we're trying to get together a 34-SNPplex using the SNAPShot technology. After PCR we clean-up using ExoSAP-IT or Columns to get rid of primers and dNTPs, we start the SNAPShot reaction and clean up using SAP to get rid of unincorporated ddNTPs. The problem we're experiencing is high background noise in the electropherogram. The noise peaks are mainly due to incorporation of ddATPs from amplicons (as they are of equel size) used in the SNAPShot reaction.
Can anybody recommend some procedure to get rid of these unwanted peaks?
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SNAPShot clean up
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