Dr. Bernard Yurke 1 Protocol for mixing DNA origami samples from ...

Created by: Hieu Bui Date: 05 – 29 – 2009
Advisor: Dr. Bernard Yurke
Protocol for mixing DNA origami samples from Caltech
General Safety procedures
1. Personal protective equipment must wear during the experiment (mandatory: lab
coat, gloves, and goggles). Gloves and splash goggles are kept on the shelf under
the sample prep counter in ET 109.
2. After handling chemicals, washing hands is mandatory before eating or leaving
the lab area. When the work is done for the day and the chemicals are put away,
and the gloves and goggles are removed, wash hands again before going on to
other tasks.
3. Copies of the MSDS for all solutions (DNA oligomers, TAE buffer, and
Magnesium chloride) must be kept in ET 109.
4. Contaminated solid waste, such as used gloves, pipette tips, and centrifuge tubes
will be disposed of in the bucket labeled “Solid Waste” in MEC 109 and the lid
will be replaced on the bucket after waste is added. If the bucket is full, contact
Environmental Health and Safety to come pick it up.
Supplies needed:
1. Protective gloves and splash goggles
2. Pipettes & tips
3. Microcentrifuge tubes
4. Viral M13mp18 at 52 nM
5. Smiley, rectangle without stripe and triangle staple strands at 750 nM
6. 10X TAE Mg++
7. Milli-Q water
**Note: above solutions can be found in freezer section. Please take it out and thaw at room temperature
for 30 minutes before mixing.
Procedure:
Making 15 nM smiley face solution:
1. Pipette 10 uL smiley staple strands into a vial
2. Pipette 15 uL viral M13mp18 into vial (1)
3. Pipette 5 uL 10X TAE Mg++ into vial (1)
4. Pipette 20 uL Milli-Q water into vial (1)
5. Label properly (sample, concentration, date)
6. Place vial (1) into thermal cycler machine
7. Select program DNA2 and hit enter to anneal
8. After 2hr30min, take out the vial and store in refrigerator
Making 15 nM triangle solutions:
1. Pipette 10 uL triangle staple strands into a vial
2. Pipette 15 uL viral M13mp18 into vial (1)
3. Pipette 5 uL 10X TAE Mg++ into vial (1)
4. Pipette 20 uL Milli-Q water into vial (1)
5. Label properly (sample, concentration, date)
6. Place vial (1) into thermal cycler machine
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Created by: Hieu Bui Date: 05 – 29 – 2009
Advisor: Dr. Bernard Yurke
7. Select program DNA2 and hit enter to anneal
8. After 2hr30min, take out the vial and store in refrigerator
Making 15 nM rectangles without stripe solution:
1. Pipette 10 uL rectangle staple strands into a vial
2. Pipette 15 uL viral M13mp18 into vial (1)
3. Pipette 5 uL 10X TAE Mg++ into vial (1)
4. Pipette 20 uL Milli-Q water into vial (1)
5. Label properly (sample, concentration, date)
6. Place vial (1) into thermal cycler machine
7. Select program DNA2 and hit enter to anneal
8. After 2hr30min, take out the vial and store in refrigerator
**Note: One rectangle solution is already mixed, one just needs to re-anneal and dilute
them down to appropriate concentration to image.
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