Question

a scientist designs a primer, which is a short oligonucleotide, for use in a polymerase chain reaction (pcr). during the reaction, the primer will bind to its dna template via complementary base - pairing. the sequence and orientation of the primer is shown below.
5-cttaggtcatcagactag-3
which of the following shows the sequence and orientation of the primer’s dna template?
choose 1 answer:
a 3-aggcttgacgactcagct-5
b 5-aggcttgacgactcagct-3
c 3-gaatccagtagtctgatc-5
d 5-gaatccagtagtctgatc-3

Explanation:

Step1: Recall base - pairing rules

In DNA, adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G). Also, the two strands of DNA are antiparallel, meaning if one strand has a 5' to 3' orientation, the complementary strand has a 3' to 5' orientation. The primer sequence is \(5' - CTTAGGTCATCAGACTAG - 3'\).

Step2: Find complementary bases and reverse orientation

First, find the complementary bases for each nucleotide in the primer:

• C pairs with G
• T pairs with A
• A pairs with T
• G pairs with C

So, the complementary sequence of the primer (reading from 3' to 5' since the template should be antiparallel to the primer) is obtained by replacing each base with its complement and reversing the order (because the primer is 5' - 3', the template should be 3' - 5' relative to the primer's 5' - 3' direction).

The primer sequence: \(5' - C\ T\ T\ A\ G\ G\ T\ C\ A\ T\ C\ A\ G\ A\ C\ T\ A\ G - 3'\)

Complementary bases (from 3' to 5' direction, so we start from the 3' end of the primer and find complements):

Starting from the 3' end of the primer (\(G\) at 3' end):

• \(G\) (primer 3' end) pairs with \(C\)
• \(A\) pairs with \(T\)
• \(T\) pairs with \(A\)
• \(C\) pairs with \(G\)
• \(A\) pairs with \(T\)
• \(G\) pairs with \(C\)
• \(T\) pairs with \(A\)
• \(C\) pairs with \(G\)
• \(A\) pairs with \(T\)
• \(T\) pairs with \(A\)
• \(T\) pairs with \(A\)
• \(A\) pairs with \(T\)
• \(C\) pairs with \(G\)
• \(T\) pairs with \(A\)
• \(T\) pairs with \(A\)
• \(C\) pairs with \(G\)

Wait, a better way: Write the primer sequence and then write the complementary sequence in reverse order (since the two strands are antiparallel). The primer is \(5' - CTTAGGTCATCAGACTAG - 3'\). Let's write the complementary bases for each position (from 5' to 3' of the primer, the complementary bases will be from 3' to 5' of the template).

Primer (5' - 3'): C T T A G G T C A T C A G A C T A G

Complementary bases (3' - 5'): G A A T C C A G T A G T C T G A T C

So the template sequence (3' - 5') is \(3' - GAATCCAGTAGTCTGATC - 5'\) (which is option C).

Answer:

C. \(3' - GAATCCAGTAGTCTGATC - 5'\)