Koch Lab:Protocols/Optical Tweezers

Userboxes This equipment incorporates components from Mad City Labs This equipment incorporates components from ThorLabs This equipment incorporates components from Newport

Setup

Optical Tweezers are simple in theory but are not very simple in setup. This is why we are going to detail our setup so that others may replicate. The other reason for this section is because different people build different tweezers for different applications. We require one tweezer with sample control coming from stage movement. Other labs use bi-directional tweezers (clamping from 2 sides), multiple tweezers, advanced tweezer positioning, and more.

Basic Setup

The simplest form of OT is laser light shined through an objective. Of course with this simple setup nothing can be achieved. All you have is a trap. There is no way to detect what is happening in the trap. There is no way to move the trap. This leads to more complex designs determined from experimental need.

Our Setup

We have some requirements based on the types of experiments we do. We need beam positioning for coarse trap movement. We need a sample holder to perform experiments. We need beam expansion for trap efficiency. We need a detector for sample analysis. We need laser power control for trap stiffness. We need a fine adjustment as well (we achieve this through stage positioning). All these requirements led us to the setup we currently have.

Parts list:

Here is the parts list for our tweezers. Several parts are custom made and those will be noted below with all diagrams showing how to make them. Also included are Sketchup files for each part.

Laser

• Coherent 1064nm 4000M mounted on a custom laser mount.
• Thorlabs beam block
• Thorlabs 2" post
• Thorlabs 2" post holder
• Thorlabs rail slider
• Thorlabs 6" rail
• Thorlabs clamp x2

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Laser steering mirrors

• Newport mirror mount x2
• CVI 1064 mirrors x2
• Thorlabs 2" post x2
• Thorlabs 2" post holder x2
• Thorlabs base plate x2

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Beam expander

• Thorlabs beam expander
• Thorlabs ø2" mirror mount
• Thorlabs 1" post
• Thorlabs 1" post
• Newport translation stages x2
• Thorlabs ø1.5" post bracket
• Thorlabs ø1.5" post 6" long
• Thorlabs ø1.5" base plate

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Periscope

• Newport 14" post
• Newport rack and pinion clamp x2
• Newport translation stages x4
• Newport X-Y translation stage
• Thorlabs 1" post
• Thorlabs 1" post holder
• Thorlabs 45˚ mount
• Thorlabs ø2" mirror mount x2
• Thorlabs ø2" mirrors x2
• Thorlabs 2" post
• Thorlabs 3" post holder

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Tweezers steering optics

• Thorlabs 3" post holder
• Thorlabs 6" post
• Thorlabs 3" rail
• Thorlabs rail slider
• Thorlabs clamp x2
• Thorlabs beam block
• Thorlabs 4" post x2
• Thorlabs 4" post holder x2
• Thorlabs base plate x2
• Thorlabs ø1" 0.3" lens tube x2
• CVI 100mm ø1" lens x2
• Thorlabs 30mm threaded cage plate x3
• Thorlabs 30mm cage X-Y stage x2
• Thorlabs 30mm cage Z stage x2
• Thorlabs 2" post
• Thorlabs 2" post holder
• Thorlabs base plate

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Sample stage

• Thorlabs breadboard
• Thorlabs ø1" x 3" post x2
• Mad City Labs piezo stage
• Custom Mad City Labs base plate.
• Newport translation stages x2
• Thorlabs slim breadboard
• Thorlabs 6" post x2
• Thorlabs 6" post holder x2
• Thorlabs base plate x2

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Condenser

• Thorlabs 60mm cage cube
• Thorlabs 60mm cube cover
• Thorlabs 60mm cube kinematic stage
• Thorlabs 60mm cube optics mount
• Thorlabs SM2 end cap
• Thorlabs SM2 to SM1 thread adapter
• Omega 690nm dichroic mirror
• Thorlabs ø2" x 3" lens tube
• Old Anchor optics 1.4NA condenser.
• Custom Thorlabs SM2 to Olympus condenser mount.

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Detector

• Thorlabs 60mm cage plate
• Newport X-Y translation stage
• QPD custom mount
• Phresh photonics QPD
• Thorlabs ø1" x 0.5" lens tube
• Band pass filter
• Thorlabs 6" post
• Thorlabs 3" post holder
• Thorlabs base plate

Tweezer Figures

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Experiments

There are numerous experiments that could be performed using an Optical Tweezers. KochLab uses it for biological applications. And we separate the experiments into two regimes: DNA Applications and Kinesin Applications.

DNA Experiments

1. DNA Stretching - The essence of this technique is to stretch DNA. It is possible to label DNA so with biotin (for adhesion to a streptavidin coated microsphere) and digoxigenin (for adhesion to anti-digoxigenin). These labels allow for the creation of dsDNA tethers because of the nature of anti-dig bonding with glass. The microsphere allows our OT to probe the sample and stretch the DNA. From here there are many avenues to take. First you can reproduce worm-like chain analysis. You could also perform some protein-DNA analysis and observe the amount of force required to remove proteins bound to dsDNA. There are also experiments investigating the nature of DNA intercalaters enhanced by stretching.
2. DNA Unzipping - Steve created an unzipping construct allowing experimenters to unzip dsDNA. This works in large part because of how DNA basepairing works, how most restriction endonucleases cleave DNA, and thanks to ligation (attaching 2 dsDNA sequences together). Embedded in the unzipping construct is a nick along the sugar backbone which allows dsDNA to be pulled apart at the site of the nick. Just slightly downstream of the nick is a biotinylated nucleotide (again to be bound to a streptavidin coated microsphere) where forces from the tweezers will be applied. This construct is extremely versatile because it can be ligated to anything with a specific overhang. The sequence for this overhang can be found in a lot of popular plasmids. Currently KochLab is using this setup for genetic mapping which we call Shotgun DNA/Chromatin Mapping (SDM/SCM). Anthony also believes that this setup can be used for Telomere mapping.
3. Transcription - With careful consideration, RNA Polymerases can be affixed to a surface. If said Polymerase is in the midst of transcription, one could gain insight into the mechanism of this process. By using some form of one of the above techniques OT can be used to gain the insight. With a biotinylated DNA molecule being transcribed, OT can probe forces involved in elongation. If the setup is more like unzipping, studies can be done to understand binding of polymerases to DNA during different junctures of transcription.

Kinesin Experiments

1. Bead Motility Assay - Kinesin stalk/tail can be labeled with biotin so that a streptavidin coated microsphere can be attached to the molecular motor. In this experiment microtubules get affixed to a surface. Kinesin has been shown to walk along these MTs via ATP hydrolysis. With OT you can directly observe the motion of one kinesin walking along a MT via the microsphere (which is bound to a kinesin stalk). More advanced experiments have shown direct observation of each kinesin motor domain (the head groups) by genetically engineering the heads. The heads were engineered with short DNA oligos attached and biotinylated ends for microsphere adhesion. Other experiments lie on the horizon.