The rapid extraction of high-purity nucleic acids from complex biological samples using conventional methods is complicated. Therefore, in this study, glycine-pillar[6]arene (Gly-P6)-functionalized tapered nanochannels were constructed using 32-mer single-stranded E. coli DNA (ssDNA) as a model sequence, which can selectively transport ssDNA by multiple noncovalent forces (transport flux of 2.65 nM cm-2 h-1) under the interference of amino acids and other substances. In view of these prospective results, the selective transport of nucleic acids with nanochannels could be applied in the design of nucleic acid enrichment and separation systems in the future.