A method for incorporating single-stranded DNA (ssDNA) barcoded polynucleotides into a nucleic acid origami nanostructure, the method comprising: (a) (i) performing first strand synthesis or in-emulsion droplet amplification of a single-stranded barcode nucleic acid to generate double-stranded barcode nucleic acids, wherein the single-stranded barcode nucleic acid comprises a sequence of nucleotides that can be used to distinguish and identify nucleic acids from the same cell flanked by priming sites complementary to one side of a single-stranded 5'-5' bowtie linker nucleic acid, the priming sites flanked by a gene specific mRNA capture sequence; and (ii) providing a single-stranded 5'-5' bowtie linker nucleic acid comprising a central 5'-5' phosphodiester linker flanked on at least one side by a sequence complementary to a nucleic acid origami nanostructure and flanked on both sides of the 5'-5' phosphodiester linker by priming sites complementary to a corresponding priming site on one strand of the double-stranded barcode nucleic acid; (b) combining the double-stranded barcode nucleic acids and the 5'-5' bowtie linker nucleic acid in an oil-emulsion droplet comprising reagents for elongating a nucleic acid; (c) thermal cycling the oil-emulsion droplet of step (b) comprising the double-stranded barcode nucleic acids and the 5'-5' bowtie linker nucleic acid sufficient to result in annealing of the priming sites on the single strands of the double-stranded barcode nucleic acids to complementary priming sites on the 5'-5' bowtie linker nucleic acid and elongation of ssDNA barcoded 5'-5' bowtie polynucleotides thereby yielding an elongation droplet comprising elongation products; (d) extracting elongation products from the elongation droplet; (e) purifying ssDNA barcoded 5'-5' bowtie polynucleotides from the extracted elongation products, wherein the ssDNA barcoded 5'-5' bowtie polynucleotides comprise from the 5' bowtie linkage extending to a 3' end: at least one side of the 5'-5' linker comprises a sequence complementary to a nucleic acid origami nanostructure, and both sides of the 5'-5' linker comprise a first priming site, a barcode sequence complementary to a barcode on an opposing arm of the 5'-5' bowtie polynucleotide, a second priming site and a mRNA capture sequence complementary to an mRNA of a gene of interest; and (f) incorporating the purified ssDNA barcoded 5'-5' bowtie polynucleotides into a nucleic acid origami nanostructure. (a) (i) performing first strand synthesis or in-emulsion droplet amplification of a single-stranded barcode nucleic acid to generate double-stranded barcode nucleic acids, wherein the single-stranded barcode nucleic acid comprises a sequence of nucleotides that can be used to distinguish and identify nucleic acids from the same cell flanked by priming sites complementary to one side of a single-stranded 5'-5' bowtie linker nucleic acid, the priming sites flanked by a gene specific mRNA capture sequence; and (ii) providing a single-stranded 5'-5' bowtie linker nucleic acid comprising a central 5'-5' phosphodiester linker flanked on at least one side by a sequence complementary to a nucleic acid origami nanostructure and flanked on both sides of the 5'-5' phosphodiester linker by priming sites complementary to a corresponding priming site on one strand of the double-stranded barcode nucleic acid; (b) combining the double-stranded barcode nucleic acids and the 5'-5' bowtie linker nucleic acid in an oil-emulsion droplet comprising reagents for elongating a nucleic acid; (c) thermal cycling the oil-emulsion droplet of step (b) comprising the double-stranded barcode nucleic acids and the 5'-5' bowtie linker nucleic acid sufficient to result in annealing of the priming sites on the single strands of the double-stranded barcode nucleic acids to complementary priming sites on the 5'-5' bowtie linker nucleic acid and elongation of ssDNA barcoded 5'-5' bowtie polynucleotides thereby yielding an elongation droplet comprising elongation products; (d) extracting elongation products from the elongation droplet; (e) purifying ssDNA barcoded 5'-5' bowtie polynucleotides from the extracted elongation products, wherein the ssDNA barcoded 5'-5' bowtie polynucleotides comprise from the 5' bowtie linkage extending to a 3' end: at least one side of the 5'-5' linker comprises a sequence complementary to a nucleic acid origami nanostructure, and both sides of the 5'-5' linker comprise a first priming site, a barcode sequence complementary to a barcode on an opposing arm of the 5'-5' bowtie polynucleotide, a second priming site and a mRNA capture sequence complementary to an mRNA of a gene of interest; and (f) incorporating the purified ssDNA barcoded 5'-5' bowtie polynucleotides into a nucleic acid origami nanostructure.