A method of placing a single target molecule on a feature of a substrate, said substrate comprising a plurality of features separated by interstitial regions that lack a target polynucleotide, the method comprising: a. hybridizing a plurality of first and second capture primers immobilized to a feature on a substrate with at least one double stranded target polynucleotide, said double stranded target polynucleotide comprising a target region flanked by first and second capture primer binding regions complementary to said first and second capture primers, wherein the second strand of the double stranded target polynucleotide is linked to a target molecule, and wherein the first capture primer binding region of the first strand of the double stranded target polynucleotide is identical to the first capture primer, the second capture primer binding region of the first strand of the double stranded target polynucleotide is 100% complementary to the second capture primer, and wherein the first capture primer binding region of the second strand of the double stranded target polynucleotide is 100% complementary to the first capture primer, the second capture primer binding region of the second strand of the double stranded target polynucleotide contains at least one nucleotide difference from the second capture primer so that the second primer binding region in the double stranded target polynucleotide contains a base pair mismatch and b. amplifying said at least one target polynucleotide at an average amplification rate that exceeds an average transport rate of a target polynucleotide to a feature to produce a plurality of clonal amplicons complementary to said target polynucleotide wherein said amplifying comprises an isothermal amplification and wherein said target molecule comprises a polypeptide, carbohydrate, amino acid, monosaccharide, hapten, ligand, antigen, analyte, small molecule organic compound or inorganic compound. a. hybridizing a plurality of first and second capture primers immobilized to a feature on a substrate with at least one double stranded target polynucleotide, said double stranded target polynucleotide comprising a target region flanked by first and second capture primer binding regions complementary to said first and second capture primers, wherein the second strand of the double stranded target polynucleotide is linked to a target molecule, and wherein the first capture primer binding region of the first strand of the double stranded target polynucleotide is identical to the first capture primer, the second capture primer binding region of the first strand of the double stranded target polynucleotide is 100% complementary to the second capture primer, and wherein the first capture primer binding region of the second strand of the double stranded target polynucleotide is 100% complementary to the first capture primer, the second capture primer binding region of the second strand of the double stranded target polynucleotide contains at least one nucleotide difference from the second capture primer so that the second primer binding region in the double stranded target polynucleotide contains a base pair mismatch and b. amplifying said at least one target polynucleotide at an average amplification rate that exceeds an average transport rate of a target polynucleotide to a feature to produce a plurality of clonal amplicons complementary to said target polynucleotide wherein said amplifying comprises an isothermal amplification and wherein said target molecule comprises a polypeptide, carbohydrate, amino acid, monosaccharide, hapten, ligand, antigen, analyte, small molecule organic compound or inorganic compound.