Zinc finger proteins and gene modulation tools MCQs With Answer

Introduction:

The following quiz on Zinc finger proteins and gene modulation tools is tailored for M.Pharm students studying Principles of Drug Discovery. It focuses on molecular structure, DNA recognition rules, engineering strategies, nuclease fusion technologies (ZFNs), and therapeutic and epigenetic applications of zinc finger-based tools. Questions examine design principles (modular assembly, selection methods), delivery and off-target considerations, and comparisons with other programmable platforms such as TALENs and CRISPR. This set of 20 MCQs with answers reinforces deeper mechanistic understanding and practical constraints relevant to using zinc finger proteins as precision modulators in drug discovery and gene therapy research.

Q1. What is the canonical amino acid motif of classical DNA-binding zinc finger proteins that coordinates a zinc ion?

• Cys2His2 (C2H2) motif coordinating Zn2+
• Cys4 (C4) motif coordinating Zn2+
• His2Asp2 (H2D2) motif coordinating Mg2+
• Cys3His1 (C3H1) motif coordinating Ca2+

Correct Answer: Cys2His2 (C2H2) motif coordinating Zn2+

Q2. Approximately how many base pairs does a single C2H2 zinc finger typically recognize in the major groove?

• 2 base pairs
• 3 base pairs
• 4 base pairs
• 6 base pairs

Correct Answer: 3 base pairs

Q3. What is the approximate length (in amino acids) of a typical C2H2 zinc finger motif?

• 12–15 amino acids
• 28–30 amino acids
• 40–50 amino acids
• 60–75 amino acids

Correct Answer: 28–30 amino acids

Q4. Which nuclease domain is most commonly fused to zinc finger arrays to create zinc finger nucleases (ZFNs)?

• FokI endonuclease domain
• Cas9 nuclease domain
• EcoRI restriction endonuclease
• Cre recombinase

Correct Answer: FokI endonuclease domain

Q5. Which DNA repair pathway is primarily responsible for producing small insertions or deletions (indels) after ZFN-induced double-strand breaks?

• Homology-directed repair (HDR)
• Nucleotide excision repair (NER)
• Non-homologous end joining (NHEJ)
• Base excision repair (BER)

Correct Answer: Non-homologous end joining (NHEJ)

Q6. What is the typical spacer length between ZFN binding sites required for efficient FokI dimerization and cleavage?

• 1–3 base pairs
• 5–7 base pairs
• 12–20 base pairs
• 20–30 base pairs

Correct Answer: 5–7 base pairs

Q7. Which practical advantage do engineered zinc finger proteins have over CRISPR/Cas systems for some therapeutic deliveries?

• They are always more specific than CRISPR/Cas
• They are smaller in coding size, easing AAV delivery
• They do not require design or optimization
• They edit RNA instead of DNA

Correct Answer: They are smaller in coding size, easing AAV delivery

Q8. Which selection-based platform was developed to account for context-dependent interactions when engineering functional zinc finger arrays?

• Modular assembly without selection
• OPEN (Oligomerized Pool ENgineering)
• Random shuffling without screening
• CRISPR library screening

Correct Answer: OPEN (Oligomerized Pool ENgineering)

Q9. For high specificity in genome targeting, engineered zinc finger arrays typically contain how many fingers?

• 1 finger
• 3–6 fingers
• 10–12 fingers
• 20 or more fingers

Correct Answer: 3–6 fingers

Q10. Which effector domain is commonly fused to zinc finger proteins to create transcriptional repressors?

• VP64 transcriptional activation domain
• KRAB repressor domain
• TET1 catalytic domain
• GFP fluorescent protein

Correct Answer: KRAB repressor domain

Q11. Which engineering strategy reduces off-target cleavage by ZFNs that arises from homodimerization of FokI?

• Using higher expression plasmid doses
• Designing obligate heterodimeric FokI variants
• Removing the zinc-binding residues from fingers
• Using monomeric FokI catalytic domains

Correct Answer: Designing obligate heterodimeric FokI variants

Q12. Through which groove of DNA do C2H2 zinc fingers primarily contact bases to achieve sequence-specific recognition?

• Minor groove
• Major groove
• Intercalation between base pairs
• Backbone phosphate only

Correct Answer: Major groove

Q13. Why do zinc finger nucleases require two separate zinc finger–FokI monomers binding opposite strands for DNA cleavage?

• Because each finger only cuts single-stranded DNA
• Because the FokI catalytic domain must dimerize to be active
• Because zinc ions mediate cleavage directly
• Because one monomer provides helicase activity

Correct Answer: Because the FokI catalytic domain must dimerize to be active

Q14. Which therapeutic application was an early clinical target for ZFN-mediated gene disruption in hematopoietic cells?

• Correction of CFTR in cystic fibrosis
• CCR5 gene disruption for HIV resistance
• Replacement of dystrophin for Duchenne muscular dystrophy
• Insertion of insulin gene for diabetes

Correct Answer: CCR5 gene disruption for HIV resistance

Q15. To create a zinc finger-based transcriptional activator, which activation domain is commonly fused to the ZFP?

• KRAB repressor domain
• DNMT3A methyltransferase
• VP64 transcriptional activation domain
• Ubiquitin ligase domain

Correct Answer: VP64 transcriptional activation domain

Q16. What is the primary limitation of simple modular assembly of zinc finger modules for designing multi-finger arrays?

• Excessive DNA-binding specificity without off-targets
• Context-dependent interactions between adjacent fingers
• Inability to bind the major groove
• Requirement for RNA guides

Correct Answer: Context-dependent interactions between adjacent fingers

Q17. Which experimental selection system is commonly used to identify functional zinc finger arrays from large libraries in bacteria?

• Phage display system only
• Bacterial one-hybrid system
• Southern blot screening
• Mass spectrometry of protein–DNA complexes

Correct Answer: Bacterial one-hybrid system

Q18. For precise sequence change via homology-directed repair (HDR) after ZFN cleavage, which of the following is required?

• A donor DNA template provided during or shortly after break induction
• Only transient expression of GFP
• Complete absence of cell-cycle progression
• High concentrations of zinc ions in the media

Correct Answer: A donor DNA template provided during or shortly after break induction

Q19. To target and increase DNA methylation at a specific locus using a zinc finger platform, which effector is commonly fused to the ZFP?

• TET1 catalytic domain (demethylase)
• DNMT3A DNA methyltransferase
• VP64 activation domain
• Cas9 nuclease

Correct Answer: DNMT3A DNA methyltransferase

Q20. Compared with TALENs, engineered zinc finger arrays are generally:

• Larger in coding size and easier to modularly design
• Smaller in coding size but show context-dependent recognition
• Completely free of off-target effects
• Unable to be fused to effector domains

Correct Answer: Smaller in coding size but show context-dependent recognition

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