Question

You are planning to use PCR to amplify several regions of a piece of DNA. The sequence of your template DNA is provided below along with the sequences of all available primers. Determine where each of the primers bind and answer the following:

5' AGGGCCAAATGAGATGAGTCAAAAGCTGCCGATAACCGGATAG 3'

3' TCCCGGTTTACTCTACTCAGTTTTCGACGGCTATTGGCCTATC 5'

Primer 1: 5-TTGGCC 3

P2: 5-GTCAAA-3

p3: 5-AACCGG-3

p4: 5-CCGGTT-3

P1 can bind to the bottom strand?

P4 can bind to the molecule at only one location

Which primer pair would you use to amplify a double stranded pcr fragment of any size from this template

Which primer has the lowest melting point

Using the two selected primers and added all of the PCR components to a test tube answer the following as the polymerase chain rxn proceeds

The concentration of dNTPs will increase,decrease, stay the same, as the rxn proceeds

The concentration of Taq DNA polymerase will increase,decrease, stay the same, as the rxn proceeds

Answer 1

# 5' AGGGCCAAATGAGATGAGTCAAAAGCTGCCGATAACCGGATAG 3'

   3' CCGGTT 5' primer-1 will bind to the above strand

5'GTCAAA 3' primer-2 will bind to the below strand

3' TCCCGGTTTACTCTACTCAGTTTTCGACGGCTATTGGCCTATC 5'

#    5' AGGGCCAAATGAGATGAGTCAAAAGCTGCCGATAACCGGATAG 3'

   primer-4 will bind to the above strand    3' TTGGCC 5'

   primer-3 will bind to the below strand 5' AACCGG 3'

3' TCCCGGTTTACTCTACTCAGTTTTCGACGGCTATTGGCCTATC 5'

# p1 cannot bind to the below strand as there is no complementary strand.

# yes p4 can only bind to one location.

# primer p4 and p2 will be more suitable because replication is done from 5' to 3'

# primer-2 have the lowest melting point as there is more A,T in it.

# The concentration of dNTPs will decrease as dNTPs is being used up as rxn proceeds

# The concentration of Taq DNA polymerase will stay the same because Taq polymerase acts as a catalyst.