What is the main disadvantage of using standard Taq polymerase compared to high-fidelity polymerases like Pfu in PCR?
Answer: B
Taq polymerase lacks 3' to 5' exonuclease (proofreading) activity, resulting in ~1 error per 10,000 bases. Pfu has proofreading activity, reducing errors to ~1 per 10 million bases.
Q.22Medium
In multiplex PCR, what is the critical challenge that must be addressed when designing multiple primer sets?
Answer: B
Multiplex PCR requires careful primer design to prevent primer-primer interactions, dimer formation, and ensure specific amplification of all target sequences simultaneously.
Q.23Medium
Which DNA technology technique combines random DNA fragmentation with sequence-independent single-primer amplification (SISPA)?
Answer: B
WGA using SISPA allows amplification of entire genomes from minimal starting material by using random primers and is useful for viral and microbial genomics.
Q.24Medium
In droplet digital PCR (ddPCR), how does partitioning of the sample improve quantification accuracy compared to conventional qPCR?
Answer: B
ddPCR partitions the sample into thousands of water-in-oil emulsion droplets, allowing independent amplification and enabling absolute quantification without standard curves.
Q.25Medium
For amplifying extremely long DNA fragments (>10 kb), which specialized PCR technique is most appropriate?
Answer: B
Long-range PCR uses high-fidelity polymerases (like Pfu or Phusion), extended extension times, and optimized Mg²⁺ concentrations to amplify fragments >10 kb.
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Q.26Medium
In CRISPR-Cas9 gene editing, what is the function of the PAM (Protospacer Adjacent Motif) sequence?
Answer: B
The PAM sequence (typically NGG for Streptococcus pyogenes Cas9) is recognized by the Cas9-gRNA complex to identify and cleave target DNA at specific locations.
Q.27Medium
In next-generation sequencing (NGS) library preparation, what is the primary purpose of adapter ligation in DNA technology workflows?
Answer: B
Adapters are short synthetic DNA sequences ligated to fragmented DNA ends, enabling cluster generation, primer binding, and sequencing on NGS platforms.
Q.28Medium
In the context of DNA barcode libraries for species identification in 2024-25, which universal marker is most commonly used for plants?
Answer: B
rbcL (ribulose-1,5-bisphosphate carboxylase) and matK are standard DNA barcodes for plant identification due to appropriate evolutionary rates and amplification efficiency.
Q.29Medium
Real-time PCR (qPCR) differs from conventional PCR in that it:
Answer: B
qPCR continuously monitors the accumulation of PCR products in real-time using fluorescent reporters (SYBR Green or TaqMan probes), allowing quantification of the target DNA.
Q.30Medium
Which of the following is a common application of multiplex PCR?
Answer: A
Multiplex PCR amplifies multiple target sequences in a single reaction tube using multiple primer pairs, enabling detection of several genetic markers, genes, or pathogens simultaneously.
Q.31Medium
In reverse transcription PCR (RT-PCR), which enzyme is critical for the first step?
Answer: B
Reverse transcriptase synthesizes complementary DNA (cDNA) from an RNA template in the first step of RT-PCR, enabling amplification of RNA targets like mRNA.
Q.32Medium
What is the primary advantage of digital PCR (dPCR) over conventional qPCR?
Answer: B
dPCR partitions the PCR reaction into numerous isolated compartments, allowing absolute quantification without requiring a standard curve, and provides higher precision than qPCR.
Q.33Medium
AFLP (Amplified Fragment Length Polymorphism) technology combines which two DNA techniques?
Answer: B
AFLP combines restriction enzyme digestion with PCR amplification of specific DNA fragments, generating polymorphic banding patterns useful for genetic mapping and strain differentiation.
Q.34Medium
In forensic applications, why are microsatellites (STRs) preferred over SNPs for individual identification?
Answer: B
STRs (Short Tandem Repeats) exhibit high variability between individuals due to differences in repeat numbers, making them ideal for forensic DNA profiling and paternity testing.
Q.35Medium
What is the primary limitation of PCR when amplifying GC-rich sequences?
Answer: B
GC-rich sequences tend to form stable secondary structures (hairpins, loops), which can inhibit primer annealing and polymerase extension, reducing PCR efficiency.
Q.36Medium
In the diagnosis of genetic disorders, why is allele-specific PCR (AS-PCR) preferred for detecting known mutations?
Answer: B
AS-PCR uses primers with mismatches at the 3' end that only allow amplification when perfectly matched to the target allele, providing rapid and cost-effective mutation detection.
Q.37Medium
What is the primary advantage of using nested PCR in pathogen detection?
Answer: B
Nested PCR uses outer primers for the first amplification round and inner primers for the second round, significantly improving specificity and sensitivity for detecting low-copy pathogens.
Q.38Medium
In whole genome amplification (WGA) using multiple displacement amplification (MDA), which enzyme is used?
Answer: B
Phi29 polymerase, from bacteriophage Phi29, has high processivity and 3' to 5' exonuclease activity, making it ideal for isothermal multiple displacement amplification of entire genomes.
Q.39Medium
Which of the following statements about primer design for PCR is INCORRECT?
Answer: C
High self-complementarity and primer-dimer formation should be avoided as they reduce PCR efficiency and specificity. Primers should have minimal secondary structure.
Q.40Medium
In real-time PCR (qPCR), which fluorescent dye binds to double-stranded DNA and is commonly used for target quantification?
Answer: A
SYBR Green intercalates into double-stranded DNA and exhibits enhanced fluorescence, making it ideal for real-time monitoring of PCR amplification.
