Using optical traps to manipulate DNA
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Using optical traps to manipulate DNA
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[ID] => 559829
[post_author] => 12815
[post_date] => 2025-01-09 11:17:25
[post_date_gmt] => 2025-01-09 16:17:25
[post_content] => Practice Passage (Question 1-5)
*This passage is the property of Khan Academy and has been reformatted into an AAMC-style interface in their entirety by MedLife Mastery. MedLife Mastery does not endorse and is not an affiliate of Khan Academy.
An optical trap is a measurement device that allows minute forces to be exerted on cells and small tissues using a laser. In a standard setup (Figure 1), a collimated laser beam is passed through a lens that focuses it towards a single point. This results in a three-dimensional light field shaped like two inverted cones, which exerts a force that pushes transparent objects towards the focal point of the assembly. Photons will pass through the object from a particular angle and scatter, moving the object in a desired direction. The device works best when the object being confined is a transparent insulator, and so polystyrene beads are often used in the trap. These beads can, in turn, be connected to objects of diagnostic interest, allowing detailed manipulation of biological materials via purely optical means. To reduce the influence of environmental factors on the optical trap, experiments are performed in mechanical isolation through the use of air tables removed from heat and acoustic sources.
One such experiment is a “DNA pulling experiment,” in which a bead in an optical trap is affixed to the end of a DNA strand and tugged by moving the laser and trap. The displacement of the bead is then recorded as a function of the force exerted on it by moving the trap. The amount that the DNA strand resists pulling provides information about its secondary structures, like coils or folds, that require an applied force to disassemble.
One drawback of this technique emerges over long timescales, when the DNA strand accumulates damage due to photons from the trap passing into it and provoking chemical changes. The total photodamage to a given strand is proportional to the total number of photons that have reached it during the experiment.
Figure 1: A schematic of a simple optical trap acting on a transparent polystyrene bead.
[post_title] => Using optical traps to manipulate DNA
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[questions] => Array
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[question] => Which of the following causes likely describes the origin of the force that pushes objects towards the center of the trap?
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[answer] => 2
[description] => Reason for the Correct Answer:
Photoionization may occur, but the separated charges are both within the bead and thus cannot exert a force on the bead overall.
Thermal gradients drive free particles from hot areas to cold areas, and so heating the bead would drive it away from the trap.
Light does not induce net currents in insulators.
Only one of the answer choices works best when the bead is a transparent dielectric.
As photons enter the bead and then pass back out, the resultant momentum transfer (recoil) exerts the force that confines the bead.
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[answers] => Array
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[0] => Array
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[each_answer] => A. Light impinging on the bead inducing a net charge, on which the electric field in the light then acts
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[1] => Array
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[each_answer] => B. Recoil due to the momentum of photons exiting the transparent material
)
[2] => Array
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[each_answer] => C. Magnetic forces arising from currents induced in the bead by the light
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[3] => Array
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[each_answer] => D. Heating of the bead resulting in a thermal gradient force
)
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[1] => Array
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[quiz_unique_key] => 3873426850
[question] => Which of the following lens types focuses a laser beam towards a focal point?
[value] => Array
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[answer] => 2
[description] => Reason for the Correct Answer:
Try drawing the lenses and sketching the path of a beam incident on the lens using Snell’s Law. Remember that glass has a higher refractive index than air.
Concave surfaces tend to spread apart a collimated beam that enters them from the opposite side; convex surfaces tend to focus beams.
A convex-convex (or “converging”) lens focuses a laser beam towards a focal point.
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[answers] => Array
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[0] => Array
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[each_answer] => A. Concave
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[1] => Array
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[each_answer] => B. Convex
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[2] => Array
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[quiz_unique_key] => 83407773
[question] => Based on the diagram, which of the following likely occurs when the bead is displaced a small amount from the center of the trap?
[value] => Array
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[answer] => 1
[description] => Reason for the Correct Answer:
This question can be solved purely by considering the forces predicted in the diagram in a separate free-body diagram.
If the bead is displaced, the focal point of the optics setup does not move with it.
The bead is in a stable equilibrium—it will always return to its original position when perturbed by a small amount (as indicated by the inwards pointing force vectors in the schematic).
The bead undergoes simple harmonic motion when perturbed from the center of the trap.
)
[answers] => Array
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[0] => Array
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[each_answer] => A. The bead will undergo oscillations about the center of the trap
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[1] => Array
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[each_answer] => B. The bead will exit the trap
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[2] => Array
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[each_answer] => C. The bead will undergo predominantly Brownian motion
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[3] => Array
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[each_answer] => D. The bead will remain fixed in its new position relative to the trap
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[3] => Array
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[quiz_unique_key] => 2261298308
[question] => Which of the following features of the curve provide information about the secondary structures that unfold during the pull?
[value] => Array
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[answer] => 2
[description] => Reason for the Correct Answer:
The DNA strand and bead are essentially acting as a mass attached to a spring.
The area under the curve is the work done by the trap to unwind the spring, which does not necessarily provide information about the spring,
The y-intercept should be at the origin for all samples.
The force during the experiment is always positive, and so there are no zero crossings.
The slope of the curve is essentially the spring constant of the DNA.
The slope of the curve provides information about the secondary structures that unfold during the pull.
)
[answers] => Array
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[0] => Array
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[each_answer] => A. The zero-crossings
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[1] => Array
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[each_answer] => B. The slope
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[2] => Array
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[each_answer] => C. The area under the curve
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[3] => Array
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[each_answer] => D. The y-intercept
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[4] => Array
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[quiz_unique_key] => 2377279144
[question] => Which of the following would reduce the effects of accumulating photodamage?
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[answer] => 4
[description] => Reason for the Correct Answer:
Photodamage is the result of an excess of photons reaching the strand during an experiment.
The intensity of light is determined by the total number of photons and their energy.
Reducing the light intensity while increasing illumination time would not substantially change the total photons that hit the sample.
Performing the experiment for short intervals on multiple copies of the sequence would reduce the effects of accumulating photodamage. Less photons will reach the strand, and extra copies will ensure precision of the data as new ones will have been previously unaffected by photodamage.
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[answers] => Array
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[0] => Array
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[each_answer] => A. Reduce the intensity of the laser and perform the experiment for a longer period
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[1] => Array
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[each_answer] => B. Use a longer DNA strand
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[2] => Array
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[each_answer] => C. Use a laser with a lower-frequency beam, like a far-infrared laser
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[3] => Array
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[each_answer] => D. Use a laser with a lower-frequency beam, like a far-infrared laser
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[total_question] => 5
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