Analysis of a polynucleotide via a nanopore system

A method of analyzing a target polynucleotide that comprises at each nucleotide position a member of a set of different nucleotides, the method comprising:

• A) obtaining an expanded single-stranded polynucleotide that comprises a sequence of expanded units, wherein each expanded unit:
• a) ordinally corresponds to a particular nucleotide position of the target polynucleotide, and
• b) comprises:
• i) a clock nucleotide sequence, the clock nucleotide sequence being common among expanded units of the expanded polynucleotide, and ii) at least one signal nucleotide, the at least one signal nucleotide being indicative of the member of the set of different nucleotides at the particular nucleotide position;
• B) hybridising two or more single-stranded polynucleotides to the expanded single-stranded polynucleotide to form an expanded polynucleotide comprising two or more sections of double-stranded polynucleotide separated by single-stranded polynucleotide;
• C) translocating the expanded polynucleotide through a nanopore until a first section of double-stranded polynucleotide reaches the nanopore and halts translocation of the expanded polynucleotide;
• D) making electrical measurements dependent on the expanded polynucleotide within the pore;
• E) un-hybridising the first section of double-stranded polynucleotide such that translocation of the expanded polynucleotide through the nanopore continues;
• and
• F) determining the sequence of one or more regions of the target polynucleotide based on the measurements obtained in step E).