Virtual Labs

Protein-DNA interaction analysis by electrophoretic mobility shift assay (EMSA)

1. In an EMSA experiment sample runs from

a: Cathode to anode Explanation

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b: Anode to cathode Explanation

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c: Both a and b Explanation

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d: None of the above Explanation

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2. In EMSA the percentage of the gel should be chosen according to

a: Charge of the protein Explanation

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b: Molecular weight of the target DNA Explanation

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c: Size and number of the protein Explanation

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d: All of the above Explanation

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3. Bromophenol blue is used in EMSA

a: As a tracking dye Explanation

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b: To label protein Explanation

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c: To label DNA Explanation

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d: None of the above Explanation

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4. In EMSA DNA probe can be

a: Radiolabeled Explanation

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b: Fluorescent labeled Explanation

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c: Both a and b Explanation

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d: None of the above Explanation

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5. In EMSA low ionic strength buffer is used

a: To stabilize transient interactions Explanation

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b: To break transient interactions Explanation

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c: To inhibit hydrophobic interactions between protein-nucleic acid Explanation

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d: None of the above Explanation

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6. Factors that affect the strength and specificity of the protein–DNA interactions under study include

a: The ionic strength and pH of the binding buffer Explanation

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b: Presence of glycerol or carrier proteins (e.g., BSA) Explanation

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c: The presence/absence of divalent cations (e.g., Mg²⁺ or Zn²⁺) Explanation

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d: All of the above Explanation

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7. Before a binding reaction is performed, gels are pre-run at a constant voltage (30-90 minutes) in a cold room or using other methods to keep the gel cool

a: to remove all traces of ammonium persulfate Explanation

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b: to ensure a constant gel temperature Explanation

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c: to equilibrate any special stabilizing factors or ions that were added to the electrophoresis buffer Explanation

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d: All of the above Explanation

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8. Method alternative to Electrophoretic Mobility Shift Assay (EMSA) for studying protein-DNA interactions

a: Chromatin Immunoprecipitation (ChIP) Explanation

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b: DNA Footprinting Explanation

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c: Surface Plasmon Resonance (SPR) Explanation

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d: All of the above Explanation

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9. Why sometimes there are multiple bands in EMSA

a: Because of the dissociation occurs during electrophoresis Explanation

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b: A single DNA molecule has multiple binding sites for an individual protein Explanation

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c: Both a and b Explanation

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d: None of the above Explanation

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10. EMSA is important for

a: Studying the affinity of protein-DNA interactions Explanation

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b: Studying the specificity of protein-DNA interactions Explanation

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c: Identifying DNA-binding proteins Explanation

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d: All of the above Explanation

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