fragments for each digestion as they
would appear after electrophoresis. Below each
line write the number of base pairs.
No enzymes
EcoRI
HindIII
BamHI
EcoRI & BamHI
Sample
Wells
HindIII 17,000
BamHI 1/20,000
Size Scale in
Base pairs 8000
6000
4000
EcoRI
14,500
3000
BamHI 5,500
EcoRI 12,000
2000
EcoRI 9,000
1000
500
Below are four pieces of the same 15,000 base
pair DNA molecule. Use a vertical line to show
the cut sites for the digestion with EcoRI & BamHI.
EcoRI
Draw the fragments for each digestion as they
would appear after electrophoresis. Below each
line write the number of base pairs.
No enzymes
4000
3500
2500
5,000
Sample
Wells
Size Scale in
Base pairs 8000
BamHI
6000
6000
4000
3000
2000
4000
HindIII
3000
8000
4500
2500
2000
EcoRI and BamHI
1000
500
EcoRI
HindIII
BamHI
EcoRI & BamHI