1. James Chappell & Cheuk Ka Tong
Lab Techniques
James Chappell & Cheuk Ka Tong

2. Contents Page Restriction Enzymes Gel Electrophoresis
Blotting techniques-Southern, Northern and Western
DNA sequencing
Polymerase Chain Reaction (PCR)
Recombinant DNA
Gene Cloning
References/ Recommended Reading

3. Restriction Enzymes
Restriction Nuclease - An enzyme that cleaves a molecule of DNA at any site where a specific short sequence of nucleotides occurs.
2key types
Endonuclease- Cleaves within the DNA molecule
Exonuclease- Cleaves at the ends of the DNA molecule

4. Endonucleases
4 types - classified on subunit composition, cleavage position, sequence-specify and co-factor requirement.
Type II is the main one that is used in gene cloning.
Two key terms
Recognition sites – Nucleotide sequence that is recognised.
Cleavage sites- Phosphodiester bond that is cleaved.

5. Endonucleases
Make break the phosphodiester bond of each of the stands of the double helix.
5’----GAATTC----3’
3’----CTTAAG----5’
5’----G-3’ 5’AATTC----3’
3’----CTTAA--5’ 3’G----5’

6. Endonucleases- Recognition site + Cleavage site

7. Endonucleases- Recognition site
3 Considerations-
Sequence – Determine specificity
Length of sequence- Determines frequency
Palindrome- sequence that reads the same backwards and forwards.
Isoshizomers – Restriction enzymes that recognise the same recognition site

8. Endonucleases- Cleavage site

9. Endonucleases Applications
Allow specific cutting and removal of genes from a complex molecule of DNA.
Complementary sticky ends (cohesive ends) allow joining of DNA molecules.
"The work on restriction nucleases not only permits us easily to construct recombinant DNA Molecules and to analyze individual genes but also has led us into the new era of synthetic biology where not only existing genes are described and analyzed but also new gene arrangements can be constructed and evaluated"
‘Nobel prizes and restriction enzymes’ in GENE (1971)

10. Gel Electrophoresis
Electrophoresis - the migration of charged molecules in an electric field though a solution or solid support
Various types – defined by support used
Paper – amino acids, small peptides
Polyacrylamide – Proteins, small DNA/RNA (<500bp)
Agarose – DNA/RNA
Good preparative and analytical method

11. Gel Electrophoresis
Gel electrophoresis uses a cross-linked polymers (agarose) that contain various pores.
Pores allow molecular sieving, where molecules e.g. DNA, can be separated based upon there mobility through the gel.

12. DNA Gel Electrophoresis
Mobility = Charge + Molecular Dimensions
Charge per nucleic acid is constant
This means separation is based upon length of the DNA molecules and this is how we can separate and identify DNA molecules.

13. DNA Gel Electrophoresis
Linear DNA has a linear relationship to distance migration.
If add molecular markers of known mass can calculate mass of our fragment by plotting a linear plot.

14. DNA Gel Electrophoresis
Other factors determining mobility-
Polymer concentration e.g. Agarose
Conformation of DNA
Electrophoresis

15. DNA Gel Electrophoresis
Detection
Dye e.g. ethidium bromide
Audioradiography 32P,
Blotting (see later)
Uses
Analytical- Can determine size of DNA fragment,
Preparative – Can identify a specific fragment based on size

16. Blotting Techniques
Blotting – Transfer of DNA, RNA or Proteins, typically from a electrophoresis gel to a membrane e.g. nitrocellulose. This membrane can then be subject to further techniques such as hybridization.
Hybridization – Process where two complementary single strands of nucleic acid (DNA or RNA) form a double helix.

17. Blotting Techniques
Using specific probes that are labelled specific sequences of DNA can be identified.
There are three main hybridization techniques which vary in the sample blotted and the probes used;
Northern Blot-Transfer of an RNA sample separated and identified using DNA or RNA probes.
Southern Blot-Transfer of an DNA sample separated and identified using DNA or RNA probes.
Western Blot- Transfer of an Protein sample separated and identified typically using an antibody.

19. Applications
The main use of this technique is to identity any changes in DNA sequencing or genes expressed, e.g. comparing genes expressed by a diseased cell to genes expressed by an healthy cell.
Other uses include- Testing for hereditary disease, Evolutionary history of species, Screening e.g.food supply
Applications to synthetic biology
- identification of various parts in natural organisms,
-?more?

20. DNA Sequencing
DNA Sequencing – Determining the order of nucleotides in a DNA molecule
Key technique as it can give us information about a DNA molecule, e.g. location and order of genes, restriction sites.
In addition, for recombinant DNA gives verification of gene cloning experiments.
2 possible use’s for project – Identify sequence of new part, Checking recombinant DNA.
Various techniques are available.
The key technique used today is Dideoxy method.

21. DNA Sequencing Deoxyribonucleotide acid Dideoxyribonucleotide acid
This is essentially the monomer of DNA. Polymerization of nucleotides occurs by condensation reaction of a 5’ phosphate to a 3’ hydroxyl group
Dideoxyribonucleotide acid
There is no 3’hydroxyl group to allow polymerization.

23. Polymerase Chain Reaction (PCR)
A method for amplifying specific DNA sequences.
Components required:
- Target sequence
- A pair of primers
- dNTPs (ATGC)
- DNA polymerase

24. PCR One PCR cycle involves three steps: - Strand separation (95ºC)
- Hybridization of primers (54ºC)
- DNA synthesis (72ºC)
After n cycles, the sequence is amplified 2n-fold.

25. Polymerase Chain Reaction (PCR)
Five noteworthy features of PCR:
The sequence of the target need not be known.
The target can be much larger than the primers (>10 kb).
Primers do not have to perfectly match flanking sequences.
Stringency can be controlled by temperature and salt (MgCl2).
PCR is very sensitive.

26. Recombinant DNA Technology
The construction of new combinations of unrelated genes.
These novel combinations can be cloned and amplified by introducing them into host cells.

27. Recombinant DNA Technology
A DNA fragment of interest is covalently joined to a DNA vector.
- A vector can replicate autonomously in an appropriate host.
- Plasmids and phage λ are common vectors for cloning in E.coli.

28. Recombinant DNA Technology
The DNA fragment of interest and the plasmid vector are both cut using the same restriction enzyme.
The single-stranded ends of the fragment are complementary to those of the cut plasmid.
The DNA fragment and the cut plasmid are annealed and then joined by DNA ligase.

29. Gene Cloning One of the most useful plasmids for cloning is pBR322.
pBR322 contains genes for resistance to tetracycline and ampicillin.
Different endonucleases can cleave this plasmid at a variety of unique sites.

30. Gene Cloning
Insertion of DNA at the EcoRI site does not alter either of the genes for antibiotic resistance.
However insertion at the SalI or PstI site causes insertional inactivation.
 Basis for selection of cells containing recombinant DNA.

31. References/ Recommended Readings
Chapter 8 – Manipulating Proteins, DNA and RNA
- Molecular Biology of the Cell (4th Edition), Alberts, Johnson, Lewis, Raff, Roberts, Walter, Garland Science
2. Chapter 6- Exploring Genes
-Biochemistry (5th Edition), Berg, Tymoczko, Stryer, Freeman