Substrate Nicleotide-Determined Non-Templated Addition of Adenine by Taq DNA
Polymerase:  Implications for PCR-Based Genotyping and Cloning.  V.L. Magnuson,
D.S. Ally, S.J. Nylund, Z.E. Karanjawala, J.B. Rayman, J.I. Knapp, A.L. Lowe,
S. Ghosh and F.S. Collins.  BioTechniques 21(4): 700-709, October 1996.

The Applied Biosystems PRISM fluorescence-based genotyping system as well as the
Invitrogen TA Cloning vector system are influenced by the tendency of Taq DNA
polymerase to add an adenine nucleotide to the 3' end of PCR products after
extension.  Incomplete addition of adenine to a majority of PCR product strands
creates problems in allele-calling during genotyping and potentially diminishes
the cloning efficiency of such products.  Experiments reported here show that
certain terminal nucleotides can either inhibit or enhance adenine addition by
Taq and that PCR primer design can be used to modulate this activity.  The
methods we propose can substantially improve allele-calling for problematic
microsatellite markers when using GENOTYPER software.