1. Restriction Enzyme Digestion
Zelha Nil
Nov-09

2. Today’s Laboratory Objectives
Results of gDNA experiment: the concentration, purity, and integrity of genomic DNA
Digest genomic DNA and plasmids

3. DNA quantification
A UV spectophotometer measures the amount of light particular molecules absorb (Proteins at A280; Nucleic Acids at A260)
Lambert-Beer law describes the relationship between absorptivity coefficient and concentration and is given by the following equation:
A=εbc
Where: b= light path length
c=concentration of substance
ε=extinction coefficient
For DNA the extinction coefficient, ε= 50 ug/ml

4. DNA quantification To Quantify your DNA sample:
A260 x Dilution Factor x 50 ug/ml= concentration of nucleic acids in a sample using a 1 cm pathlength (DF=200)
To estimate the purity of your sample:
A260/A280= ratio of nucleic acids/protein
A260/A280= is optimal for DNA

5. Integrity of genomic DNA
High Quality Genomic DNA
>95% DNA will be of high molecular weight, migrating as intact band near the top of the gel
Very little evidence of smaller fragments indicated by a smear of many different sized DNA fragments

6. Our results (1.0% (w/v) agarose, EtBr staining)
L Z W W W3 W L Z T T T T L
(1.0% (w/v) agarose, EtBr staining)
L: Fermentas GeneRuler™ DNA Ladder Mix; bp DNA ladder
Z: Zelha

7. Restriction Enzymes
Phage (or viruses) invade all types of cells. Bacteria are one favorite target.
Defense mechanisms have been developed by bacteria to defend themselves from these invasions.
Bacteria have evolved a class of enzymes that destroy foreign DNA (eg. Virus DNA).
protect bacteria from bacteriophages (Viruses).
Infecting DNA is cleaved (restricted) by the restriction enzyme(s) preventing it from successfully replicating and parasitizing the cell.

8. Why the bacteria does not kill itself
Why the bacteria does not kill itself? The Restriction Enzyme Modification Systems
If everything gets cleaved, how come the bacteria does not kill itself?
Usually, organisms that make restriction enzymes also make a companion modification enzyme (DNA methyltransferase- methylase) that protects their own DNA from cleavage.
These enzymes recognize the same DNA sequence as the restriction enzyme they accompany, but instead of cleaving the sequence, they disguise it by methylating one of the bases in each DNA strand.

9. RE system
This system is composed of a restriction endonuclease enzyme and a methylase enzyme
Each bacterial species and strain has their own combination of restriction and methylating enzymes.

10. Restriction endonuclease is an enzyme that cuts DNA at internal phosphodiester bonds; different types exist and the most useful ones for molecular biology are those which cleave at a specific DNA sequence.

11. Classification of restriction enzymes
Type 1:
One enzyme with different subunits for recognition, cleavage, & methylation.
The methylation and cutting rxns both require ATP, Mg+2 and S-adenosylmethionine as cofactors.
The enzyme cuts unmodified DNA at some distance (~1000 bp away) from the recognition site (Asymmetrical recognition sequences).
Type 2s:
Asymmetric recognition sequence & cleavage occurs on one side of recognition sequence up to 20 bp away.
Type 3:
Resemble type 1 systems but have symmetrical recognition sequences.

12. Type 2:
Restriction and modification are mediated by separate enzymes so it is possible to cleave DNA in the absence of modification.
The restriction activities do not require cofactors, making them easier to use.
Most importantly; those enzymes recognize a defined, usually symmetrical sequence and cut within it.

13. Nomenclature Smith and Nathans (1973) proposed enzyme naming scheme;
Three-letter acronym for each enzyme derived from the source organism
First letter from genus
Next two letters represent species
Additional letter or number represent the strain or serotypes
For example. the enzyme HindII was isolated from Haemophilus influenzae serotype d.

14. 5’ TGACGGGTTCGAGGCCAG 3’ 3’ ACTGCCCAAGGTCCGGTC 5’
Most type 2 RE recognize and cleave DNA within particular sequences of 4 to 8 nucleotides which have two fold axis of rotational symmetry. Such sequences are often referred as palindromes:
Ex: HaeIII
5’ TGACGGGTTCGAGGCCAG 3’
3’ ACTGCCCAAGGTCCGGTC 5’

15. Ends of restriction fragments;
Blunt ends
Sticky ends
3‘ extensions
5‘ extensions
Importantly, the 5' termini of each strand in the cleavage product(s) retain the phosphoryl group from the phosphodiester bond, the 3' termini are hydroxylated.

16. Blunt ends Some restriction enzymes cut DNA at opposite base
They leave blunt ended DNA fragments
AluI
HaeIII

17. Sticky ends Most restriction enzymes make staggered cuts
Staggered cuts produce single stranded “sticky- ends”

18. Star effect Optimum conditions are necessary for the expected result.
Under extreme conditions such as elevated pH or low ionic strength, RE are capable of cleaving sequences which are similar but not identical to their recognition sequence.
EcoR1→GAATTC
EcoR1 with star activity→NAATTN
(N=any base)

19. General uses of REs Detection of RFLPs
Restriction enzyme map: The location of the restriction enzyme cleavage sites on the DNA molecule
DNA fragments from different species can be ligated to create Recombinant DNA:

20. Example Single digest with EcoRI: Double digest with EcoRI & PstI: 6kb

21. Experimental procedure
Genomic DNA isolated last week and the plasmid DNA isolated before will be digested.
Single digestion with EcoRI
Double digestion with EcoRI & HindIII

22. Group 1 &3: Single digestion Group 2&4: Double digestion
An Enzymatic Unit (u) is defined as the amount of enzyme required to digest 1 ug of DNA under optimal conditions:
2-3 u/ug of genomic DNA
1 u/ug of plasmid DNA
Stocks typically at 10 u/ul