This report has presented the development of a His3-tagbinding
DNA molecule—the H3T aptamer. The biochemical analysis
revealed that (i) the binding/elution of the H3T aptamer/His3-
tag can be controlled by sodium ion concentration and (ii)
imidazole is not necessary to efficiently release the His3-tag
from the H3T aptamer. Further investigations confirmed that
the chromatography system developed here can be used for the
purification of recombinant proteins containing the His3-tag from
an E. coli total protein extract. Comparative analysis demonstrated
that the power of the H3T aptamer-based chromatography
was superior to IMAC when purification of His3-tagged proteins
was tested. Although the presented chromatography system is
free of the disadvantages of IMAC, the H3T aptamer’s molecular
weight, which is 18.7 kDa, as well as its probably complex
three-dimensional structure, may limit the power of this technique
in the case of particular proteins. When the His3-tag is
hidden inside the protein structure, it may make the purification
of the protein difficult. However, it is this very feature that
makes binding highly selective, and hence less likely that there
will be unwanted binding with histidine-rich host protein impurities
as would be the case with the divalent metal ions used in
IMAC