FAQ: Do you have any recommendations for purification of ssDNA?

The Monarch PCR & DNA Cleanup Kit (5 μg) can be used to purify ssDNA from enzymatic reactions, as well as for general cleanup to remove potential inhibitors of PCR, etc. Single-stranded DNA binds less tightly than dsDNA, and strength of binding will be affected by length, sequence, and the formation of any secondary structure. For ssDNA <200 nt, we recommend using the Oligonucleotide Cleanup Protocol, however, it is important to note that this protocol shifts the cutoff size for DNA binding as compared to the standard protocol (18 nt versus 50 nt). For ssDNA >200nt, we recommend following the standard protocol with the 7:1 ratio of binding buffer to sample before applying the DNA to the column. It is difficult to predict the recovery efficiency of ssDNA; we therefore recommend a trial recovery with the sequence of interest before using your entire sample.