A method for controlling DNA-polymerase activity upon a partially double-stranded polynucleotide complex by blocking activity of the DNA polymerase in bulk phase using a blocking molecule released only by capture of the complex in a nanopore, the method comprising: providing two separate, adjacent pools of a medium and an interface between the two pools, the interface having a nanopore so dimensioned as to allow sequential nucleotide-by-nucleotide passage from one pool to the other pool of only one polynucleotide at a time; providing a DNA polymerase having binding activity to a partially double-stranded polynucleotide complex; providing a polynucleotide complex comprising a DNA primer-template pair, wherein each DNA primer-template pair is annealed to a blocking molecule at the first base that will be added to the primer strand, wherein the blocking molecule comprises a loop at its end that is too large to enter the nanopore, wherein the blocking molecule either inhibits binding of the polymerase at the initiation site of the DNA primer-template pair or it allows the binding but prevents DNA-strand synthesis; providing a reagent that initiates DNA-polymerase activity; introducing the reagent, the polynucleotide complex and the DNA-polymerase into a first of the two pools; and incubating the pools at a suitable temperature; applying a potential difference between the two pools at a first polarity to capture the polynucleotide complex at the nanopore, to advance a single-stranded segment of the polynucleotide complex in the nanopore toward the second of the two pools, and to dissociate the blocking molecule from the DNA primer-template pair; reversing the potential difference a first time, thereby creating a second polarity, such that the activated dsDNA/ssDNA junction is exposed for DNA-polymerase binding and/or for start of DNA-polymerase activity; and reversing the potential difference a second time to create a third polarity. providing two separate, adjacent pools of a medium and an interface between the two pools, the interface having a nanopore so dimensioned as to allow sequential nucleotide-by-nucleotide passage from one pool to the other pool of only one polynucleotide at a time; providing a DNA polymerase having binding activity to a partially double-stranded polynucleotide complex; providing a polynucleotide complex comprising a DNA primer-template pair, wherein each DNA primer-template pair is annealed to a blocking molecule at the first base that will be added to the primer strand, wherein the blocking molecule comprises a loop at its end that is too large to enter the nanopore, wherein the blocking molecule either inhibits binding of the polymerase at the initiation site of the DNA primer-template pair or it allows the binding but prevents DNA-strand synthesis; providing a reagent that initiates DNA-polymerase activity; introducing the reagent, the polynucleotide complex and the DNA-polymerase into a first of the two pools; and incubating the pools at a suitable temperature; applying a potential difference between the two pools at a first polarity to capture the polynucleotide complex at the nanopore, to advance a single-stranded segment of the polynucleotide complex in the nanopore toward the second of the two pools, and to dissociate the blocking molecule from the DNA primer-template pair; reversing the potential difference a first time, thereby creating a second polarity, such that the activated dsDNA/ssDNA junction is exposed for DNA-polymerase binding and/or for start of DNA-polymerase activity; and reversing the potential difference a second time to create a third polarity.