Name
LAB REPORT 2: Enzyme Interaction With DNA
40 points
1
(5) What is the difference between an endonuclease and an exonuclease? What effect would you
expect each to have on cut and uncut pRHR53? Why?
2
(5) What is the difference between a site-specific endonuclease and a general endonuclease? How
would you expect the lanes on a gel to differ if you cut the same DNA with each type of enzyme?
Why?
3
(5) What is the concentration of pRHR53 (consult the syllabus or GE web page)? How many g of
DNA did you use for each reaction?
4
(10) Write the Methods and Materials for Experiment 5.
5
(10) Attach a copy of the gel for Experiment 5.
6
(30) Analyze the results of your gel by completing the table. For each enzyme use a (+) or (--) to
indicate whether it acts on each substrate. In the last column, briefly describe the appearance of the
lane and explain the result.
Enzyme
Circular
Linear
Circular
SS
Linear
SS
Appearance of Lane & Explanation
No Enzyme
HindIII
DNase I
 exonuclease
T5 exonuclease
Mung Bean
nuclease
7
(5) Complete the table using information in Appendix 10 or the New England Biolabs catalog.
Enzyme
Conc
(U/ml)
# Units
per rxn
Unit Definition
BglII
HindIII
DNase I
 exonuclease
T5 exonuclease
Mung Bean
nuclease*
*stock was diluted 1/10
8
(10) Write the Methods and Materials for Experiment 6.
9
(10) Attach a copy of the gel for Experiment 6
10
(30) Analyze the results of your gel by completing the table. For each substrate check the appropriate
box to indicate whether or not it was cut by each REase.
Substrate
REase
none
 DNA treated
with M.EcoRI
R.EcoRI
R.BamHI
none
 DNA treated
with M.BamHI
R.EcoRI
M.BamHI
Cut
Uncut
Explanation
11
(20) Complete the table using information in Appendix 10 or the New England Biolabs catalog.
Indicate where the cuts are made and use an asterisk to indicate the base that is modified by the
MTase.
Enzyme
Recognition
Sequence
Conc
(U/ml)
Unit Definition
M.EcoRI
R.EcoRI
M.BamHI
R.BamHI
12 (5) What is the concentration of  DNA (consult Appendix 10)? How many g of  DNA did you use in
each reaction?
13 (5) Draw a diagram of S-adenosyl methionine.
Grade = Total Points x 40 points
150