Q.18 Which one of the following techniques can be used to compare the expression of a large
number of genes in two biological samples in a single experiment?
(A) Polymerase chain reaction (B) DNA microarray
(C) Northern hybridization (D) Southern hybridization

The correct answer is: (B) DNA microarray.​​

Introduction

In molecular biology, choosing the right technique to compare gene expression between two samples is crucial for accurate large-scale transcript profiling. Among polymerase chain reaction, DNA microarray, Northern hybridization and Southern hybridization, only DNA microarray can simultaneously assess the expression of thousands of genes in a single experiment using two biological samples.​

Why DNA microarray is correct (Option B)

• A DNA microarray is a solid surface (like a glass slide) containing thousands of immobilized DNA spots (probes) corresponding to different genes.​

• cDNA from two biological samples (e.g., control and treated) is labeled with different fluorescent dyes and hybridized to the same array, allowing direct comparison of expression levels for a very large number of genes in a single experiment.​

• Fluorescent signal intensity ratios at each spot reflect relative expression of each gene between the two samples, enabling genome‑wide expression profiling.​

Therefore, DNA microarray is the technique that can be used to compare the expression of a large number of genes in two biological samples simultaneously.​

Why the other options are incorrect

(A) Polymerase chain reaction (PCR)

• PCR is an amplification method that exponentially copies a specific DNA fragment using sequence‑specific primers and a thermostable DNA polymerase.​

• Although quantitative PCR (qPCR/RT‑qPCR) can measure expression levels, it is typically used for a limited set of genes (tens at most) per run, not for thousands of genes in a single experiment with simultaneous comparison on the same platform.​

So, PCR is powerful but not designed for high‑throughput genome‑wide expression comparison in one experiment.

(C) Northern hybridization

• Northern blotting detects specific RNA molecules by separating RNA on a gel, transferring it to a membrane, and hybridizing with labeled nucleic acid probes.​

• It is low‑throughput, usually used to analyze one or a few transcripts at a time, so it cannot efficiently compare expression of a very large number of genes simultaneously in two samples.​

Hence, Northern hybridization is unsuitable for large‑scale expression comparison.

(D) Southern hybridization

• Southern blotting is used to detect specific DNA sequences (often genomic DNA), such as gene presence, copy number or restriction fragment patterns.​

• It does not measure gene expression levels (which depend on RNA abundance) and is not used for transcriptome‑wide comparison between samples.​

Therefore, Southern hybridization is incorrect for comparing gene expression across many genes.

Key exam takeaway

• To compare the expression of a large number of genes in two biological samples in a single experiment, the best and correct technique is DNA microarray (Option B).​

• PCR, Northern and Southern techniques are valuable but limited in throughput or do not directly measure global gene expression.​