We describe glass nanocapillaries with single-stranded DNA molecules (ssDNA) covalently attached to the capillary surface. These DNA-functionalized nanocapillaries selectively facilitate the translocation of target ssDNA that is complementary to the probe ssDNA. In addition, the complementary target ssDNA exhibits an event duration time longer than that of the noncomplementary target ssDNA. The temperature dependence measurements of translocation events show that the longer duration time is a result of an interaction between probe and target ssDNA and is dependent on the base pair binding strength. These results demonstrate that single-base mismatch transport selectivity can be achieved using the DNA-functionalized nanocapillaries.