Plasmid Mapping Exercises PDF
Plasmid Mapping Exercises PDF
Plasmid Mapping Exercises PDF
Plasmid Mapping
Restriction enzymes are proteins that separate a DNA molecule at a specific location (locus). Think of them as molecular scissors.
The terms "cut," "digest," or "restrict" may be used to describe the action of a restriction enzyme. Whenever a DNA molecule is cut with
a restriction enzyme, the resulting pieces often need to be reassembled in a map representing the relative locus where the restriction
enzyme cut the DNA molecule.
This is because scientists are usually trying to determine where a specific gene is located in a certain piece of DNA. They start by using
restriction enzymes that act close to either end of the gene of interest. Once the gene has been located on a piece of DNA, it is often
useful to determine where the piece of DNA was originally located. To do this, scientists try to construct a map of the original piece of
DNA using their experimental data.
Because plasmids are rings or circles of DNA, a restriction enzyme that cuts a plasmid once results in a linear piece of DNA that has the
same number of base pairs as the original plasmid. A restriction enzyme that cuts a plasmid twice results in 2 linear pieces of DNA
whose total number of base pairs equals the number of base pairs in the original plasmid. When 2 restriction enzymes cut the same
plasmid, it is referred to as a double digest. It is usually necessary to use at least 2 restriction enzymes to map a plasmid. However, it is
not uncommon for as many as 6 or 8 restriction enzymes to be used.
Plasmid maps normally take the form of a circle. The name of the restriction enzyme and the relative locus where the enzyme cuts the
plasmid are shown on the map. The center of the map is labeled with the total number of base pairs in the plasmid. When teaching
students how to create a plasmid map, it is helpful to use some type of 3-D circular object that you can cut up to demonstrate the
process, e.g., string, rope, or rubber tubing
Mapping a plasmid is basically a game of logic. The key is to remember to account for all experimental data. Think of it as taking a clock
apart and putting it back together again with no parts remaining. We have listed 13 plasmid map problems that we have collected over
the years, most of which are not original. These exercises are a great way to get students to start thinking like scientists. Plasmid
mapping can be done from at least 3 different views. You can present any one of the 3 views to your students, and they should be able
to come up with the other 2.
Start by showing your students how to solve one or 2 simple problems to give them a feel for the process. We have included a sample
plasmid map problem (with a solution guide) for this purpose. Some students will demonstrate a knack for solving these problems while
others will suffer and rue the day plasmid maps entered their classroom—remember, these are basically logic problems. We suggest that
you let students work together in pairs if they wish.
There is no one certain way to do plasmid mapping. Just look for answers that account for all of the experimental data. It is a good idea
for a few students to present their method of plasmid mapping to the whole class. This reinforces the process for the problem solvers
and assists those having trouble. Perhaps the ultimate assessment is to have your students make up some plasmid mapping problems
for their classmates to solve. Consider saving the best problems for reuse in subsequent classes. These make great activities for down
time, e.g., when gels are setting up or during electrophoresis. Have fun with them.
After your students have had a chance at pen and paper problems, they will probably be ready for a more realistic DNA mapping
problem. Carolina DNA mapping kits are a great way to make electrophoresis much more than just running a gel. These kits really get
your students involved—hands on and minds on!
# of
EcoRI
Blank Blank EcoRI BamHI BamHI Blank Blank Blank Base
mm Pairs
0
1
2
Plasmid mapping: Exercise # 1 3
Instructions 4
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6 40
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7
represents about 37–38 bp. 8 24
9
Experimental data 10
11 16
Number of base pairs per band 12
BamHI 24.0 12.0 4.0 13
14
EcoRI 40.0
15 12
EcoRI / 16
16.0 12.0 8.0 4.0
BamHI 17
18
19
20 8
21
22
23
24
25
26 4
27
28
29
30
31
32
33
34
35
36
# of
BamHI
Blank Blank BamHI HindIII base
HindIII Blank Blank Blank
mm pairs
0
1
2
Plasmid mapping: Exercise # 2 3
Instructions 4 52
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7 26
represents about 37–38 bp. 8
9
Experimental data 10
11
Number of base pairs per band 12
BamHI 52.0 13
14 14
HindIII 26.0 12.0 8.0 6.0 15 12
BamHI / 16
14.0 12.0 8.0 6.0
HindIII 17
18
19
20 8
21
22
23
24 6
25
26
27
28
29
30
31
32
33
34
35
36
# of
EcoRI EcoRI EcoRI
Blank Standard HindIIII BamHI BamHI Blank Blank Blank base
HindIII mm pairs
0
1
2
Plasmid mapping: Exercise # 3 3
Instructions 4
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7
represents about 37–38 bp. 8
9
Experimental data 10
11
# of base pairs per band 12
EcoRI / 13
42.8 9.2
HindIII 14 80.0
15
EcoRI /
48.0 4.0 16
BamHI 17
EcoRI / 18 48.0
BamHI / 38.8 9.2 4.0 19 44.0
20 42.8
HindIII
21 40.0
Size 22 38.8
80.0 44.0 40.0 10.0
Standard 23
24
25
26
27
28
29
30
31 10.0
32 9.2
33
34
35 4.0
36
# of
EcoRI
Blank Blank EcoRI BamHI BamHI Blank Blank Blank base
mm pairs
0
1
2
Plasmid mapping: Exercise # 4 3
Instructions 4
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6 40
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7
represents about 37–38 bp. 8
9 22
Experimental data 10
11 16
Number of base pairs per band 12
EcoRI 40.0 13
14
BamHI 22.0 12.0 15 12
EcoRI / 16
16.0 12.0 6.0
BamHI 17
18
19
20
21 6
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
# of
EcoRI EcoRI BamHI
Blank BamHI EcoRI HindIII base
HindIII BamHI HindIII Blank
mm pairs
0
1
2 87.2
Plasmid mapping: Exercise # 5 3
Instructions 4 79.6
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7 72.2
represents about 37–38 bp. 8
9
Experimental data 10
11 64.6
Number of base pairs per band 12
BamHI 87.2 13
14
EcoRI 87.2 15
HindIII 87.2 16
17
EcoRI / 18
79.6 7.6
HindIII 19
EcoRI / 20
72.2 15.0 21 22.6
BamHI
22
BamHI / 23
64.6 22.6
HindIII 24
25
26
27
28 15
29
30
31
32
33
34
35
36 7.6
# of
EcoRI EcoRI BamHI
Blank BamHI EcoRI HindIII base
HindIII BamHI HindIII Blank
mm pairs
0
1 47.8
2
Plasmid mapping: Exercise # 6 3
Instructions 4 33.2
Determine the number of base pairs (bp) in the whole plasmid, and then
5 31.2
determine a scale for your plasmid map. Visualizing the map as a clock face is
helpful. For example, if the total number of base pairs going around the map is 6
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7 28.0
represents about 37–38 bp. 8 24.2
9 20.2
Experimental data 10 19.0
11 18.2
Number of base pairs per band 12
BamHI 33.2 18.2 13
14 15.0
EcoRI 31.2 20.2 15
HindIII 47.8 3.6 16
17
EcoRI / 18 8.6
20.2 19.0 8.6 3.6
HindIII 19
EcoRI / 20
28.0 15.0 5.2 3.2 21 5.4
BamHI
22 5.2
BamHI / 23
24.2 18.2 5.4 3.6
HindIII 24
25
26
27
28 3.6
29 3.2
30
31
32
33
34
35
36
# of
BamHI
Blank Blank BamHI HindIII base
HindIII Blank Blank Blank
mm pairs
0
1 46.0
2 42.0
Plasmid mapping: Exercise # 7 3
Instructions 4 36.0
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6 31.0
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7
represents about 37–38 bp. 8 24.0
9 22.0
Experimental data 10
11
Number of base pairs per band 12
HindIII 42.0 31.0 14.0 13
14 15.0
BamHI 46.0 36.0 5.0 15 14.0
BamHI / 16
24.0 22.0 15.0 14.0 7.0 5.0
HindIII 17
18
19
20
21 7.0
22
23 5.0
24
25
26
27
28
29
30
31
32
33
34
35
36
# of
BamHI
Blank Blank BamHI EcoRI base
EcoRI Blank Blank Blank
mm pairs
0
1 50.0
2
Plasmid mapping: Exercise # 8 3
Instructions 4
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7
represents about 37–38 bp. 8 23.0
9
Experimental data 10
11
Number of base pairs per band 12 15.0
BamHI 23.0 12.0 9.0 6.0 13
14
EcoRI 50.0 15 12.0
BamHI / 16
15.0 12.0 9.0 8.0 6.0 17 9.0
EcoRI
18 8.0
19
20
21 6.0
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
# of
BamHI
Blank Blank BamHI EcoRI base
EcoRI Blank Blank Blank
mm pairs
0
1
2
Plasmid mapping: Exercise # 9 3
Instructions 4
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7
represents about 37–38 bp. 8
9 20.0
Experimental data 10
11
Number of base pairs per band 12
BamHI 20.0 13
14
EcoRI 11.0 6.0 3.0 15
BamHI / 16 11.0
7.0 6.0 4.0 3.0
EcoRI 17
18
19
20 7.0
21 6.0
22
23
24
25
26 4.0
27
28
29 3.0
30
31
32
33
34
35
36
# of
BamHI
Blank Blank BamHI HindIII base
HindIII Blank Blank Blank
mm pairs
0
1
2
Plasmid mapping: Exercise # 10 3 40.0
Instructions 4
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7
represents about 37–38 bp. 8
9
Experimental data 10
11 16.0
# of base pairs per band 12
BamHI 12.0 9.0 6.0 13
14
HindIII 40.0 15 12.0
BamHI / 16
16.0 12.0 6.0 17 9.0
HindIII
18
19
20
21 6.0
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
# of
HindIII
Blank Blank EcoRI HindIII base
EcoRI Blank Blank Blank
mm pairs
0
1
2
Plasmid mapping: Exercise # 11 3
Instructions 4
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7
represents about 37–38 bp. 8 20.0
9
Experimental data 10
11
Number of base pairs per band 12
EcoRI 11.0 6.0 3.0 13
14
HindIII 20.0 15
HindIII/ 16 11.0
8.0 6.0 3.0
EcoRI 17
18 8.0
19
20
21 6.0
22
23
24
25
26
27
28
29 3.0
30
31
32
33
34
35
36
# of
BamHI EcoRI EcoRI EcoRI
Blank BamHI HindIII base
HindIII BamHI Frag. A Frag. B Blank
HindIII mm pairs
0
1
2
Plasmid mapping: Exercise # 12 3
Instructions 4
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7
represents about 37–38 bp. 8 19.5
9
Experimental data 10
11
Number of base pairs per band 12
BamHI 19.5 13
14
HindIII 19.5 15 12.0
BamHI / 16
12.0 7.5
HindIII 17 10.5
18 8.0
EcoRI /
19
BamHI / 10.5 4.5 3.0 1.5 20 7.5
HindIII 21
EcoRI 22
(Fragment 10.5 1.5 23
A) 24
25 4.5
EcoRI 26
(Fragment 4.5 3.0 27
B) 28
29 3.0
30
31
32
33
34
35 1.5
36
# of
Blank BamHI EcoRI HindIII PstI Blank Blank Blank base
mm pairs
0
1
2
Plasmid mapping: Exercise # 13-A 3
Instructions 4
Determine the number of base pairs (bp) in the whole plasmid, and then
5 30.0
determine a scale for your plasmid map. Visualizing the map as a clock face is
helpful. For example, if the total number of base pairs going around the map is 6 28.0
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7 26.0
represents about 37–38 bp. 8
9 22.0
Experimental data 10
11 18.0
Number of base pairs per band 12
BamHI 22.0 18.0 13
14 14.0
EcoRI 26.0 14.0 15 12.0
HindIII 30.0 10.0 16
17 10.0
PstI 28.0 12.0 18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
# of
EcoRI BamHI BamHI HindIII EcoRI EcoRI
Blank BamHI base
PstI HindIII PstI HindIII PstI Blank
mm pairs
0
1
2
Plasmid mapping: Exercise # 13-B 3
Instructions 4
Determine the number of base pairs (bp) in the whole plasmid, and then
determine a scale for your plasmid map. Visualizing the map as a clock face is 5
helpful. For example, if the total number of base pairs going around the map is 6
50, then 6:00 represents 25 bp, 3:00 represents about 12–13 bp, and 9:00 7 26.0
represents about 37–38 bp. 8 24.0
9 22.0
Experimental data 10
11 18.0
Number of base pairs per band 12 16.0
EcoRI / 13
14.0 12.0 10.0 4.0 14 14.0
BamHI
15 12.0
BamHI / 16
18.0 10.0 8.0 4.0
PstI 17 10.0
BamHI / 18
16.0 14.0 8.0 2.0
HindIII 19
20
HindIII / 21
24.0 6.0 4.0
PstI 22 8.0
EcoRI / 23
26.0 10.0 2.0
HindIII 24
25 6.0
EcoRI / 26
22.0 8.0 6.0 4.0
PstI 27
28
29
30 4.0
31
32
33
34
35
36
37 2.0
PstI 24
25 6.0
BamHI / 26
EcoRI / 27
12.0 10.0 4.0 2.0
HindIII / 28
PstI 29
30 4.0
31
32
33
34
35
36
37 2.0