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CleanSEQ on the ABI 3100


Removal of unincorporated dye-terminators is required prior to sequence delineation on capillary electrophoresis instrumentation. CleanSEQ has proven an efficient and highly effective dye-terminator removal system with the ABI 3700 and 3730xl sequencers. Samples run on the ABI 3100 are more prone to evaporation and exposure to air before machine injection which can have deleterious effects on sample integrity including the appearance of dye blobs. This application note will demonstrate the effective use of CleanSEQ for dye-terminator removal in combination with the ABI 3100.


Introduction
CleanSEQ has proven to outperform many other dye-terminator removal technologies when used in conjunction with the high throughput ABI PRISM 3700 and 3730xl sequencers. The ABI 3100 is a lower throughput instrument that unlike the 3700 and 3730xl systems, has historically given more reproducible results with formamide elution and injection. Formamide acts to reduce sample evaporation which helps maintain sample integrity. Formamide, however, is well known to significantly reduce signal strengths.

CleanSEQ is a magnetic bead dye-terminator removal system based on SPRI chemistry. Experimentation during CleanSEQ development indicated that samples eluted in water were of high quality and produced sequences with long Phred20 read lengths and much higher signal intensities than samples eluted in formamide. Our standard CleanSEQ protocol, therefore, recommends the elution of sequencing products in water (Figure 1). We believe the septa seals on the 3100 may not effectively prevent exposure to air, potentially s
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