1. CHAPTER 4 DNA CLONING (cont.) MISS NUR SHALENA SOFIAN

2. Steps in Gene Cloning : The use of pBR322 as vector Contains genes that confer resistance to antibiotics: ampicillin and tetracycline Also contains one cutting site for RE e.g. EcoRI, PstI, HindIII, SalI E.g - Cut the foreign DNA and plasmid with PstI yielding both DNA with sticky ends - combining both DNA and ligate them together

3. Transform the recombinant plasmid into host E. coli To make the E.coli permeable to the extracellular plasmid, incubate the cells with calcium salt solution / electroporation – cells are competent PROBLEMS : HOW CAN ONCE SORTED OUT THE RIGHT RECOMBINANTS? – Religated plasmid – Religated insert – Recombinants

4. Foreign DNA which has been cut with PstI is inserted within Amp R gene After transformation, cells are grown in media of tetracycline – cells with plasmid will grow Grow copies of the original colonies with ampicillin which kills cells with plasmid including foreign DNA

5. Screening With Replica Plating Replica plating transfers clone copies from original tetracycline plate to a plate containing ampicillin A sterile velvet transfer tool can be used to transfer copies of the original colonies Desired colonies are those that do NOT grow on the new ampicillin plate

6. pUC plasmids are based on pBR322 – having MCS The procedure shown seeks to clone the human β-globin gene into a plasmid vector The vector carries two important genes amp R  Confers antibiotic resistance to the host cell lacZ  Encodes β-galactosidase Provides a means by which bacteria that have picked up the cloned gene can be identified Steps in Gene Cloning: The use of pUC as vector

7. Nonrecombinant: recircularized Recombinant: vector plus inserted cloned gene Selection for vector: ampicillin resistance Selection for recombinant vs. nonrecombinant vector: β-galactosidase activity Selection for gene of interest?

8. The growth media contains two relevant compounds: IPTG (isopropyl-b-D-thiogalactopyranoside) A lactose analogue that can induce the lacZ gene X-Gal (5-bromo-4-chloro-3-indoyl-β-D-galactoside) A colorless compound that is cleaved by β-galactosidase into a blue dye The color of bacterial colonies will therefore depend on whether or not the β-galactosidase is functional If it is, the colonies will be blue If not, the colonies will be white In this experiment Bacterial colonies with recircularized vectors form blue colonies While those with hybrid vectors form white colonies

10. Note: In this case, the β-globin gene was inserted into the plasmid It is also possible for any other DNA fragment to be inserted into the plasmid And it is possible for the plasmid to circularize without an insert This is called a recircularized vector This is termed a hybrid vector

11. Cells that are able to take up DNA are called competent cells This step of the procedure is termed transformation.

13. PROBLEMS: cloning into pUC can give false-positive results having white colonies without inserts – vector religating itself Treating with alkaline phosphatase – removes the 5’-phosphates necessary for ligation Vector cannot religate to itself but can ligate to the inserts which retain its 5’-phosphates

14. The net result of gene cloning is to produce an enormous amount of copies of a gene During transformation, a single bacterial cell usually takes up a single copy of the hybrid vector Amplification of the gene occurs in two ways: 1. The vector gets replicated by the host cell many times 2. The bacterial cell divides approximately every 30 minutes Recombinant DNA technology is not only used to clone genes Sequences such as telomeres, centromeres and highly repetitive sequences can be cloned as well

15. Steps in Gene Cloning: The use of phage as vector

16. A plaque is a clear area on an otherwise opaque bacterial lawn on the agar surface of a petri dish It is caused by the lysis of bacterial cells as a result of the growth and reproduction of phages Plaques

17. Other phage vectors used in gene cloning λ phage – can accommodate large foreign DNA – usually useful in constructing genomic libraries e.g. Charon 4 λ phage can accept 20kb DNA Cosmids – behaving as both plasmids and phages. Having ‘cos’ sites and plasmid origin of replication. Large inserts of 40-50kb M13 phage – filamentous phage. DNA inserts can be in single stranded form Phagemids – having the same characteristics as cosmids and produce ssDNA e.g pBluescript

18. Eukaryotic Vectors Ti plasmid of Agrobacterium tumefacians carrying genes into plant cells YAC BAC – designed for cloning huge pieces of DNA