# Biomod/2017/StJohns:Results

## Contents

- 1 Results
- 1.1 Effect of Trehalose on VLP Binding
- 1.2 Tightening of Bands as a Result of Removing Hinge Staples
- 1.3 Distinction Between the Bound and Unbound Version of Unhinged Claw to VLP
- 1.4 FRET Signaling of Bound and Unbound Claw
- 1.5 Yield Produced by Cross-Linking
- 1.6 Binding triangle with fluorescently labeled DNA strand 40%
- 1.7 Purity Check and Quantifying Methylene Blue Strands
- 1.8 Quantifying Methylene Blue strands on Triangle
- 1.9 Attachment of MB strands to Side-Triangle
- 1.10 Fluorescence Polarization Results

## Results

**NOTE:**
**Unless otherwise stated, the agarose gels run (Fig. 12-19) were 0.5X TBE ~10mM Mg ^{2+} 1% denaturing, with 0.5X TBE 10mM Mg^{2+} buffer, run at 25°C and 450-700 volthours.
**

**All gel images have been uploaded in JPEG form, but TIFF forms can be made available upon request.**

### Effect of Trehalose on VLP Binding

**1% Agarose gel; 650 Vhrs **

Lanes

- 0.05 pmol Triangle blunt
- 0.05 pmol Triangle blunt + 0.20 pmol T
_{21}VLP - 0.05 pmol Triangle sticky
- 0.05 pmol Triangle sticky + 0.20 pmol wild type VLP
- 0.05 pmol Triangle sticky + 0.20 pmol old T
_{21}VLP - 0.05 pmol Triangle sticky + 0.20 pmol new T
_{21}VLP (fresh) - 0.05 pmol Triangle sticky + 0.20 pmol new T
_{21}VLP (1 week frozen)

### Tightening of Bands as a Result of Removing Hinge Staples

**1% Agarose; 700 Vhrs**

Lanes:

- 0.05 pmol hinged claw blunt
- 0.05 pmol unhinged claw blunt
- 0.05 pmol hinged claw sticky
- 0.05 pmol unhinged claw sticky

### Distinction Between the Bound and Unbound Version of Unhinged Claw to VLP

**1% Agarose; 690 Vhrs**

Lanes:

- 0.05 pmol unhinged claw blunt
- 0.05 pmol unhinged claw blunt + 0.20 pmol T
_{21}VLP - 0.05 pmol unhinged claw sticky
- 0.05 pmol unhinged claw sticky + 0.20 pmol T
_{21}VLP

### FRET Signaling of Bound and Unbound Claw

**1% Agarose; 680 Vhrs**

Lanes:

- 0.05 pmol unhinged claw sticky (donor only)
- 0.05 pmol unhinged claw sticky (donor only) + 0.20 pmol T
_{21}VLP - 0.05 pmol unhinged claw sticky (acceptor only)
- 0.05 pmol unhinged claw sticky (acceptor only) + 0.20 pmol T
_{21}VLP - 0.05 pmol unhinged claw sticky (donor+acceptor)
- 0.05 pmol unhinged claw sticky (donor+acceptor) + 0.20 pmol T
_{21}VLP

### Yield Produced by Cross-Linking

**20% Denaturing Acrylamide; 400 Vhrs**

Lanes:

- Marker
- 0.05 pmol Triangle + 25 mmol 8 MOP (Crosslinked 0min)
- 0.05 pmol Triangle + 25 mmol 8 MOP (Crosslinked 30 min)
- 0.05 pmol Triangle + 25 mmol 8 MOP (Crosslinked 90 min)
- 0.05 pmol Triangle + 25 mmol 8 MOP (Crosslinked 270 min)
- 0.05 pmol Triangle + 5 mmol 8 MOP (Crosslinked 0 min)
- 0.05 pmol Triangle + 5 mmol 8 MOP (Crosslinked 30 min)
- 0.05 pmol Triangle + 5 mmol 8 MOP (Crosslinked 90 min)
- 0.05 pmol Triangle + 5 mmol 8 MOP (Crosslinked 270 min)
- Plasmid

#### Increased Reaction Time Led to Increased Crosslinking Yield

### Binding triangle with fluorescently labeled DNA strand 40%

**1% Agarose; 680 Vhrs**

Lanes:

- ~0.05pm Uncrosslinked Triangle + T
_{21}Fluorescent Strand - ~0.05pm Uncrosslinked Triangle + T
_{21}Fluorescent Strand - ~0.05pm Uncrosslinked Triangle + T
_{21}Fluorescent Strand - ~0.05pm Crosslinked Triangle (270 min) + T
_{21}Fluorescent Strand - ~0.05pm Crosslinked Triangle (270 min) + T
_{21}Fluorescent Strand - ~0.05pm Crosslinked Triangle (480 min)+ T
_{21}Fluorescent Strand

### Purity Check and Quantifying Methylene Blue Strands

**20% Acrylimide Gel; 794 Vhrs (Imaged using scan for MB before staining)**

Lanes:

- 10 bp Ladder
- 5.0 pmol (TCA)
_{7}MB - 5.0 pmol T
_{21}MB - 0.5 pmol (TCA)
_{7}MB - 0.5 pmol T
_{21}MB - 0.05 pmol (TCA)
_{7}MB - 0.05 pmol T
_{21}MB - 5.0 pmol A
_{21}C10 - 5.0 pmol (TCA)
_{7}MS2 - 0.5 pmol Claw XII ATTO
- Denaturing Dye
- Blank

### Quantifying Methylene Blue strands on Triangle

#### Prestain

**1% Agarose Gel; 487 Vhrs (Imaged using scan for MB before staining)**

Lanes:

- 1kb Ladder
- 0.05 pmol Triangle Blunt + 5.0 pmol T
_{21}MB - 0.05 pmol Triangle Blunt + 5.0 pmol (TCA)
_{7}MB - 0.05 pmol Up Triangle(15) A
_{21}+ 5.0 pmol T_{21}MB - 0.05 pmol Up Triangle(15) A
_{21}+ 5.0 pmol (TCA)_{7}MB - 0.05 pmol Up Triangle(15) (TGA)
_{7}+ 5.0 pmol T_{21}MB - 0.05 pmol Up Triangle(15) (TGA)
_{7}+ 5.0 pmol (TCA)_{7}MB - 0.05 pmol Up Triangle(7) A
_{21}+ 5.0 pmol T_{21}MB - 0.05 pmol Up Triangle(7) A
_{21}+ 5.0 pmol (TCA)_{7}MB - 0.05 pmol Up Triangle(7) (TGA)
_{7}+ 5.0 pmol T_{21}MB - 0.05 pmol Up Triangle(15) (TGA)
_{7}+ 5.0 pmol (TCA)_{7}MB

#### SYBR Stain

**1% Agarose Gel; 487 Vhrs (SYBR stain)**

Lanes:

- 1kb Ladder
- 0.05 pmol Triangle Blunt + 5.0 pmol T
_{21}MB - 0.05 pmol Triangle Blunt + 5.0 pmol (TCA)
_{7}MB - 0.05 pmol Up Triangle(15) A
_{21}+ 5.0 pmol T_{21}MB - 0.05 pmol Up Triangle(15) A
_{21}+ 5.0 pmol (TCA)_{7}MB - 0.05 pmol Up Triangle(15) (TGA)
_{7}+ 5.0 pmol T_{21}MB - 0.05 pmol Up Triangle(15) (TGA)
_{7}+ 5.0 pmol (TCA)_{7}MB - 0.05 pmol Up Triangle(7) A
_{21}+ 5.0 pmol T_{21}MB - 0.05 pmol Up Triangle(7) A
_{21}+ 5.0 pmol (TCA)_{7}MB - 0.05 pmol Up Triangle(7) (TGA)
_{7}+ 5.0 pmol T_{21}MB - 0.05 pmol Up Triangle(15) (TGA)
_{7}+ 5.0 pmol (TCA)_{7}MB

### Attachment of MB strands to Side-Triangle

#### Prestain

**1% Agarose Gel; 581 Vhrs (Imaged using scan for MB before staining)**

Lanes:

- 1kb Ladder
- 0.05 pmol Up Triangle(15) A
_{21}+ 5.0 pmol T_{21}MB - 0.05 pmol Up Triangle(15) (TGA)
_{7}+ 5.0 pmol (TCA)_{7}MB - 0.05 pmol Side Triangle(15) A
_{21}+ 5.0 pmol T_{21}MB - 0.05 pmol Side Triangle(15) A
_{21}+ 5.0 pmol (TCA)_{7}MB - 0.05 pmol Side Triangle(15) (TGA)
_{7}+ 5.0 pmol T_{21}MB - 0.05 pmol Side Triangle(15) (TGA)
_{7}+ 5.0 pmol (TCA)_{7}MB

#### SYBR Stain

**1% Agarose Gel; 581 Vhrs (SYBR stain)**

Lanes:

- 1kb Ladder
- 0.05 pmol Up Triangle(15) A
_{21}+ 5.0 pmol T_{21}MB - 0.05 pmol Up Triangle(15) (TGA)
_{7}+ 5.0 pmol (TCA)_{7}MB - 0.05 pmol Side Triangle(15) A
_{21}+ 5.0 pmol T_{21}MB - 0.05 pmol Side Triangle(15) A
_{21}+ 5.0 pmol (TCA)_{7}MB - 0.05 pmol Side Triangle(15) (TGA)
_{7}+ 5.0 pmol T_{21}MB - 0.05 pmol Side Triangle(15) (TGA)
_{7}+ 5.0 pmol (TCA)_{7}MB