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    ​For the template sequence given below, which one of the following combination of primers can hypothetically be used to amplify the target region (Ign
    Question

    For the template sequence given below, which one of the following combination of primers can hypothetically be used to amplify the target region (Ignore Tm & length parameters for the primers)? 5'- A T C G A C T A G NNNNNNNNNNNNNNNNN C C T A A T G C A G - 3'

    A.

    Primer 1: 5'- T A G C G T C - 3'
    Primer 2: 5'- G A C G T A - 3'

    B.

    Primer 1: 5'- C T G C A T - 3'
    Primer 2: 5'- A T C G A C - 3'

    C.

    Primer 1: 5'- A T C G A C - 3'
    Primer 2: 5'- G A C G T A - 3'

    D.

    Primer 0: 5'- T A G C G T C - 3'
    Primer 2: 5'- G A C G T A - 3'

    Correct option is B

    Explanation-

    We are given a template DNA sequence
    This means the actual target sequence lies between:
    Start: A T C G A C T A G
    End: C C T A A T G C A G
    We need to select two primers:
    Primer 1: Binds to the start of the bottom (template) strand — it should be complementary to the 3' end of the top strand, and run 5' to 3'
    Primer 2: Binds to the end of the top strand — it is complementary to the 3' end of the bottom strand, and runs 5' to 3'
    Option b:
    Primer 1: 5′-C T T G C A T-3′
    → This binds to the 3′ end of the bottom strand, complementary to A T G C A A G, which is the reverse complement of the 3' end of the top strand.
    Primer 2: 5′-A T C G G A C-3′
    → This binds to the top strand, at the 5' end, complementary to the start region.
    Together, these primers flank the target region correctly and face inward, allowing amplification.

    Incorrect Options:
    Option a: Primers point away from each other or are not complementary to the correct ends.
    Option c: Both primers bind in the same region or orientation.
    Option d: Similar issue — primers do not properly flank the target region.

     Final Answer: Option b is correct

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