Consider the following 45 base-pair (bp) DNA sequence:

1 10 20 30 40
| . | . | . | . | .
5’-CGCACCTGTGTTGATCACCTAGCCGATCCACGGTGGATCCAAGGC-3’
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3’-GCGTGGACACAACTAGTGGATCGGCTAGGTGCCACCTAGGTTCCG-5’

Tip: If you want to see a review of PCR, we recommend this amazing animation and virtual lab made by the University of Utah.

You also have a collection of short DNA primers:

Primer 1: 5’-CGTGGA-3’
Primer 2: 5’-TGTGTT-3’
Primer 3: 5’-ATCCAA-3’
Primer 4: 5’-CCTTGG-3’
You put together several reaction mixtures, run them in the thermocycler under conditions that should produce a product if the reaction mixture is correct.

All mixtures contain:

5’-CGCACCTGTGTTGATCACCTAGCCGATCCACGGTG
GATCCAAGGC-3’

The 45 bp DNA fragment
DNA polymerase that can function at high temperature
The necessary buffer conditions
For each mixture, indicate whether or not the PCR reaction would produce a product. If a product would be produced, give the length of that product in base-pairs (bp); if no product would be produced, give zero “0” for the length.

1
Added: dATP, dGTP, dCTP, Primer 2, Primer 4
- unanswered

2
Added: dATP, dGTP, dCTP, dTTP, Primer 2
- unanswered
3
Added: dATP, dGTP, dCTP, dTTP, Primer 2, Primer 4
- unanswered
4
Added: dATP, dGTP, dCTP, dTTP, Primer 1, Primer 3
- unanswered
5
Added: dATP, dGTP, dCTP, dTTP, Primer 2, Primer 3

To determine whether a PCR reaction would produce a product for each mixture, you need to check if the primers match the DNA sequence and if all necessary nucleotides (dATP, dGTP, dCTP, and dTTP) are present in the reaction.

Let's go through each mixture one by one:

Mixture 1:
Primer 2 matches the DNA sequence at position 13-18 (TGTGTT). Primer 4 does not have a match in the DNA sequence. However, for PCR to occur, both primers need to bind to opposite strands of the DNA. Since Primer 4 does not have a complementary sequence, no product would be produced. The length of the product would be 0 bp.

Mixture 2:
Primer 2 matches the DNA sequence at position 13-18 (TGTGTT). All necessary nucleotides (dATP, dGTP, dCTP, and dTTP) are present. Both primers would bind to the DNA and provide a template for synthesis. Since all conditions for PCR are met, a product would be produced. To calculate the length of the product, count the base pairs between the binding sites of the two primers: 13-18 (6 bp). Therefore, the length of the product would be 6 bp.

Mixture 3:
Primer 2 matches the DNA sequence at position 13-18 (TGTGTT). Primer 4 does not have a match in the DNA sequence. Similar to Mixture 1, since both primers need to bind to opposite strands of the DNA, no product would be produced. The length of the product would be 0 bp.

Mixture 4:
Primer 1 matches the DNA sequence at position 1-6 (CGTGGA). Primer 3 matches the DNA sequence at position 26-31 (ATCCAA). All necessary nucleotides are present. Both primers would bind to the DNA and provide a template for synthesis. Therefore, a product would be produced. To calculate the length of the product, count the base pairs between the binding sites of the two primers: 1-6 (6 bp) and 26-31 (6 bp). The total length of the product would be 12 bp.

Mixture 5:
Primer 2 matches the DNA sequence at position 13-18 (TGTGTT). Primer 3 matches the DNA sequence at position 26-31 (ATCCAA). All necessary nucleotides are present. Both primers would bind to the DNA and provide a template for synthesis. A product would be produced. To calculate the length of the product, count the base pairs between the binding sites of the two primers: 13-18 (6 bp) and 26-31 (6 bp). The total length of the product would be 12 bp.

So, to summarize the results for each mixture:
1. No product (0 bp)
2. Product (6 bp)
3. No product (0 bp)
4. Product (12 bp)
5. Product (12 bp)