Poor DNA recovery could be due to one or a combination of the following factors:

• Binding of DNA to the column/wells was inefficient.

  Binding of the DNA is dependent on both pH and salt concentration. Ensure that an appropriate amount of Binding Buffer C was used for the volume of the PCR reaction.

• The appropriate amount of ethanol was not added to the Wash Concentrate.

  The Wash Solution A has been specifically designed to contain the appropriate amount of components. Ensure that the Wash Solution A was prepared using the correct amount of ethanol.

• Binding Buffer C was not completely removed in the wash step.

  Traces of salt left on the column/wells from the binding step may interfere with the elution of the DNA. Ensure that the columns/wells are washed with the Wash Solution A.

• Proper Elution Buffer was not used.

  The provided Elution Buffer B has been optimized for high elution recoveries. If water or TE buffer is used instead, ensure the pH is around 8.

• Elution Buffer B was not placed directly onto the column bed.

  It is important that the Elution Buffer B be placed directly onto the column bed, as this helps to increase recovery by ensuring an even passing of the buffer through the column. Do not pipette the Elution Buffer B onto the side of the column.

Purified DNA may not be performing well in downstream applications due to:

• Insufficient washing of plate with bound DNA.

  Traces of salt from the binding step may remain in the sample if the columns/wells are not properly washed with the Wash Solution A. Ensure that the columns/wells are washed with the Wash Solution A for 2 minutes during the washing step. Salt may interfere with downstream applications, and thus must be washed from the column.

• Eluted DNA contains residual ethanol.

  Ensure that the drying step is performed after the second DNA wash to remove all traces of ethanol.

Well clogging could be due to the following reasons:

• Insufficient Vacuum.

  Ensure that a vacuum pressure of at least -650 mbar or -25 in. Hg is developed.

• Centrifuge temperature is too low.

  Ensure that the centrifuge remains at room temperature throughout the procedure. Temperatures below 15°C may cause precipitates to form that can cause the wells to clog.