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?
Polymerase chain reaction
DNA microarray
Northern hybridization
Southern hybridization
ANSWER
The official key is B: DNA microarray
Official answer: BSource: Official answer key, GATE 2019 BT (IIT Madras)
The question requires a technique that: (1) measures gene expression (RNA transcript levels), (2) for a large number of genes, (3) comparing two biological samples, (4) in a single experiment.
Option (A) PCR: amplifies/quantifies one or a small targeted set of specific DNA/cDNA sequences per run; not designed for large-scale, genome-wide comparison in a single experiment. Eliminated.
Option (B) DNA microarray: a chip carrying thousands to tens of thousands of gene-specific probe spots. cDNA from two samples (commonly labelled with two different fluorophores, e.g. Cy3/Cy5) is hybridized to the chip simultaneously, and the relative fluorescence at each spot reflects the relative expression of that gene between the two samples. This is exactly a large-scale, two-sample, single-experiment comparison. Matches all requirements.
Option (C) Northern hybridization: detects and semi-quantifies one specific RNA species per blot using a single labelled probe; not suited to comparing large numbers of genes at once. Eliminated.
Option (D) Southern hybridization: probes for specific genomic DNA sequences, not gene expression (RNA) at all, and again targets only one or a few sequences per blot. Eliminated.
Only DNA microarray satisfies both the 'large number of genes' and the 'simultaneous two-sample, single-experiment' requirements.
KEY IDEA
A DNA microarray carries thousands of gene-specific probe spots on a single chip; fluorescently labelled cDNA from two samples is hybridized to it simultaneously, so the relative signal at each spot gives a genome-scale, single-experiment comparison of gene expression between the two samples — something PCR, Northern and Southern hybridization each do only one (or a few) targets at a time.
WATCH OUT FOR
Confusing DNA microarray (measures RNA/gene expression via labelled cDNA hybridized to probe spots) with Southern hybridization (detects specific DNA sequences, not expression) — the word "DNA" in "DNA microarray" misleads some students into picking a genomic-DNA technique like (D) instead.
From the GATE 2019 BT paper. Every question of this paper · Download the full paper · All 9 Assays & electrophoresis questions, with notes
