1. Transformation
2. Plasmid isolation
3. PCR
4. DNA purification
5. Restriction digestion
6. Ligation
7. SEM assay
8. DLS assay
9. Spectrophotometry assay
10. Reagents

Transformation

Preparation of competent cells - TSS method

For E. coli cells to take up a foreign plasmid, they have to first be made competent - their cell walls must be weakened and made permeable to incoming DNA. This is traditionally done using divalent cations, which mask the negative charge of the phospholipid membrane, allowing the negatively-charged DNA to approach the cell without significant repulsion. The Transformation and Storage Solution (TSS) contains Mg++.

Day 1

Step	Description	Rationale
1	Prepare a primary inoculum of E. coli in 5 mL LB in a test tube.	-
2	Incubate overnight at 37°C, 170 rpm.	-

Day 2

Step	Description	Comments
1	Inoculate 1 mL overnight culture in 100 mL LB medium (1% inoculum)	This protocol yields one aliquot of competent cells per mL of culture. Depending on how many aliquots of competent cells you wish to make, you can vary the volume of LB medium used.
2	Incubate at 37°C, 170 rpm until the OD reaches 0.4 (~1 h 45 min for E. coli DH5α cells)	This is the early exponential phase; cells are physiologically ideal for the preparation of competent cells.
From this point, cells should always be placed in the cold (below 4°C), all buffers should be ice-cold, and all plasticware/glassware should be pre-chilled.
3	Place the culture at 4°C for 45 min	-
4	Spin down the culture at 10000 rpm, 10 min, 4°C	-
5	Resuspend the cell pellet in 1 mL ice-cold TSS buffer	-
6	Spin down the culture at 10000 rpm, 10 min, 4°C	-
7	Make 50-100 µL aliquots in chilled microfuge tubes, snap-freeze in liquid nitrogen and store at -80°C for long-term storage	-

Heat-shock transformation

Step	Description	Rationale
1	Thaw the competent cells on ice for 20 min	-
2	Add 1-5 µL of plasmid DNA (10 pg - 100 ng) directly into the competent cells.	-
3	Gently flick the microfuge tube to mix the cells and the DNA.	-
4	Incubate on ice for 30 min.	-
5	Heat-shock the cells at 42°C for ~45 s	The optimal heat-shock duration varies from 30 s to 90 s depending on strain, batch, and method of preparation. In our experiments, 45 s gave us a high enough transformation efficiency to proceed.
6	Place the cells on ice for 5 min	-
7	Add 950 µL SOC medium.	-
8	Incubate at 37°C, 220 rpm for 1-2 h.	The optimal incubation time varies depending on strain and antibiotic resistance marker used for selection. This step allows the few transformants to replicate and increase their plasmid number in the following generations.
9	Spread plate 100 µL of the culture on a selection plate.	-
10	Spin down the remaining culture at 5000 rpm, 10 min, resuspend in ~100 µL medium, and spread plate on a selection plate.	-
11	Incubate plates overnight at 37°C until transformant colonies are seen.	-

Plasmid isolation

Miniprep

Midiprep

PCR

Simple PCR

Overhang PCR

Colony PCR

DNA purification

Chloroform extraction

Gel purification

Restriction digestion

Single digestion

Double digestion

Overnight digestion

Ligation

Simple ligation

Sequential ligation

Multi-ligation

Scanning Electron Microscopy (SEM) assay

Dynamic Light Scattering (DLS) assay

Spectrophotometry assay

Stocks

LB medium

TSS buffer

Reagent	Volume	Final concentration
2x LB medium	0.5 mL	5% (v/v)
PEG 3350	0.5 mL	5% (v/v)
DMSO	0.5 mL	5% (v/v)
2M MgCl2	0.5 mL	0.1 MgCl2
MilliQ water	8 mL	Up to 10 mL

Alkaline lysis solution I<h2>

Reagent	Volume	Final concentration
glucose	-	50 mM
Tris-Cl (pH 8.0)	-	25 mM
EDTA (pH 8.0)	-	10 mM
MilliQ water	-	-

   <h2>Alkaline lysis solution II<h2>

Reagent	Volume	Final concentration
1 N NaOH	2 mL	0.2 N
10% SDS (w/v)	1 mL	1% (w/v)
MilliQ water	7 mL	Up to 10 mL

   <h2>Alkaline lysis solution III<h2>	

Reagent	Volume	Final concentration
5 M KOAc	60 mL	3 M
glacial acetic acid	11.5 mL	11.5% (v/v)
MilliQ water	28.5 mL	Up to 100 mL

<h2>Chloramphenicol stock solution

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