Abstract: The present disclosure provides methods of sequencing polynucleotides and compounds, compositions useful for sequencing of polynucleotides. The chemical compounds include nucleotides and their analogs which possess a sugar moiety comprising a cleavable chemical group capping the 3?-OH group and a base that is attached to a detectable label through a cleavable linker comprising a disulfide bond. In addition, the disulfide bond(s) can be cleavable by a reducing reagent. In addition, after the disulfide bond(s) is/are cleaved by the reducing reagent, there is no free thiol group linked to the nucleotides. Examples of chemical compounds according to the present disclosure are shown as Formulae (IV) and (V).

Abstract: The present disclosure relates to method of monitoring a solid-phase reaction on a surface of a substrate by taking measurements at a plurality of positions on the surface. Properties of the surface are determined based on the measurements taken. Based on the properties determined, the extent of the solid-phase reaction is determined. This method can be achieved by using an ellipsometer and measuring the changes in thickness of the surface before and after the solid-phase reaction.

Abstract: The present disclosure provides methods, device, and system for a hybridization assay to detect nucleic acid targets. The assay may use a probe array format with addressable microwells. Each microwell may retain a plurality of copies of one probe which may be complementary to a portion of a specific nucleic acid target. The plurality of copies of probes may be produced from a pooled library of probe sequences by amplification techniques, including, rolling circle amplification and emulsion-PCR. Detection of hybridization may rely on methods using ion-sensitive field effect transistor (ISFET) and optical detectors to detect signals indicating the presence of the nucleic acid targets.

Abstract: The present disclosure relates to methods, processes and systems for enzymatic synthesis of oligonucleotide from a single-stranded, immobilized primer in the presence of a polymerase. Using the disclosed methods single-stranded oligonucleotides can be synthesized enzymatically from a single-stranded, immobilized primer in the presence of deoxyribonucleotide triphosphates or ribonucleotide triphosphates. Dideoxyribonucleotide triphosphates, deoxyribonucleotide triphosphates with reversible terminators, or ribonucleotide triphosphates with reversible terminators can be added enzymatically to the end of the primer or its extension products. According to the disclosed method, a single-stranded primer can bind to a template such that the thus-formed double-stranded structure can allow the polymerase to extend the primer at 3? end.

Abstract: The present disclosure provides methods, device, and system for biochips manufacturing including a wafer processing apparatus such as a spin cell platform, a synthesizer, a wafer handling robot, an ultraviolet aligner, and a wafer centering device. The wafer processing apparatus uses a nozzle in a lid to disperse a solution to the surface of a wafer. Further, the wafer is positioned on top of a vacuum chuck and does not spin while the solution is dispensed over the surface of the wafer via surface tension, thereby permitting the first solution to react with a reagent on the surface. Further, when dispensing the first solution, a separation gap between the lid and the wafer is at a predetermined distance, for example, from about 20 micrometer to about 200 micrometer.

Abstract: The present disclosure relates to methods, processes and systems for enzymatic synthesis of oligonucleotide from a single-stranded, immobilized primer in the presence of a polymerase. Using the disclosed methods single-stranded oligonucleotides can be synthesized enzymatically from a single-stranded, immobilized primer in the presence of deoxyribonucleotide triphosphates or ribonucleotide triphosphates. Dideoxyribonucleotide triphosphates, deoxyribonucleotide triphosphates with reversible terminators, or ribonucleotide triphosphates with reversible terminators can be added enzymatically to the end of the primer or its extension products. According to the disclosed method, a single-stranded primer can bind to a template such that the thus-formed double-stranded structure can allow the polymerase to extend the primer at 3? end.

Abstract: The present disclosure relates to processes for suspending stretched nucleic acids over surface features. These processes can be used to prepare stretched nucleic acids that are more active in enzymatic reactions and other reactions than those laid down on a flat surface. These processes can be achieved by using a photoresist layer on top of a substrate, stretch a nucleic acid on top of the surface, and then remove part of the photoresist to form surface features that suspend the stretched nucleic acid. Furthermore, the formation of a hydrogel layer over the stretched nucleic acid and the surface features can transfer the stretched nucleic acid to the hydrogel for further reactions, including enzymatic reactions.

Abstract: The present disclosure provides methods of sequencing polynucleotides and compounds, compositions useful for sequencing of polynucleotides. The chemical compounds include nucleotides and their analogs which possess a sugar moiety comprising a cleavable chemical group capping the 3?-OH group and a base that is attached to a label through a cleavable linker comprising a disulfide bond. In addition, both the disulfide bond and the cleavable chemical group are cleavable by a chemical reagent. Furthermore, after the disulfide bond is cleaved by the chemical reagent, there is no free thiol group linked to the base of the nucleotides according to the fragmentation reaction shown below as an example. Example compounds according to the present disclosure are shown as Formula (I): wherein w is 1-5; X is O, S, or BH3; B is a nucleotide base or an analog thereof, L1-3 are linkers; and D1 is a label.

Abstract: The present disclosure relates to processes for derivatizing a surface of a substrate with a covalently bonded thin film of poly(methylsilsesquioxane)-bonded polymers as a platform for the synthesis of a biomolecule array. These processes can also be used to prepare a surface of a substrate for an in situ solid-phase synthesis of biomolecule array.

Abstract: Provided herein are methods and compositions for the sequencing of long nucleic acids, such as DNA. The methods and compositions are suited for the spatial labeling and sequencing of long nucleic acid molecules.

Abstract: The present invention provides methods and systems for sequencing long nucleic acid fragments. In one aspect of the invention, methods, systems and reagent kits are provided for sequencing nucleic acid target sequences. Some embodiments of the methods, systems and reagent kits are particularly suitable for sequencing a large number of fragments, particularly long fragments.

Abstract: The present disclosure relates to processes for inverting oligonucleotide probes in an in situ synthesized array. These processes can be used to reverse the orientation of probes with respect to the substrate from 3?-bound to 5?-bound. These processes can also be used to reduce or eliminate the presence of truncated probe sequences from an in situ synthesized array.

Abstract: The present disclosure describes systems and methods to construct genomic DNA fragments library by stretching genomic DNA over an adapter-modified chip; using an enzyme cocktail comprising a first restriction enzyme, a ligase, and a second restriction enzyme to cut the genomic DNA into fragments and ligate the fragments to the adapters on the chip; and amplifying thus-obtained DNA by PCR amplification.

Abstract: The methods, systems, kits and reagents provided herein relate to the synchronization of dephased/prephased nucleic acid molecules during sequencing reactions. The methods, systems, kits and reagents provided herein can be utilized to improve the efficiency and accuracy of sequencing technologies.

Abstract: Provided herein are methods and compositions for analyzing epigenetic modifications of genomes. The methods and compositions are suited for complete epigenome sequencing of any modification for which an antibody or an affinity binding agent has been developed. In one aspect, provided herein is a method for analyzing epigenetic modification of a genome. In some embodiments of aspects provided herein, the method further comprises sequencing a sequencing library to generate sequence reads, and assembling the sequence reads with aid of a positional barcode sequence information. In some embodiments of aspects provided herein, the method further comprises determining a location of at least two different epigenetic modifications of the nucleic acid. Another aspect of the present disclosure provides a kit for analyzing an epigenetic modification of a nucleic acid.

Abstract: The present disclosure relates to processes for inverting oligonucleotide probes in an in situ synthesized array. These processes can be used to reverse the orientation of probes with respect to the substrate from 3?-bound to 5?-bound. These processes can also be used to reduce or eliminate the presence of truncated probe sequences from an in situ synthesized array.

Abstract: Provided herein are methods and compositions for the fabrication of patterned arrays, such as nucleotide arrays. The methods and compositions are suited for the transfer and reorientation of array components.

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

Abstract: A reagent storage and dispensing apparatus comprises a housing, storage wells disposed within an internal volume of the housing, and a valve. The housing comprises a shared outlet chamber. The wells can be selected to be in fluid communication with the shared outlet channel through individual outlet channels. The valve is coupled to the housing and is rotated to select a well to be in fluid communication with the shared outlet channel while preventing the remaining wells from being in fluid communication. As the valve is rotated, the wells and their individual outlet channels remain stationary. To dispense fluid from or draw fluid into the selected well, positive or negative pressure, respectively, is introduced into the internal volume. Pressurization of the internal volume also pressurizes the plurality of wells, though the valve allows only fluid flow for the selected well.

Abstract: The present disclosure provides methods, device, and system for wafer processing. The wafer processing apparatus uses lid dispenser to disperse at least one reagent to the surface of the wafer. Further, the wafer is positioned on top of a rotatable vacuum chuck configured to spread at least one reagent over the surface of the wafer via a centrifugal force or surface tension, thereby permitting the at least one reagent to react with an additional reagent. Further, when dispensing the at least one reagent, a separation gap between the lid dispenser and the wafer is at a predetermined distance, for example, from 50 ?m to 2 mm.