Solution to PS 8 #10

No, there will be no double stranded DNA amplified if the DNA primers are pointing out instead of pointing inwards towards each other. In each cycle of the reaction, the primers will bind to their target sites and the polymerase will make one copy of the DNA flanking each side of the desired region.  There will be no increase in bnding sites for the primers and no exponential amplification.

Amplificaton product after first generation with  correct primers and direction of DNA replication marked in red.

-------5' AGCG------------------------------------TCTGA 3'------
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<--AGACT 5'------

-------5' AGCG>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-------3' TCGC------------------------------------AGACT 5'-------
 
 

Product and direction of replication if complement of primers is used (shown in Blue).  In this case the desired fragment of DNA  is never amplified:

-------5' AGCG------------------------------------TCTGA 3'------
<<<< 3' TCGC-5'

                                                                    5' TCTGA 3'>>>>>>
-------3' TCGC------------------------------------AGACT 5'-------


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