Design primers that can be used to copy a nucleic acid strand into a complementa

Question

Design primers that can be used to copy a nucleic acid strand into a complementary strand:

5’ TACGGTCGTTTACGC------------------------------------CTGCCCAATGCGTGC 3’

The sequence of the 5’ and 3’ ends of a DNA template are given above. The dashed line indicates the rest of the DNA sequence.

A) Design a primer of 15 nucleotides in length that can be used to prime synthesis of the template strand above.

B) Having copied the template into its complementary sequence – now design a 15 nucleotide primer that can be used to prime synthesis from the newly synthesised DNA strand.

For both primers show the direction of the primer.

Explanation / Answer

DNA synthesis proceeds in the 5' to 3' direction and needs a primer at the 5' end that offers a free 3' hydroxyl group for DNA polymerase.

A. Therefore, the sequence complementary to the 3' end of the given template can act as its primer. The 3' end has the sequence: 5'CTGCCCAATGCGTGC3'. The complementary sequence, which will act as its primer, will be: 5'GCACGCATTGGGCAG3'.

B. The newly synthesized DNA will be complementary to the given template strand. Therefore, the 5' end sequence of the given template strand itself can act as a primer for the synthesis of the newly synthesized DNA strand. The sequence, whcih can act as primer for the newly synthesized strand, is: 5'TACGGTCGTTTACGC3'.

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