Q.Which one of the following represents the correct annealing of primers to the DNA to be amplified in the PCR ? (A) [diagram: two template strands each with a short primer annealed] (B) [diagram: two template strands each with a short primer annealed] (C) [diagram: two template strands each with a short primer annealed] (D) [diagram: two template strands each with a short primer annealed]

PCR amplification requires two primers that flank the target DNA sequence on opposite strands. Each primer must anneal to its complementary sequence in an orientation that allows DNA polymerase to synthesize toward the other primer, effectively copying the region in between.

The correct arrangement shows:

• One primer binding to the 3′ end of the sense strand (running 5′→3′ left to right)
• The second primer binding to the 3′ end of the antisense strand (running 5′→3′ right to left)
• Both primers oriented so their 3′-OH groups point toward each other, enabling extension inward to amplify the target segment

Common mistakes include primers facing outward (extension would move away from the target) or both primers on the same strand (no amplification of the complementary region). The primers must be complementary to opposite strands and convergent in their synthesis direction. …

The polymerase chain reaction depends entirely on the precise placement and orientation of primers. To understand which diagram is correct, you need to grasp what primers actually do and how DNA polymerase works.

DNA polymerase can only add nucleotides to the 3' end of an existing strand — it synthesizes in the 5' to 3' direction exclusively. This directional constraint shapes everything about primer design. When you want to amplify a specific segment of DNA, you need two primers: one that binds to the 3' end of the sense strand and another that binds to the 3' end of the antisense strand. Because the two strands of DNA run antiparallel (one 5' to 3', the other 3' to 5'), the primers must face each other from opposite ends of the target region.

Picture the target sequence you want to amplify sitting between two boundary points. The forward primer anneals to one template strand at one boundary, with its 3' end pointing inward toward the target. The reverse primer anneals to the complementary strand at the other boundary, also with its 3' end pointing inward. When polymerase extends both primers, the new strands grow toward each other, copying the entire region in between.