Abstract: Methods and compositions relate to the sorting and cloning of high fidelity nucleic acids using high throughput sequencing. Specifically, nucleic acid molecules having the desired predetermined sequence can be sorted from a pool comprising a plurality of nucleic acids having correct and incorrect sequences.

Abstract: Aspects of the invention relate to methods, compositions for synthesizing high fidelity oligonucleotides.

Abstract: Disclosed are devices and methods to synthesize polynucleotides and libraries of polynucleotides such as libraries of oligonucleotides. In exemplary embodiments, the device includes a support having a plurality of features. Each feature contains a plurality of oligonucleotides. Within each feature, each of the plurality of oligonucleotides includes an identical predetermined subunit sequence of X nucleosides and a degenerate sequence of Y nucleosides. A predetermined combination of a subset of the features can be used to produce a polynucleotide having a predetermined sequence of Z nucleosides.

Abstract: Disclosed are methods for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides. In exemplary embodiments, the methods involve synthesis and/or amplification of different oligonucleotides immobilized on a solid support, release of synthesized/amplified oligonucleotides in solution to form droplets, recognition and removal of error-containing oligonucleotides, moving or combining two droplets to allow hybridization and/or ligation between two different oligonucleotides, and further chain extension reaction following hybridization and/or ligation to hierarchically generate desired length of polynucleotide products.

Abstract: Disclosed are devices and methods to synthesize polynucleotides and libraries of polynucleotides such as libraries of oligonucleotides. In exemplary embodiments, the device includes a support having a plurality of features. Each feature contains a plurality of oligonucleotides. Within each feature, each of the plurality of oligonucleotides includes an identical predetermined subunit sequence of X nucleosides and a degenerate sequence of Y nucleosides. A predetermined combination of a subset of the features can be used to produce a polynucleotide having a predetermined sequence of Z nucleosides.

Abstract: Methods and apparatus relate to the synthesis of high fidelity polynucleotides and to the reduction of sequence errors generated during synthesis of nucleic acids on a solid support. Specifically, design of support-bound template oligonucleotides is disclosed. Assembly methods include cycles of annealing, stringent wash and extension of polynucleotides comprising a sequence region complementary to immobilized template oligonucleotides. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products.

Abstract: In exemplary implementations of this invention, a photoelectrode includes a semiconductor for photocarrier generation, and a catalyst layer for altering the reaction rate in an adjacent electrolyte. The catalyst layer covers part of the semiconductor. The thickness of the catalyst layer is less than 60% of its minority carrier diffusion distance. If the photoelectrode is a photoanode, it has an OEP that is more than the potential of the valance band edge but less than the potential of the Fermi level of the semiconductor. If it is a photocathode, it has an RHE potential that is less than the potential of the conduction band edge but more than the potential of the Fermi level of the semiconductor. The absolute value of difference (OEP minus potential of valence band edge, or RHE potential minus potential of conduction band edge) is greater than zero and less than or equal to 0.2V.

Abstract: Methods and devices relate to the isolation of nucleic acids of interest from within a population of nucleic acids such as libraries of nucleic acid sequences.

Abstract: Disclosed are methods for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides. In exemplary embodiments, the methods involve synthesis and/or amplification of different oligonucleotides immobilized on a solid support, release of synthesized/amplified oligonucleotides in solution to form droplets, recognition and removal of error-containing oligonucleotides, moving or combining two droplets to allow hybridization and/or ligation between two different oligonucleotides, and further chain extension reaction following hybridization and/or ligation to hierarchically generate desired length of polynucleotide products.

Abstract: Methods and compositions relate to the assembly of high fidelity nucleic acids. Specifically, nucleic acid molecules having a desired predetermined sequence can be assembled after failure to assemble in conventional assembly. Aspects of the disclosure relate to methods of assembling a target nucleic acid molecule having a desired or predetermined sequence.

Abstract: Methods and devices relate to the isolation of nucleic acids of interest from within a population of nucleic acids such as libraries of nucleic acid sequences.

Abstract: Aspects of the disclosure relate to compositions and methods for site-directed DNA nicking and/or cleaving, and use thereof in, for example, polynucleotide assembly.

Abstract: Methods for designing and producing non-random libraries of nucleic acids are presented. In particular, synthesis of nonrandom libraries by multiplexed polynucleotide synthesis is utilized. Each library member may encode a promoter, ribosomal binding site and polypeptide.

Abstract: Systems and methods are provided to evaluate a search engine using search results retrieved from a plurality of different search engines. For example, a controller can randomly distribute a set of pre-formulated queries to a plurality of computers to query the search engines at random times to obtain search results and combine the search results to evaluate the completeness of a query result provided by a particular search engine. The controller may simulate the random queries from users using a set of computers and may reduce the burden on the search engines by spreading out the query activities over a period of time, such as a month.

Abstract: Methods and apparatus relate to reduction of sequence errors generated during synthesis of nucleic acids on a microarray chip. The error reduction can include synthesis of complementary stands (to template strands), using a short universal primer complementary to the template strands and polymerase. Heteroduplex can be formed be melting and re-annealing complementary stands and template strands. The heteroduplexes containing a mismatch can be recognized and cleaved by a mismatch endonuclease. The mismatch-containing cleaved heteroduplexes can be removed from the microarray chip using a global buffer exchange. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products.

Abstract: A pipetting system identifies and records data regarding pipetting events, including the time and well into which a pipette dispenses liquid and the volume of liquid dispensed into the well. The pipetting system also measures and records other data regarding the context of pipetting events. This other data includes the speed of pipetting, the pressure exerted on a plunger of the pipette by a finger of a user, and the temperature, humidity and lighting conditions at a well tray into which the liquid is dispensed. The pipetting system includes a pipette that has multiple cylinders and multiple corresponding pistons. Each cylinder has different diameter. Thus, a down-stroke of the pistons causes each of the cylinders to expel a different amount of air. A rotatable mechanism selects which cylinder is connected by an airway to a pipette tip and which other cylinders vent directly to the ambient atmosphere.

Abstract: Methods and apparatus relate to the synthesis of polynucleotides having a predefined sequence on a support. Assembly methods include primer extension to generate overlapping construction oligonucleotides and assembly of the polynucleotides of interest onto an anchor support-bound oligonucleotides. Methods and apparatus for selection of polynucleotides having the predefined sequence and/or length are disclosed.

Abstract: Methods and apparatus relate to reduction of sequence errors generated during synthesis of nucleic acids on a microarray chip. The error reduction can include synthesis of complementary stands (to template strands), using a short universal primer complementary to the template strands and polymerase. Heteroduplex can be formed be melting and re-annealing complementary stands and template strands. The heteroduplexes containing a mismatch can be recognized and cleaved by a mismatch endonuclease. The mismatch-containing cleaved heteroduplexes can be removed from the microarray chip using a global buffer exchange. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products.

Abstract: Disclosed are devices and methods to synthesize polynucleotides and libraries of polynucleotides such as libraries of oligonucleotides. In exemplary embodiments, the device includes a support having a plurality of features. Each feature contains a plurality of oligonucleotides. Within each feature, each of the plurality of oligonucleotides includes an identical predetermined subunit sequence of X nucleosides and a degenerate sequence of Y nucleosides. A predetermined combination of a subset of the features can be used to produce a polynucleotide having a predetermined sequence of Z nucleosides.

Abstract: Disclosed are devices and methods to synthesize polynucleotides and libraries of polynucleotides such as libraries of oligonucleotides. In exemplary embodiments, the device includes a support having a plurality of features. Each feature contains a plurality of oligonucleotides. Within each feature, each of the plurality of oligonucleotides includes an identical predetermined subunit sequence of X nucleosides and a degenerate sequence of Y nucleosides. A predetermined combination of a subset of the features can be used to produce a polynucleotide having a predetermined sequence of Z nucleosides.