Abstract: Electrically controlled hybridization is used to selectively assemble oligonucleotides on the surface of a microelectrode array. Controlled activation of individual electrodes in the microelectrode array attracts oligonucleotides in solution to specific regions of the array where they hybridize to other oligonucleotides anchored on the array. The oligonucleotides that hybridize may provide locations for subsequent oligonucleotides to hybridize. The active electrodes and the oligonucleotides in solution may be varied during each round of synthesis. This allows for multiple oligonucleotides each with different and specific sequences to be created in parallel. This is accomplished without the use of phosphoramidite chemical synthesis or template-independent DNA polymerase enzymatic synthesis. Oligonucleotides created with these techniques may be used to encode digital data. Fully assembled oligonucleotides may be separated from the array and sequenced, stored, or otherwise processed.

Abstract: De novo polynucleotide synthesis is performed with a substrate-bound polymerase. The polymerase is attached to a solid substrate such as a microelectrode array. The polymerase adds nucleotides to growing polynucleotides strands that are also attached to the solid substrate. Spatial control of polymerase activity is achieved by changing the rate of nucleotide polymerization at selected locations on the surface of the solid substrate. The rate of polymerization is changed by inhibiting or promoting activity of the polymerase. In some implementations, activation of electrodes in the microelectrode array changes the rate of nucleotide polymerization. Nucleotides are added to the growing polynucleotide strands at areas where the polymerase is active. By varying the locations where the substrate-bound polymerase is active and the species of nucleotide added, a population of polynucleotides with different, arbitrary sequences is synthesized on the surface of the solid substrate.

Abstract: Recycling information is associated with objects through the use of molecular tags. The recycling information may describe the type of material that the object is made from as well as provide instructions for recycling. The molecular tags may be polynucleotides or other types of molecules including inorganic molecules. The molecular tags may be embedded within the object or attached to the surface of the object. At the end of the object's life, the molecular tags are read and the recycling information is used to appropriately recycle the object.

Abstract: High surface area coatings are applied to solid substrates to increase the surface area available for solid-phase synthesis of polymers. The high surface area coatings use three-dimensional space to provide more area for functional groups to bind polymers than an untreated solid substrate. The polymers may be oligonucleotides, polypeptides, or another type of polymer. The solid substrate is a rigid supportive layer made from a material such as glass, a silicon material, a metal material, and plastic. The coating may be thin films, hydrogels, microparticles. The coating may be made from a metal oxide, a high-? dielectric, a low-? dielectric, an etched metal, a carbon material, or an organic polymer. The functional groups may be hydroxyl groups, amine groups, thiolate groups, alkenes, n-alkenes, alkalines, N-Hydroxysuccinimide (NHS)-activated esters, polyaniline, aminosilane groups, silanized oxides, oligothiophenes, and diazonium compounds.

Abstract: Array-based enzymatic oligonucleotide synthesis creates a large number of polynucleotides using an uncontrolled and template independent polymerase such as terminal deoxynucleotidyl transferase (TdT). Spatial control of reaction conditions on the surface of the array allows creation of polynucleotides with a variety of arbitrary sequences. Spatial control may be implemented by removing protecting groups attached to nucleotides only at a selected location on the array or by other techniques such as location-specific regulation of enzymatic activity. The ratio of polynucleotides with protecting groups to unprotected polynucleotides used during a cycle of synthesis is adjusted to control the length of homopolymers created by the polymerase. Digital information may be encoded in the enzymatically synthesized polynucleotides.

Abstract: Electrically controlled hybridization is used to selectively assemble oligonucleotides on the surface of a microelectrode array. Controlled activation of individual electrodes in the microelectrode array attracts oligonucleotides in solution to specific regions of the array where they hybridize to other oligonucleotides anchored on the array. The oligonucleotides that hybridize may provide locations for subsequent oligonucleotides to hybridize. The active electrodes and the oligonucleotides in solution may be varied during each round of synthesis. This allows for multiple oligonucleotides each with different and specific sequences to be created in parallel. This is accomplished without the use of phosphoramidite chemical synthesis or template-independent DNA polymerase enzymatic synthesis. Oligonucleotides created with these techniques may be used to encode digital data. Fully assembled oligonucleotides may be separated from the array and sequenced, stored, or otherwise processed.

Abstract: Techniques for random access of particular DNA strands from a mixture of DNA strands are described. DNA strands that encode pieces of the same digital file are labeled with the same identification sequence. The identification sequence is used to selectively separate DNA strands that contain portions of the same digital file from other DNA strands. A DNA staple positions DNA strands with the identification sequence adjacent to sequencing adaptors. DNA ligase joins the molecules to create a longer molecule with the region encoding the digital file flanked by sequencing adaptors. DNA strands that include sequencing adaptors are sequenced and the sequence data is available for further analysis. DNA strands without the identification sequence are not joined to sequencing adaptors, and thus, are not sequenced. As a result, the sequencing data produced by the DNA sequencer comes from those DNA strands that included the identification sequence.

Abstract: Neural networks can be implemented with DNA strand displacement (DSD) circuits. The neural networks are designed and trained in silico taking into account the behavior of DSD circuits. Oligonucleotides comprising DSD circuits are synthesized and combined to form a neural network. In an implementation, the neural network may be a binary neural network in which the output from each neuron is a binary value and the weight of each neuron either maintains the incoming binary value or flips the binary value. Inputs to the neural network are one more oligonucleotides such as synthetic oligonucleotides containing digital data or natural oligonucleotides such as mRNA. Outputs from the neural networks may be oligonucleotides that are read by directly sequencing or oligonucleotides that generate signals such as by release of fluorescent reporters.

Abstract: A universal template strand built with universal base analogs is used as a template for polynucleotide synthesis. The universal template strand can hybridize to any sequence of nucleotides. A new polynucleotide is synthesized by using a polymerase to extend a primer hybridized to the universal template strand. Unlike primer extension in polymerase chain reactions, base pairing with nucleotides in the template strand does not specify the sequence of the new polynucleotide. Instead, the sequence of the new polynucleotide is specified by the order of addition of protected nucleotides. After addition of a single species of protected nucleotide, the blocking group is removed and another protected nucleotide is added. The order of nucleotide addition can be varied to create any sequence. After synthesis, the polynucleotide can be dehybridized from the universal template strand. The universal template strand may then be reused to synthesize a different polynucleotide.

Abstract: Array-based enzymatic oligonucleotide synthesis creates a large number of polynucleotides using an uncontrolled and template independent polymerase such as terminal deoxynucleotidyl transferase (TdT). Spatial control of reaction conditions on the surface of the array allows creation of polynucleotides with a variety of arbitrary sequences. Spatial control may be implemented by removing protecting groups attached to nucleotides only at a selected location on the array or by other techniques such as location-specific regulation of enzymatic activity. The ratio of polynucleotides with protecting groups to unprotected polynucleotides used during a cycle of synthesis is adjusted to control the length of homopolymers created by the polymerase. Digital information may be encoded in the enzymatically synthesized polynucleotides.

Abstract: Techniques for random access of particular DNA strands from a mixture of DNA strands are described. DNA strands that encode pieces of the same digital file are labeled with the same identification sequence. The identification sequence is used to selectively separate DNA strands that contain portions of the same digital file from other DNA strands. A DNA staple positions DNA strands with the identification sequence adjacent to sequencing adaptors. DNA ligase joins the molecules to create a longer molecule with the region encoding the digital file flanked by sequencing adaptors. DNA strands that include sequencing adaptors are sequenced and the sequence data is available for further analysis. DNA strands without the identification sequence are not joined to sequencing adaptors, and thus, are not sequenced. As a result, the sequencing data produced by the DNA sequencer comes from those DNA strands that included the identification sequence.

Abstract: An authentication assay using embedded deoxyribonucleic acid (DNA) taggants includes a substrate and a sample of an authenticity label collected from a product. The substrate has a plurality of assay locations, each of which includes a reporter oligonucleotide bound to the substrate. The reporter oligonucleotide includes a first region with a single-stranded toehold sequence, a second region with a universal sequence, and a third region with a unique sequence, the second and third regions being prehybridized with a complementary strand. The sample includes at least one fluorophore-labeled DNA taggant complementary to the first and second regions of the reporter oligonucleotide. Incubation of the substrate with the sample results in a toehold-mediated DNA strand displacement reaction that exchanges the complementary strand for the fluorophore-labeled DNA taggant. Excitation of the fluorophore molecule attached to the DNA taggant produces a pattern of light emitted at one or more assay locations.

Abstract: A universal template strand built with universal base analogs is used as a template for polynucleotide synthesis. The universal template strand can hybridize to any sequence of nucleotides. A new polynucleotide is synthesized by using a polymerase to extend a primer hybridized to the universal template strand. Unlike primer extension in polymerase chain reactions, base pairing with nucleotides in the template strand does not specify the sequence of the new polynucleotide. Instead, the sequence of the new polynucleotide is specified by the order of addition of protected nucleotides. After addition of a single species of protected nucleotide, the blocking group is removed and another protected nucleotide is added. The order of nucleotide addition can be varied to create any sequence. After synthesis, the polynucleotide can be dehybridized from the universal template strand. The universal template strand may then be reused to synthesize a different polynucleotide.

Abstract: Sequential assembly of oligonucleotide hairpins is used to create oligonucleotides that encode a specific sequence of arbitrary information. Each oligonucleotide hairpin includes a payload region in the loop region of the hairpin. The payload region encodes arbitrary information such as a binary digit. Overhang regions on the oligonucleotide hairpins hybridize to anchor strands attached to a substrate. The hybridized oligonucleotide hairpins are covalently attached to the anchor strands by ligase. Invading strands are used to open the hairpin structures by also hybridizing to the anchor strand and displacing the double-stranded stem region of the hairpin. This process is repeated with another oligonucleotide hairpin that hybridizes to the end of the previously added oligonucleotide hairpin. A microelectrode array may be used to control the location of hybridization and create multiple different oligonucleotides in parallel.

Abstract: Sequential assembly of oligonucleotide hairpins is used to create oligonucleotides with specific sequences. Each oligonucleotide hairpin includes a payload region containing one or more nucleotides that are added to the end of an anchor strand. Overhang regions on the oligonucleotide hairpins hybridize to anchor strands attached to a substrate. The hybridized oligonucleotide hairpins are covalently attached to the anchor strands by the activity of ligase. The oligonucleotide hairpins include an enzyme cleavage region which, when cleaved, separates the payload region from the remainder of the oligonucleotide hairpin. The oligonucleotide hairpin is separated from the anchor strand by denaturation and washed away. This process is repeated with additional oligonucleotide hairpins to add additional nucleotides to the ends of the anchor strands. A microelectrode array may be used to control the location of hybridization and create multiple oligonucleotides in parallel.

Abstract: This disclosure describes an efficient method to copy all polynucleotides encoding digital data of digital files in a polynucleotide storage container while maintaining random access capabilities over a collection of files or data items in the container. The disclosure further describes a process whereby random-access and sequencing of the polynucleotides are combined in a single step.

Abstract: The efficiency of polymer synthesis is increased by reducing the number of monomer addition cycles needed to create a set of polymer strands. The number of cycles depends on the sequences of the polymer strands and the order in which each type of monomer is made available for addition to the growing strands. Efficiencies are created by grouping the polymer strands into batches such that all the strands in a batch require a similar number of cycles to synthesize. Efficiencies are also created by selecting an order in which the monomers are made available for addition to the growing polymer strands in a batch. Both techniques can be used together. With these techniques, the number of cycles of monomer addition and commensurate reagent use may be reduced by over 10% as compared to naïve synthesis techniques.

Abstract: De novo polynucleotide synthesis is performed with a substrate-bound polymerase. The polymerase is attached to a solid substrate such as a microelectrode array. The polymerase adds nucleotides to growing polynucleotides strands that are also attached to the solid substrate. Spatial control of polymerase activity is achieved by changing the rate of nucleotide polymerization at selected locations on the surface of the solid substrate. The rate of polymerization is changed by inhibiting or promoting activity of the polymerase. In some implementations, activation of electrodes in the microelectrode array changes the rate of nucleotide polymerization. Nucleotides are added to the growing polynucleotide strands at areas where the polymerase is active. By varying the locations where the substrate-bound polymerase is active and the species of nucleotide added, a population of polynucleotides with different, arbitrary sequences is synthesized on the surface of the solid substrate.

Abstract: Neural networks can be implemented with DNA strand displacement (DSD) circuits. The neural networks are designed and trained in silico taking into account the behavior of DSD circuits. Oligonucleotides comprising DSD circuits are synthesized and combined to form a neural network. In an implementation, the neural network may be a binary neural network in which the output from each neuron is a binary value and the weight of each neuron either maintains the incoming binary value or flips the binary value. Inputs to the neural network are one more oligonucleotides such as synthetic oligonucleotides containing digital data or natural oligonucleotides such as mRNA. Outputs from the neural networks may be oligonucleotides that are read by directly sequencing or oligonucleotides that generate signals such as by release of fluorescent reporters.

Abstract: De novo polynucleotide synthesis is performed with a substrate-bound polymerase. The polymerase is attached to a solid substrate such as a microelectrode array. The polymerase adds nucleotides to growing polynucleotides strands that are also attached to the solid substrate. Spatial control of polymerase activity is achieved by changing the rate of nucleotide polymerization at selected locations on the surface of the solid substrate. The rate of polymerization is changed by inhibiting or promoting activity of the polymerase. In some implementations, activation of electrodes in the microelectrode array changes the rate of nucleotide polymerization. Nucleotides are added to the growing polynucleotide strands at areas where the polymerase is active. By varying the locations where the substrate-bound polymerase is active and the species of nucleotide added, a population of polynucleotides with different, arbitrary sequences is synthesized on the surface of the solid substrate.