Methods, systems, and apparatuses to encode data for storage in genetic materials. For example, a computing system may segment user data into a plurality of data blocks and generate seed data characterizing a plurality of fountain code seeds. Additionally, the computing system may, for each data block, implement a set of operations that generate one or more data packets. In some instances, the set of operations may include, for each of the plurality of fountain code seeds, determining a bit value and corresponding metaCode value and determining which of the fountain code seeds has a metaCode value of the bit value that matches a value of the bit position identified in the metadata. Moreover, the computing system may, for each data packet, cause an implementation of a second set of operations that synthesize a polynucleotide strand in accordance with at least bit values of the corresponding data packet.
Disclosed herein is a multiplex microarray having serially attached non-functionalized biomolecules attached to a polymer coating covering each electrode of an array of electrodes for assays and a method of making the multiplex microarray. The method comprises serially blocking the electrodes of the microarray with a blocking protein, electropolymerizing pyrrole or a functionalized pyrrole on the electrodes where the biomolecule is not present during polymerization, exposing the microarray to a biomolecular solution containing a non-functionalized biomolecule for attachment to the polymer coating, and then repeating the steps to form the multiplex microarray.
Functionalized aryldiazonium salts and films formed by electrografting of functionalized aryldiazonium salts are provided. Methods for purifying functionalized aryldiazonium salts and for coating solid support systems with functionalized aryldiazonium salts are also provided. These coated solid support systems can be used, for example, in methods of oligonucleotide synthesis.
C25B 11/095 - Electrodes formed of electrocatalysts on a substrate or carrier characterised by the electrocatalysts material consisting of at least one catalytic element and at least one catalytic compoundElectrodes formed of electrocatalysts on a substrate or carrier characterised by the electrocatalysts material consisting of two or more catalytic elements or catalytic compounds at least one of the compounds being organic
C25D 9/02 - Electrolytic coating other than with metals with organic materials
C25F 1/00 - Electrolytic cleaning, degreasing, pickling, or descaling
Provided herein are methods and compositions for oligonucleotide synthesis utilizing universal linker phosphoramidites. Methods and reagents are described with DNA synthesis using controlled pore glass (CPG) solid supports, and on platinum coated electrodes for electrochemical DNA synthesis. The universal linkers can be used as spacers in single-column PCR primer synthesis to generate 2 strands with free 3′-hydroxy termini after cleavage. The methods and compositions utilize a solid support system for synthesis of oligonucleotides, wherein the support has platinum electrodes and a universal linker, optionally wherein the platinum electrode is coated with an amine. The methods and compositions further describe use of universal linker phosphoramidites and the platinum electrode is coated with a monosaccharide, or a disaccharide.
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
C07C 247/04 - Compounds containing azido groups with azido groups bound to acyclic carbon atoms of a carbon skeleton being saturated
C07C 275/10 - Derivatives of urea, i.e. compounds containing any of the groups the nitrogen atoms not being part of nitro or nitroso groups having nitrogen atoms of urea groups bound to acyclic carbon atoms of an acyclic and saturated carbon skeleton being further substituted by singly-bound oxygen atoms
Systems and devices for reagent delivery are described. In one example, a disclosed fluidic device comprises: a plurality of first inlet ports; a first common channel; a plurality of first valves each associated with one first inlet port; a plurality of second inlet ports; a second common channel; a plurality of second valves each associated with one second inlet port; a plurality of outlet ports; a third common channel; a plurality of third valves each associated with one outlet ports; a first shutoff valve fluidically coupled between the first and the third common channels; and a second shutoff valve fluidically coupled between the second and the third common channels. Each first or second valve is fluidically coupled between a first or second inlet port and the first or second common channel. Each third valve is fluidically coupled between an outlet port and the third common channel.
Methods, systems, and apparatuses to encode data for storage in genetic materials. For example, a computing system may segment user data into a plurality of data blocks and generate seed data characterizing a plurality of fountain code seeds. Additionally, the computing system may, for each data block, implement a set of operations that generate one or more data packets. In some instances, the set of operations may include, for each of the plurality of fountain code seeds, determining a bit value and corresponding metaCode value and determining which of the fountain code seeds has a metaCode value of the bit value that matches a value of the bit position identified in the metadata. Moreover, the computing system may, for each data packet, cause an implementation of a second set of operations that synthesize a polynucleotide strand in accordance with at least bit values of the corresponding data packet.
G06N 3/12 - Computing arrangements based on biological models using genetic models
G06F 7/74 - Selecting or encoding within a word the position of one or more bits having a specified value, e.g. most or least significant one or zero detection, priority encoders
G06F 5/08 - Methods or arrangements for data conversion without changing the order or content of the data handled for changing the speed of data flow, i.e. speed regularising having a sequence of storage locations, the intermediate ones not being accessible for either enqueue or dequeue operations, e.g. using a shift register
Functionalized aryldiazonium salts and films formed by electrografting of functionalized aryldiazonium salts are provided. Methods for purifying functionalized aryldiazonium salts and for coating solid support systems with functionalized aryldiazonium salts are also provided. These coated solid support systems can be used, for example, in methods of oligonucleotide synthesis.
Provided herein are methods and compositions for oligonucleotide synthesis utilizing universal linker phosphoramidites. Methods and reagents are described with DNA synthesis using controlled pore glass (CPG) solid supports, and on platinum coated electrodes for electrochemical DNA synthesis. The universal linkers can be used as spacers in single-column PCR primer synthesis to generate 2 strands with free 3'-hydroxy termini after cleavage. The methods and compositions utilize a solid support system for synthesis of oligonucleotides, wherein the support has platinum electrodes and a universal linker, optionally wherein the platinum electrode is coated with an amine. The methods and compositions further describe use of universal linker phosphoramidites and the platinum electrode is coated with a monosaccharide, or a disaccharide.
C07D 487/02 - Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups in which the condensed system contains two hetero rings
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
B82B 3/00 - Manufacture or treatment of nanostructures by manipulation of individual atoms or molecules, or limited collections of atoms or molecules as discrete units
9.
Electrochemical deblocking solution for electrochemical oligomer synthesis on an electrode array
There is disclosed an electrochemical deblocking solution for use on an electrode microarray. There is further disclosed a method for electrochemical synthesis on an electrode array using the electrochemical deblocking solution. The solution and method are for removing acid-labile protecting groups for synthesis of oligonucleotides, peptides, small molecules, or polymers on a microarray of electrodes while substantially improving isolation of deblocking to active electrodes. The method comprises applying a voltage or a current to at least one electrode of an array of electrodes. The array of electrodes is covered by the electrochemical deblocking solution.
C25B 3/04 - Electrolytic production of organic compounds by reduction
C25B 3/02 - Electrolytic production of organic compounds by oxidation
C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
C25B 3/00 - Electrolytic production of organic compounds
C07D 213/16 - Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom containing only hydrogen and carbon atoms in addition to the ring nitrogen atom containing only one pyridine ring
C07C 309/30 - Sulfonic acids having sulfo groups bound to carbon atoms of six-membered aromatic rings of a carbon skeleton of non-condensed six-membered aromatic rings of six-membered aromatic rings substituted by alkyl groups
There is disclosed an electrode array architecture employing continuous and discontinuous circumferential electrodes. There is further disclosed a process for the neutralization of acid generated at anode(s) by base generated at cathode(s) circumferentially located to each other so as to confine a region of pH change. The cathodes can be displayed as concentric rings (continuous) or as counter electrodes in a cross pattern (discontinuous). In this way reagents, such as acid, generated in a center electrode are countered (neutralized) by reagents, such as base, generated at the corners or at the outer ring.
Disclosed herein is a multiplex microarray having serially attached non-functionalized biomolecules attached to a polymer coating covering each electrode of an array of electrodes for assays and a method of making the multiplex microarray. The method comprises serially blocking the electrodes of the microarray with a blocking protein, electropolymerizing pyrrole or a functionalized pyrrole on the electrodes where the biomolecule is not present during polymerization, exposing the microarray to a biomolecular solution containing a non-functionalized biomolecule for attachment to the polymer coating, and then repeating the steps to form the multiplex microarray.
There is disclosed an electrode array device having an adsorbed porous reaction layer for improved synthesis quality. The array comprises a plurality of electrodes on a substrate, wherein the electrodes are electronically connected to a computer control system. The array has an adsorbed porous reaction layer on the plurality of electrodes, wherein the adsorbed porous reaction layer comprises a chemical species having at least one hydroxyl group. In the preferred embodiment, the reaction layer is sucrose. A method for preparing an electrode array for improved synthesis quality is disclosed. The method comprises a cleaning method and a method of attachment of a reaction layer. The cleaning method comprises a plasma cleaning method and a chemical cleaning method. The reaction layer is attached after cleaning by exposing the microarray to a solution containing the chemical species having at least one hydroxyl group.
There is disclosed a microarray having base cleavable linkers and a process of making the microarray. The microarray has a solid surface with known locations, each having reactive hydroxyl groups. The density of the known locations is greater than approximately 100 locations per square centimeter. Optionally, oligomers are synthesized in situ onto the cleavable linkers and subsequently cleaved using a cleaving base. Optionally, the oligomers are cleaved and recovered as a pool of oligomers.
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
C40B 50/18 - Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creationParticular methods of cleavage from the solid support using a particular method of attachment to the solid support
C12Q 1/6837 - Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
14.
Neutralization and containment of redox species produced by circumferential electrodes
There is disclosed an electrode array architecture employing continuous and discontinuous circumferential electrodes. There is further disclosed a process for the neutralization of acid generated at anode(s) by base generated at cathode(s) circumferentially located to each other so as to confine a region of pH change. The cathodes can be displayed as concentric rings (continuous) or as counter electrodes in a cross pattern (discontinuous). In this way reagents, such as acid, generated in a center electrode are countered (neutralized) by reagents, such as base, generated at the corners or at the outer ring.
Disclosed herein is a multiplex microarray having serially attached non-functionalized biomolecules attached to a polymer coating covering each electrode of an array of electrodes for assays and a method of making the multiplex microarray. The method comprises serially blocking the electrodes of the microarray with a blocking protein, electropolymerizing pyrrole or a functionalized pyrrole on the electrodes where the biomolecule is not present during polymerization, exposing the microarray to a biomolecular solution containing a non-functionalized biomolecule for attachment to the polymer coating, and then repeating the steps to form the multiplex microarray.
C09D 4/00 - Coating compositions, e.g. paints, varnishes or lacquers, based on organic non-macromolecular compounds having at least one polymerisable carbon-to-carbon unsaturated bond
C40B 40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
16.
MULTIPLEX MICROARRAY OF SERIALLY DEPOSITED BIOMOLECULES ON A MICROARRAY
Disclosed herein is a multiplex microarray having serially attached non-functionalized biomolecules attached to a polymer coating covering each electrode of an array of electrodes for assays and a method of making the multiplex microarray. The method comprises serially blocking the electrodes of the microarray with a blocking protein, electropolymerizing pyrrole or a functionalized pyrrole on the electrodes where the biomolcule is not present during polymerization, exposing the microarray to a biomolecular solution containing a non-functionalized biomolecule for attachment to the polymer coating, and then repeating the steps to form the multiplex microarray.
C08F 2/58 - Polymerisation initiated by direct application of electric current
H01L 27/28 - Devices consisting of a plurality of semiconductor or other solid-state components formed in or on a common substrate including components using organic materials as the active part, or using a combination of organic materials with other materials as the active part
There is disclosed a microarray having base cleavable linkers and a process of making the microarray. The microarray has a solid surface with known locations, each having reactive hydroxyl groups. The density of the known locations is greater than approximately 100 locations per square centimeter. Optionally, oligomers are synthesized in situ onto the cleavable linkers and subsequently cleaved using a cleaving base. Optionally, the oligomers are cleaved and recovered as a pool of oligomers.
C40B 50/18 - Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creationParticular methods of cleavage from the solid support using a particular method of attachment to the solid support
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
18.
Microarray having a base cleavable sulfonyl linker
The present invention provides a microarray having base cleavable, sulfonyl-containing linkers and a process to make the microarray. Oligonucleotides of any sequence may be synthesized on the microarray having the cleavable linker. The oligonucleotides may be cleaved and recovered as a pool of oligonucleotides having a three prime phosphate moiety. Specifically, the microarray is an electrode containing microarray, and the oligonucleotides are electrochemically synthesized.
C40B 40/00 - Libraries per se, e.g. arrays, mixtures
C40B 40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof
C40B 40/12 - Libraries containing saccharides or polysaccharides, or derivatives thereof
C40B 50/00 - Methods of creating libraries, e.g. combinatorial synthesis
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C07H 21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
19.
Process and apparatus for measuring binding events on a microarray of electrodes
There is disclosed a process and apparatus for reading electrical current of electrodes on a microarray of electrodes. Those electrodes having binding events are detected by a difference in electrical current flow. Enzymes on targets catalyze the conversion of substrate to product, which is detectable by electrochemical reduction at each electrode on the microarray of electrodes. The apparatus has an integration circuit that provides a voltage output that is measured and recorded over time and used to calculate an average current flow. A potentiometer equalizes voltage at electrodes undergoing measurement compared to grounded electrodes.
There is disclosed a process for performing an isolated Pd(II) mediated oxidation reaction electrochemically. The inventive process is performed on an electrode array device having a plurality of separately addressable electrodes. Preferably, the Pd(II) mediated oxidation is a Wacker reaction. Specifically, there is disclosed a process for conducting an isolated Pd(II) mediated oxidation on a plurality of electrodes, comprising providing an electrode array device having a plurality of electrodes with a conductive electrode surface and a matrix or coating material over the electrodes surfaces; providing a solution bathing the electrode array matrix or coating material and electrode surfaces, wherein the solution comprises a transition metal species and a confining agent; and biasing one or a plurality of electrodes (“selected electrode or electrodes”) with a voltage or current to regenerate the transition metal species required for the isolated Pd(II) mediated oxidation, whereby the confining agent limits diffusion of the transition metal species to a volume surrounding each selected electrode surface.
C07D 311/08 - Benzo [b] pyrans, not hydrogenated in the carbocyclic ring with oxygen or sulfur atoms directly attached in position 2 not hydrogenated in the hetero ring
21.
Electrochemical deblocking using a hydrazine derivative
A method for electrochemical removal of acid-labile protecting groups on an electrode microarray using an organic solution is disclosed. The solution comprises a hydrazine derivative and a salt in an organic solvent. The hydrazine derivative has at least one hydrazine group having at least one hydrogen. The hydrazine derivative provides acidic reagent when an electrode is active and isolates the acidic reagent to the area around the active electrode. The salt is an organic salt or ionic liquid having a concentration sufficient to provide electrochemical conductivity under an applied voltage. During the applied voltage, acidic reagent is generated, which removes acid-labile protecting groups thereby allowing continued addition of monomers to build a custom microarray of oligonucleotides, peptides, or other polymers.
patents
