MCQs on Gel Electrophoresis, Oligonucleotide & Microarrays – 2
1 - Question
A piece of DNA that is to be separated is crushed and soaked into the buffer. The majority of DNA diffuses, how can it be separated?
a) Filtration and centrifugation
b) Filtration or centrifugation
c) Allowing to sediment
d) By passing through a silica column
Explanation: As the target DNA is crushed and soaked into the buffer, the majority of it diffuses into the gel. It can be separated via filtration or separation. It is simply termed as recovering the DNA from the gel by diffusion.
2 - Question
Another method of DNA recovery is termed as freeze-squeeze. The correct statement for it is?
a) The slice containing DNA is cut and frozen into liquid oxygen
b) Freezing doesn’t have any effect on the DNA structure
c) After freezing centrifugation is carried out through glass wool plug
d) The substance used for centrifugation allows the gel to pass through but the liquid is retained
Explanation: It is also a method for obtaining DNA from gels. The slice containing DNA is cut and frozen into liquid nitrogen. Freezing in liquid nitrogen leads to disruption of structure. As the centrifugation by glass wool plug is carried out after freezing out, the gel is retained by it. The liquid which is containing dissolved DNA will be allowed to pass through.
3 - Question
If further electrophoresis is used for recovery of DNA from gels, the method is termed as ____________
a) secondary electrophoresis
b) recovery electrophoresis
c) denaturing electrophoresis
Explanation: If electrophoresis is used further for recovery, the method is termed as electro-elution. There are different electro-elution methods which are used such as dialysis tube or membrane is used.
4 - Question
The DNA is sliced and is placed into the dialysis tube containing buffer. Further electrophoresis is performed. After it, the DNA moves out of the gel but is retained by buffer.
Explanation: As further electrophoresis is carried out, the DNA moves out of the gel but is retained by the buffer. From the buffer, it can be obtained via pipetting.
5 - Question
UV shadowing is used at times for visualising the DNA. Which of the statements is correct for it?
a) In this method, the DNA bands are visualized because they fluoresce under UV
b) The DNA bands won’t fluoresce but will absorb the UV light
c) It is not suitable for visualizing single stranded molecules
d) It is less preferred over the use of ethidium bromide
Explanation: In this method, the DNA bands won’t fluoresce but will absorb the UV light. This leads to the formation of a non-fluorescent shadow on the screen. It is suitable for visualising single stranded species because the mode of action is not intercalating as in the case of use of ethidium bromide. It is preferred over it because ethidium bromide is often difficult to remove
6 - Question
The greatest separation is obtained in which portion of the gel?
a) Lower portion where the anode is
b) Lower portion where the cathode is
c) The separation is uniform all over
d) It varies according to the quantity of the size of the molecules to be separated
Explanation: The greatest separation is obtained in the lower portion of the gel where the anode is. Thus the smaller molecules are having the greatest separation because they are the one which travels farther in the gel.
7 - Question
Which of the statements is correct for non uniform separation obtained other than the conventional one?
a) It can be obtained via applying strong field towards the cathode
b) It can be obtained via applying the same field on both the sides
c) The separation is greater on the side of stronger field
d) Its is greater towards the weaker field
Explanation: Conventionally, separation is greater towards the lower portion i.e. where the anode is. In order to obtain greater separation towards the cathode, the stronger field is applied here. As the field is weaker on the anode side, the molecules retard as they move towards anode and are less separated.
8 - Question
How can gradient in the field strength be obtained?
a) It can be obtained via varying the amount of current, keeping the resistance constant
b) It can be obtained via varying the amount of resistance, keeping the current constant
c) Both can be varied, but resistance is having more effect
d) Buffer-gradient gels can be used with decreasing concentration of buffer at the bottom
Explanation: The gradient field strength can be obtained via varying the resistance because the current flowing throughout the gel needs to remain constant. To vary the resistance, often buffer-gradient gels and wedge gels can be used. Wedge gels are thick and thus are having lower resistance at the bottom. Whereas buffer-gradient gels with increasing concentration at the bottom are used. As the concentration increases at the bottom, resistance decreases.
9 - Question
If the molecules to be separated are larger than the size for conventional electrophoresis, which type of gels can be used?
a) Wedge gels
b) Buffer-gradient gels
c) Pulse field gels
d) Varying the amount of agarose will carry out the separation
Explanation: In the case, if the molecules to be separated are very large, say the chromosomes are to be separated. In this case, pulse-field gels are used. It is termed as pulse field gel electrophoresis (PFGE).
10 - Question
Which of the following statement is correct for the method of separation of large molecules?
a) The large DNA molecules can pass through the matrix in any direction, not necessarily in the direction parallel to the movement
b) The separation can be carried out if the fields are at right angles to each other
c) The time of pulse should be less than that of the reorientation time
d) Separation is not of the megabase level
Explanation: For the separation of large DNA molecules, the electric fields are often applied at right angles to each other. Usually, the large molecules pass through the matrix only in the direction of the movement. In rest directions, the movement is blocked by the gel matrix. The time of the pulse is greater than that of the reorientation time. Thus, smaller molecules have greater time for movement. DNA of megabase size can also be separated.