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primer binding - (Jun/15/2009 )

I read few papers related to PCR, some mentioned primer binding is specified primarily by 3`end sequence of the primer,while other mentioned that even single nucleotide variation in primer can change the patterns of amplified DNA when viewed after DNA electrophoresis. So plz help me.... :o

-where am I?-

3' end specificity is more important than 5' end because if there are mismatches at 5' end, 3'end of the primer can still bind to its homologous sequence. That is why introducing 3' clamps (GCs) can increase primer specificity.