1. Restriction Digestion and Analysis of Lambda DNA Kit

2. What can you do with the Restriction Digestion and Analysis of Lambda DNA Kit?
Understand the use of restriction enzymes as biotechnology tools
Become familiar with principals and techniques of agarose gel electrophoresis
Generate a standard curve from a series of DNA size fragments
Estimate DNA fragment sizes from agarose gel data

3. What are restriction enzymes?
Evolved by bacteria to protect against viral DNA infection
Endonucleases = cleave within DNA strands
3,139 known enzymes

4. How does it work? Enzyme Site Recognition
Each enzyme digests (cuts) DNA at a specific sequence  restriction site
Enzymes recognize 4-, 6- or 8- base pair, palindromic sequences
Isoschizomers recognize identical sequences, but have different optimum reaction conditions and stabilities
Can be unambiguous or ambiguous
Unambiguous
Ambiguous

5. Palindromic Sequences
5’ versus 3’ overhang: Sticky Ends
5’ GAATTC 3’
3’ G 5’
5’ G ’
3’ CTTAAG 5’
Enzyme cuts 
5’ G ’
3’ CTTAA 5’
5’ AATTC 3’
3’ G 5’
Generates 5’ overhang
5’ and 3’ versus Blunt ends

6. Common Restriction Enzymes
5’ GAATTC 3’
3’ CTTAAG 5’
EcoRI
Escherichia coli
5’ overhang
HindIII
Haemophilus influensae
PstI
Providencia stuartii
3’ overhang
5’ AAGCTT 3’
3’ TTCGAA 5’
5’ CTGCAG 3’
3’ CACGTC 5’

7. What is needed for restriction digestion?
Template DNA, uncut DNA, often bacterial phage DNA
DNA standard or marker, a restriction enzyme of known fragment sizes
Restriction enzyme(s), to cut template DNA
Restriction Buffer, to provide optimal conditions for digestion

8. Lambda Phage DNA Genomic DNA of a bacterial virus
Attacks bacteria by inserting its nucleic acid into the host bacterial cell
Replicates rapidly inside host cells until the cells burst and release more phages
Harmless to man and other eukaryotic organisms

9. Restriction Enzyme Digestion
Restriction Buffer provides optimal conditions
NaCl provides the correct ionic strength
Tris-HCl provides the proper pH
Mg2+ is an enzyme co-factor

10. DNA Digestion Temperature
Why incubate at 37C?
Body temperature is optimal for these and most other enzymes
What happens if temperature is too hot or cool?
Too hot = enzyme may be denatured, killed
Too cool= enzyme activity lowered, requiring longer digestion time

11. Agarose Gel Electrophoresis
Electrolysis: the splitting of water using electricity
current splits water into hydrogen ions (H+) and hydroxyl ions (OH-)
Electrophoresis: a method of separating charged molecules in an electrical field; DNA has an overall negative charge
Used to separate DNA fragments by size

12. Components of an Electrophoresis System
Power supply and chamber, a source of negatively charged particles with a cathode and anode
Buffer, a fluid mixture of water and ions
Agarose gel, a porous material that DNA migrates through
Gel casting materials
DNA ladder, mixture of DNA fragments of known lengths
Loading dye, contains a dense material and allows visualization of DNA migration
DNA Stain, allows visualizations of DNA fragments after electrophoresis
Ions: atoms that have a positive or negative charge because they have lost or gained electrons.
Electrophoresis: migration of ions at different speeds is a basic principal

13. - + Cathode Anode Buffer Dyes Agarose gel Power Supply
The electrode at which electrons enter the gel box from the power supply (along the black wire) is called the cathode and is negative (-). The electrode at which electrons leave the box and re-enter the power supply (along the red wire) is called the anode and carries a positive charge (+). The flow of electrons sets up a potential energy difference between the electrodes. This is known as potential, and is measured in volts. It establishes an electric field through which the ions in the gel box fluid migrate. The migration of ions in the fluid creates electrical current which is measured in milliamperes (milliamps).

14. Bio-Rad’s Electrophoresis Equipment
Power Supplies
Precast Ready
Agarose Gel

15. Electrophoresis Buffer
TAE (Tris-acetate-EDTA) and TBE (Tris- borate-EDTA) are the most common buffers for duplex DNA
Establish pH and provide ions to support conductivity
Concentration affects DNA migration
Use of water will produce no migraton
High buffer conc. could melt the agarose gel

16. Agarose Gel A porous material derived from red seaweed
Acts as a sieve for separating DNA fragments; smaller fragments travel faster than large fragments
Concentration affects DNA migration
Low conc. = larger pores better resolution of larger DNA fragments
High conc. = smaller pores better resolution of smaller DNA fragments

17. DNA Staining Allows DNA visualization after gel electrophoresis
Ethidium Bromide
Bio-Safe DNA stains

18. Complete a Gel Electrophoresis simulation at:
Agarose Gel
DNA Fragments
Complete a Gel Electrophoresis simulation at:

19. Restriction Enzyme Digest and Analysis Procedures

20. Actual Results of Restriction Enzyme Digestion
Lane 1, DNA markers (HindIII lambda digest)
lane 2, uncut lambda DNA
lane 3, lambda DNA digested with PstI
lane 4, lambda DNA digested with EcoRI
lane 5, lambda DNA digested with HindIII

21. Analysis of DNA Fragments
Determine restriction fragment sizes
Create standard curve using DNA marker
Measure distance traveled by restriction fragments
Determine size of DNA fragments

22. DNA Marker Standard Curve
Size (bp) Distance (mm)
23, 9, 6, 4, 2, 2,

23. Factors Affecting Restriction Enzyme Digestion
Temperature, restriction enzymes are sensitive to prolonged periods of exposure to heat
Cross contamination of restriction enzymes
Buffer, optimum pH
Incubation temperature, maintain optimum temperature during restriction enzyme activity
And Finally…Don’t forget to ADD your restriction enzyme to the reaction!!!