Nanopore sequencing using charge blockade labels

A method for determining sequence information about at template nucleic acid molecule comprising

• providing a substrate having at least one nanopore, the at least one nanopore having a top opening and a bottom opening, and having a single polymerase enzyme attached proximal to an opening, the polymerase enzyme complexed with a primed template nucleic acid;
• contacting the substrate with a sequencing reaction mixture comprising reagents required for polymerase mediated nucleic acid synthesis including two or more different types of nucleotide analogs, each comprising a current blockade label attached to the phosphate portion of the nucleotide analogs such that the current blockade label is cleaved upon incorporation of the nucleotide into a growing strand,
• providing a voltage drop across the nanopore such that the current blockage label produces a change in current through the nanopore;
• measuring the current through the nanopore over time to detect the incorporation of nucleotides into the growing strand;
• and
• identifying the type of nucleotide incorporated into the growing strand using current blockage characteristics, thus determining sequence information about the template nucleic acid molecule.