DNA motion in gel electrophoresis
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DNA motion in gel electrophoresis
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[ID] => 556514
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[post_date] => 2025-01-09 07:21:58
[post_date_gmt] => 2025-01-09 12:21:58
[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.
Gel electrophoresis is a commonly used method to separate DNA fragments. In Classic Gel Electrophoresis (CGE), negatively-charged DNA fragments are loaded into lanes in a block of agarose gel. A constant electric field is applied to the system, which causes the DNA fragments to migrate toward the opposite end of the block. DNA fragments are separated because shorter fragments can move through pores in the agarose gel more quickly than longer fragments. Groups of DNA fragments of the same length migrate together and can be visualized as bands in the gel.
Figure 1: Schematic Representation of CGE. The arrow indicates the direction of net DNA migration. Dark bands in the gel represent groups of DNA molecules of identical length. ‘A’ indicates the site of DNA loading. ‘B’ indicates the area through which DNA molecules migrate.
CGE can only separate DNA fragments between 5 and 20,000 base pairs in length. Pulsed Field Gel Electrophoresis (PFGE) is a powerful technique that can separate DNA fragments differing by as many as 106 base pairs. There are several variants of PFGE, all of which share the essential characteristic that the orientation of the electric field is abruptly changed thousands of times during the procedure. As the electric field changes direction, the DNA molecules reorient themselves before migrating in a new direction. Typically, smaller molecules are able to reorient themselves more quickly and therefore migrate farther. One currently available PFGE apparatus utilizes electrodes arranged in a hexagonal array, in which each electrode can be controlled independently. The electrodes are turned on in alternating arrangements to produce straight, distortion-free, lanes of DNA migration.
Figure 2: Example electrode array for PFGE. The small bars at the top of the block show where DNA loading would occur. ‘A’ shows the relative electrode potentials when the -45° field angle is activated. ‘B’ shows the relative electrode potentials when the +45° field angle is activated.
[post_title] => DNA motion in gel electrophoresis
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[question] => A researcher tests a novel PFGE electrode array on a sample of DNA she hopes to analyze. Which quantity would help her determine if this electrode array would function well for this sample and other similar samples?
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[answer] => 4
[description] => Reason for the Correct Answer:
The passage says that for PFGE to be successful, electric fields must cause “straight, distortion-free lanes of DNA migration.” To verify that this electrode array works, we need to know the direction of DNA migration.
Speed does not include direction, so it would not help us decide if the novel electrode array is helpful. Additionally, speed is based on distance traveled, which impossible to determine for a DNA molecule that is moving back and forth as the electric field changes.
Knowing the instantaneous velocity of DNA would not be helpful, since the instantaneous velocity will change as the electric field changes throughout the course of PFGE.
The average velocity of the DNA would provide information about the speed and direction of the DNA molecule during the entire course of PFGE. This would tell a researcher if the electrode array worked well or not.
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[answers] => Array
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[0] => Array
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[each_answer] => A. instantaneous speed of a DNA molecule in the PFGE
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[1] => Array
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[each_answer] => B. instantaneous velocity of a DNA molecule in the PFGE
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[2] => Array
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[each_answer] => C. average speed of a DNA molecule in the PFGE
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[3] => Array
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[each_answer] => D. average velocity of a DNA molecule in the PFGE
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[1] => Array
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[quiz_unique_key] => 3873426850
[question] => Which of the following paths most closely represents the net displacement of a DNA molecule undergoing PFGE in the apparatus shown in Figure 2?
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[answer] => 1
[description] => Reason for the Correct Answer:
The DNA is negatively charged, so it will move downward diagonally when the ‘A’ field is on. It will move downward in the opposite diagonal direction when the ‘B’ field is on.
The passage says that in PFGE, the orientation of the electric field changes periodically. This means the actual DNA molecule changes direction multiple times.
The actual DNA molecule would move back and forth in the direction of the two electric fields. The lateral component of this motion would cancel, causing net downward migration.
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[each_answer] => A.
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[1] => Array
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[each_answer] => B.
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[each_answer] => C.
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[each_answer] => D.
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[2] => Array
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[quiz_unique_key] => 83407773
[question] => In the PFGE in apparatus shown in Figure 2, what could be a direction of the net displacement vector of a DNA molecule when the -45o pulses are run for a greater time than the +45o pulses?
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[answer] => 2
[description] => Reason for the Correct Answer:
Use Figure 2 to establish an axis for yourself. 0o would be perfectly downwards, -45° would be downward and to the left, and 45° would be downward and to the right.
Under normal PFGE conditions, when the -45°pulses are run for the same amount of time as the 45°pulses, the DNA is displaced downwards 0°. The lateral components would cancel out.
When the -45°pulses are run for a greater time than the 45°pulses, the DNA will be displaced more toward the -45°direction, but not completely because there are still 45°pulses. The only number that is between 0°and -45°is -20°.
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[each_answer] => A. -45°
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[each_answer] => B. -20°
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[each_answer] => C. 0°
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[each_answer] => D. 20°
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[question] => Which of the following is the difference between CGE and PFGE?
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Speed is equal to distance / time, while velocity is equal to displacement / time.
In CGE, the DNA travels in approximately a straight line. In PFGE, the DNA molecule is constantly changing direction as the direction of the electric field changes.
In CGE, the distance that a DNA molecule travels is roughly identical to its displacement (since it travels in a straight line). In PFGE, the DNA molecule travels much more distance than its displacement. Therefore, one difference between CGE and PFGE is that “in CGE, the average speed of a DNA molecule is more similar to its average velocity than in PFGE.”
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[each_answer] => A. In CGE, the average speed of a DNA molecule is more similar to its average velocity than in PFGE.
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[each_answer] => B. In CGE, there is no difference between the instantaneous velocity of average velocity of a DNA molecule.
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[each_answer] => C. In PFGE, the DNA molecules travel less total distance than in CGE when net migration is the same.
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[each_answer] => D. In PFGE, there is a linear net migration of DNA molecules.
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[question] => A researcher carries out PFGE on a sample of DNA that can be visualized as two bands after a period of time. Which of the following must increase as the PFGE continues?
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[answer] => 2
[description] => Reason for the Correct Answer:
All of the DNA is loaded at the same place. If the sample has separated into two distinct bands, it is because one group of molecules has traveled faster than another.
As time goes on, the faster DNA band will continue to get farther away from the slower DNA band.
Therefore, the “distance between the bands of DNA” must increase.
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[each_answer] => A. velocity of the DNA fragments
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[each_answer] => B. distance between the DNA bands
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[each_answer] => C. strength of the electric field
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[each_answer] => D. density of DNA in each band
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CGE can only separate DNA fragments between 5 and 20,000 base pairs in length. Pulsed Field Gel Electrophoresis (PFGE) is a powerful technique that can separate DNA fragments differing by as many as 106 base pairs. There are several variants of PFGE, all of which share the essential characteristic that the orientation of the electric field is abruptly changed thousands of times during the procedure. As the electric field changes direction, the DNA molecules reorient themselves before migrating in a new direction. Typically, smaller molecules are able to reorient themselves more quickly and therefore migrate farther. One currently available PFGE apparatus utilizes electrodes arranged in a hexagonal array, in which each electrode can be controlled independently. The electrodes are turned on in alternating arrangements to produce straight, distortion-free, lanes of DNA migration.
