# Biomod/2012/TeamSendai/Experiment

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Team Sendai Top

# Gate formation

## AFM image

スケールバーの表示。これが筒であるという根拠。

# Porter functionality

We carried out electrophoresis to see if the target moved and hybridized to Porter of higher bonding energy and if the target was successfully transported through the three Porters.

## Electrophoresis

### DNA sequences

NameSequence (5' to 3')Tm (°C)
Target ACTAGTGAGTGCAGCAGTCGTACCA---
Porter 1 TGGTACGACAAAAAAAATGCTGCACAAAAAAAATCACTAGTAAAAAAAAAA54.8
Porter 2 TGGTACGACAAAAAAAAGCACTCACTAGTAAAAAAAAAA63.9

### Protchol

First, we mixed Porter1 and the target for reaction. Second, we added Porter2, expecting that the target would be passed from Porter1 to Porter2. Finally, we added Porter3, expecting that the target would be passed from Porter2 to Porter3.We waited for 15 minutes at each step, letting the target attach to a Porter of higher bonding energy.

The final concentration of samples were follows.
The target DNA: 0.5 μM
Porter 1,2,3: 1.0 μM
Dilution was performed with 1 x TAE Mg2+. The total volume was 5 μM.

Electrophoresis were performed with:
20% acrylamide gel
1×TAE as running buffers
Constant volt 100 V, 3h

### Results

If the target has passed well through Porters, bands of the target hybridizing with Porter1, 2, and 3 should appear from the left side.In the gel, bands are above each Porter.The result shows that target hybridized with available Porter during the 15 minutes, and then it moved to the Porter that has higher bonding energy during another 15 minutes. Therefore, this indicates that Porter (1, 2, and 3) successfully work as “porter” of the target.

### Comparison of Porter and Toehold

We saw that Porter catches the target more effectively than the toehold structure by our simulations. In addition, we actually confirmed this idea through experiments.

### Protchol

We compared the carrier set of the target as below.

```1. Porter1 and Porter2
2. Toehold A and toehold B
```

First, we mixed the target and Porter1. At the same time, we also mixed the target and toehold A.Second, we added Porter2 to the sample of Porter1 and the target. At the same time, we added toehold B to the sample of toehold B and the target. We waited for 15 minutes at each step, for the sample to react.
The final concentration of samples were follows.
The target DNA: 0.5 μM
Porter 1,2,3: 1.0 μM
Toehold A,B: 1.0 μM
Dilution was performed with 1 x TAE Mg2+. The total volume was 5 μM.

Electrophoresis were performed with:
20% acrylamide gel
1×TAE as running buffers
Constant volt 100 V, 3h

### Results

Fig 2. Lanes are (1) porter1, (2) porter2, (3) Target, (4) toehold A, (it is not indicated in the picture) (5) toehold B, (6) target and porter1, (7) target and porter1 and 2, (8) target and porter2, (9) target and toehold A, (10) target and toehold A and toehold B, (11) target and toehold B, (12) 20kb ladder

The target was passed between porters (lane 7). But the target didn’t attach to toehold A (lane 9). So, the target cannot be delivered by the toehold structure (lane 10)
Similar to the interaction of Porters and the target, Porter1 and Porter2 attached to the target respectively (figure2: lane6 and 8). Also, the target was passed between Porters (lane 7).As for the toehold structure, the target hybridized with toehold B. On the other hand, in the lane of the target and toehold A, the band of the target is still strong (lane 9). So, the target didn’t hybridize with toehold A. It follows that toehold A cannot catch the target only in 15 minutes, and that the target cannot be delivered by using toehold structures. Therefore, we concluded that Porter structure, which has some loops, is more effective and efficient than toehold in terms of catching the target.

# Membrane

## Making mini-gate

We prepared a preliminary step to that cell gate insert into the liposome. We designed a smaller tube and attempted to insert into liposomes using it.

Similar to the cell gate, we stretched single-stranded DNA of 10 bases that can be modified cholesterol from the side of this tube.

We attached cholesterol to the single-stranded DNA, and 　confirmed by electrophoresis.

We expected that these enter into the hydrophobic portion of the liposome. Then, it is likely to that the tube stick to the liposome.

## Making liposome

We examined the appropriate composition of the liposome. And　we decided the composition; DOPC:DSPE-PEG2000: Fructose =　100:1:1000.

### General methods for formation and functional analysis of liposome with DNA

At first, the lipids mixture as follows was prepared.

DOPC　5mM 10μL

DSPE-PEG2000　0.5mM　1μL

Fructose 10mM　50μL

Tube 20μL

Chloroform 70μL

We dry a sample of that composition under argon gas condition.

For liposome formation, 125μL of 1×TAE　Mg2+ were added and incubate for 1 h at room temperature.

When indicated, 1 mM Lucifer Yellow fluorescein was added 1/50 fold of total volume (20 μM final). For DNA staining 1/100 fold Hoechst was added after liposome formations. Fluorescence of DNA by Hoechst was observed by a fluorescence microscope.

As this picture, we observed liposome.　So there seems to be some liposome.

## Confirming Gate attaches to the membrane

We use fluorescein to confirm that the tube insert into the liposome.

For example, We put Lucifer Yellow fluorescein into big liposome and made a hole using the α- Hemorijin into liposomes. Then, we observed that fluorescein was flowing out from it. Alpha-hemolysin is toxin which makes a hole in the cell and is often used in experiments liposome system.

The figure shows that fluorescein flowing out from a liposome.

Therefore, we are sure that observing fluorescein would be a confirmatory experiment which our tube stuck to the liposome or not.

FigureA1 Vesicles dyed by lucifer yellow.Positive control
This is the image of the vesicle which putting α-hemolysin. Dotted yellow line is the position of vesicle.And yellow line area is a domain of a graph expressed by "FigureA2'"'
FigureA2 Gray scale graph
This is the gray scale graph using ImageJ soft.The area of this graph is expressed by FigureA1's yellow line. Z-axis's gray scale is separated to 256 gradation.The differences between maximum and minimum of the gray scale are about 0 gradation.

FigureB1 Vesicles dyed by lucifer yellow Negative control
This is the image only vesicles. Yellow line area is a domain of a graph expressed by "FigureB2'"'
FigureB2 Gray scale graph
This is the gray scale graph using ImageJ soft.The area of this graph is expressed by FigureB1's yellow line. Z-axis's gray scale is separated to 256 gradation.The differences between maximum and minimum of the gray scale are about 10 gradation.

FigureC1 Vesicles dyed by lucifer yellow.
This is the image of the vesicle which putting the cholesterol modified mini "cylinder". Yellow line area is a domain of a graph expressed by "FigureC2'"'
FigureC2 Gray scale graph
This is the gray scale graph using ImageJ soft.The area of this graph is expressed by FigureC1's yellow line. Z-axis's gray scale is separated to 256 gradation.The differences between maximum and minimum of the gray scale are about 5 gradation.

## Biacore

### What's Biacore?

Biacore is the device that monitors the interaction between the biological molecules using optical phenomena called surface plasmon resonance (SPR) in real time, without the use of labels. To study an interaction, one of the interaction partners is immobilized onto the sensor surface of a Biacore sensor chip. Immobilization occurs by direct coupling to the surface or via a suitable molecule already coupled to the surface. It is necessary to choose the most suitable sensor tip by contents of the kind of molecules to immobilize and the analysis.

We used sensor tip L1. The matrix is that: lipophilic groups are covalently attached to carboxymethylated dextran, making the surface suitable for direct attachment of lipid membrane vesicles such as liposomes. After attachment, the lipid bilayer structure is retained, facilitating the study of interactions involving transmembrane receptors in membrane-like environments.

### Immobilization of lipid

1. Set a sensor tip L1 and running buffer on the SPR sensor.

2. Inject 5% Triton X-100 25 μL when the sensor gram becomes steady.

3. Inject lipid suspended in running buffer 100 μL when the sensor gram becomes steady again.

4. Inject 10mM NaOH 5 μL.

5. Inject the lipid 50 μL.

6. Inject 10mM NaOH 5 μL.

7. Repeat 5-6 until the baseline of the sensor gram does not rise.

8. Check the rise in RU levels is 100 RU or under after injection of 100 μg/mL BSA 25 μL.

Running buffer: 10 mM HEPES 150 mM NaCl pH =7.0

BSA: Bovine Serum Albumin

### Measurements of samples

Inject sample 10 μL and start measurement. After end of measurement, inject 10 mM NaOH 5 μL. It is necessary to unify measurement time and RU levels when inject sample.

Sample 1:

min-gate (4.2 nM) 50 μL

Cholesterol 12 μL

Running buffer 38 μL

Sample2:

min-gate 50 (4.2 nM) μL

Running buffer 50 μL