The disclosed technology relates to a molecular synthesis device. In one aspect, the molecular synthesis device comprises a synthesis array having an array of synthesis locations and an electrode arranged at each synthesis locations. The molecular synthesis device further comprises a non-volatile memory having an array of bit cells and a set of wordlines and a set of bitlines. Each bit cell comprises a non-volatile memory transistor having a control gate connected to a wordline, a first source/drain terminal, and a second source/drain terminal connected to a bitline. The electrode at each synthesis locations of the synthesis array is connected to the first source/drain terminal of a corresponding bit cell of the non-volatile memory.

Disclosed herein are formulations, substrates, and arrays for the synthesis of PNA chains and PNA-DNA chimera on microarrays. In some embodiments, the formulations include a photo-protective compound that shields any PNA monomers, PNA polymers, or PNA-DNA chimera already attached to a microarray from radiation exposure during the synthesis of the PNA or PNA-DNA chains. In some embodiments, substrates and arrays comprise a porous or a planar layer for synthesis and attachment of PNA or DNA monomers, or PNA or PNA-DNA polymers. In some embodiments, disclosed herein are formulations and methods for high efficiency coupling of PNA monomers or PNA polymers to a microarray substrate.

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.

Provided herein are methods and compositions for coating surfaces with polymers. The methods and compositions are suited for conducting biological reactions.

The invention describes a high-throughput method for simultaneously and selectively mixing one molecule with a plurality of other molecules. The resulting molecule-molecule complexes can then be captured on a surface, creating a microarray. This microarray can then be used to characterize and measure the molecule-molecule complexes (e.g. for reactions to other molecules).

In one example, a flow cell includes a substrate, an electrode positioned on the substrate, and a patterned material positioned on the electrode. In this example, the patterned material includes depressions separated by interstitial regions, and a functionalized surface of the electrode is exposed at each of the depressions. In this example, the flow cell further includes a primer grafted to the functionalized surface in each of the depressions. In another example, a flow cell includes a substrate and a patterned electrode positioned on the substrate. In this other example, the patterned electrode includes depressions separated by interstitial regions, and a functionalized surface of the substrate exposed at each of the depressions. In this other example, a primer is grafted to the functionalized surface in each of the depressions.

The present invention provides methods, compositions, and systems for distributing single polymerase molecules into array regions. In particular, the methods, compositions, and systems of the present invention result in a distribution of single polymerase molecules into array regions at a percentage that is larger than the percentage expected to be occupied under a Poisson distribution.

Embodiments of the present invention provide substrates having controllably co-located polymers of different sequences. Methods are provided that allow the fabrication of arrays of polymers on a substrate having controllably co-located polymers in regions of the array. For example, polymers of nucleic acids and peptides having different sequences and or compositions can be co-located within a region of a substrate. Also provided are arrays of DNA polymers wherein polymers having two different sequences are co-located within a region of an array. The co-located DNA polymers can comprise complementary DNA that is able to hybridize and form double stranded DNA. Arrays having regions comprising double stranded DNA are provided.

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.

A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.