The Central Dogma. 1) A simplified model. 2) Played out across life. 3) Many points for control.

Transcription

1 Molecular Biology

2 The Central Dogma 1) A simplified model. 2) Played out across life. 3) Many dis@nct points for control.

3 Molecular Biology DNA: four bases (GC,AT) (2 bits) code in 3 base codons informa@on storage and propaga@on, gene@c regula@on Protein: folded polypep@de of 20 amino acids mo@lity, metabolism, reproduc@on, gene@c regula@on, transport, etc. Manipula0ng DNA Protein Rela0onships: Revolu@onized biological research (e.g. crystallography, fluorescent proteins as markers) and medicine (e.g. drug manufacture)

4 Overview of Cloning Steps to produce new DNAs that can be used as tools to ask deep biological questions. We are going to see how to construct plasmids which include key features such as the GFP protein, antibiotic resistance, etc. Big Message: Much of the brilliant trickery of modern molecular biology is tied to getting your DNA of interest into some organism.

5 The tools of basic subcloning 1) Plasmids 2) Enzymes 3) Ligase 4) PCR 5) E. coli (and many more)

6 So, what s a plasmid? Plasmid: circular piece of DNA with origin of replication that propagates as separate genetic material in bacterial cells. Plasmids have key features such as: origin of replication, promoter for gene of interest, antibiotic resistance,

7 Plasmid Structure of of pze21 Venus(YFP) Promoter RNA polymerase binding site, regulator Origin of Replica7on site where plasmid begins for division, controls copy number and hence regulates Restric7on Sites sequence specific DNA cleavage sites, leaves s7cky ends for proper insert Kanamycin encodes gene for Kanamycin (fungal) resistance, imparts severe advantage in proper media Non descript DNA contain other sites for gene

8 Building A Stock of Plasmids

9 Molecular Biology By Cut and Paste: Building a Plasmid In order to construct the relevant fusion, we need to do a variety of cutting, amplifying and pasting operations. Once that is done, we need to do a series of controls and checks to make sure we produced what we think we did.

10 Molecular Biology By Cut and Paste: Building a Plasmid Another view of the procedure

11 Restriction Enzymes and Cutting

12 New England Biolabs Website This list shows the sites on the phage lambda genome that will be cut by various restriction enzymes.

13 The Idea of Ligation When we have our fragments (YFP and protein) to insert into the plasmid, we have to glue them in using an enzyme called DNA ligase. In living cells, this is relevant to supercoiling, recombination, DNA repair, replication, etc.

14 Aph 162 Subcloning Genotype Phenotype E. coli expressing protein β-galactosidase E. coli expressing fluorescent protein from jellyfish (YFP)

15 Subcloning Cloning Vector plasmid / (double) digest / gel purifica@on Vector + Insert Insert Liga@on Transforma@on

16 Subcloning Cloning Vector plasmid / (double) digest / gel purifica@on Vector + Insert Insert PCR Liga@on Transform (Electropora@on)

17 The First Cycle of PCR Once we have some copies of our DNA fragments of interest, we need to generate a huge number of copies of these fragments for the purposes of actually generating large quantities of the insert. Video

18 Polymerase Chain High temp (98C) DNA denatures Forward Primer Reverse Primer Lower temp (62C) Primers anneal

19 Polymerase Chain Lower temp (62C) Primers anneal Free Raise temp (72C) Polymerase extends DNA

20 Polymerase Chain 35 cycles = 2 35 copies

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22 PCR Revisited: Constructing the Insert

23 Plasmid HindIII KpnI

24 Plasmid Structure pze21 LacZ pze21 Venus(YFP) HindIII KpnI

25 Vector / Insert Liga@on Vector + Insert + Ligase fluorescent cells blue cells white cells

26 Polymerase Chain