Abstract: The present invention features compositions and methods for quantifying detection of a target oligonucleotide in a sample in real time. These methods are compatible with target oligonucleotides amplified using a NEAR reaction.

Abstract: The invention provides compositions and methods for modifying the 3?-terminal ends of nucleic acids using DNA polymerase ? terminal transferase activity.

Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Abstract: Devices, containers, and methods are provided for performing biological analysis in a closed environment. Illustrative biological analyses include high density nucleic acid amplification and detection and immuno-PCR.

Abstract: Disclosed is a method for the cell-free expression of peptides or proteins in a liquid filled digital microfluidic device. The droplets having the components required for cell-free protein expression can be manipulated by electrokinesis in order to enhance levels of protein expression in the droplets.

Abstract: The present disclosure relates to multifunctional verification molecules, including molecules according to formula (I): G-L-(B)K-Q-U, wherein G, L, B, K, Q, and U are defined herein. The present disclosure also relates to methods of preparing and using such multifunctional verification molecules to remove defective multifunctional molecules and to quantify synthetic yield.

Abstract: One or more enzymes are used to repair damage in synthetic DNA molecules that encode digital information. The enzymes are included in a repair mixture containing one or more of DNA polymerase, DNA ligase, T4 Endonuclease, Endonuclease IV, Endonuclease VIII, and uracil glycosylase. The repair mixture may also contain one or more of a buffering solution, oxidized nicotinamide adenine dinucleotide (NAD+), and deoxyribose nucleoside triphosphates (dNTPs). The synthetic DNA molecules are incubated with the repair mixture for approximately four hours. Use of the repair solution allows recovery of the digital information from damaged DNA molecules.

Abstract: Modifications to both hardware and enzymatic reactions used in single cell analyses such as but not limited to Seq-well that enable significant increases in the yield of transcripts per cell, portability and ease of use, increased scalability of the assay, and linkage of transcript information to other measurements made in the picowell arrays are disclosed.

Abstract: The invention relates to an optimal selection method of gene chip probes for cancer screening. The method is characterized in that the gene chip probes capable of being used for cancer screening are obtained through three stages of constructing a point mutation site (SNV) group, constructing a candidate probe group and verifying and confirming probes on the basis of nucleic acid data of a confirmed case of a selected cancer.

Abstract: Devices, containers, and methods are provided for performing biological analysis in a closed environment. Illustrative biological analyses include nucleic acid amplification and detection and immuno-PCR.

Abstract: A bottleneck in the Next Generation Sequencing (NGS) workflow is the quantification of libraries for accurate pooling and loading of the sequencing instrument flow cell or chip. Disclosed herein are methods that improve performance and reduce time compared to existing methods.

Abstract: Methods for labeling and imaging the accessible genome using a transposase are disclosed. In some embodiments, a bifunctional transposase complex or transposome is used to insert adaptors comprising chemical tags selectively at accessible sites in the genome where active regulatory DNA is located. Various chemical tags can be used for labeling DNA at insertion sites, including, for example, fluorescent dyes for fluorescence imaging, metal particles for electron microscopy or magnetic manipulation of DNA, isotopic labels, or biotin or other ligands, haptens, substrates, or inhibitors that are recognized by streptavidin, antibodies, enzymes, or receptors. Labeling DNA in this manner can be used to provide spatial information regarding the positioning of regulatory DNA in the genome and makes possible the imaging and sorting of cells based on the status of their regulatory DNA.

Abstract: The present disclosure is concerned with compositions and methods for reducing the steps used in the generation of monoclonal clusters by combining the enzymes used for linearization and removal of unused surface primers.

Abstract: The invention includes a mutant Taq polymerase or biologically active fragment thereof, which can significantly extend and amplify a target sequence in comparison to wild type Taq polymerase, where the extension mixture includes asymmetrical cyanine dye, including SYBR Green I. The mutant Taq polymerase, or a biologically active fragment thereof, has one or more substitutions differing from the wild type as shown in Table I.

Abstract: The present invention relates to the evaluation of the performance of a component using a pair of dimer-forming primers. The method using the pair of dimer-forming primers according to the present invention can be used not only for evaluating the performance of components including a nucleic acid polymerase but also as an internal control in the detection of a target nucleic acid sequence.

Abstract: A polynucleotide sequencing method comprises (i) removing a label and a blocking moiety from a blocked, labeled nucleotide incorporated into a copy polynucleotide strand that is complementary to at least a portion of a template polynucleotide strand; and (ii) washing the removed label and blocking moiety away from the copy strand with a wash solution comprising a first buffer comprising a scavenger compound. Removing the label and blocking moieties may comprise chemically removing the moieties. The first buffer may also comprise an antioxidant and may be used in a scanning buffer used during a nucleotide detection step.

Abstract: The invention relates to reagents and methods for improving the efficiency of multiplex nucleic acid amplification, in particular where overlapping amplicons are to be generated. The invention also relates to reagents and methods for improving the efficiency of multistep nucleic acid amplification, in particular the performance of two separate amplification reactions designed to occur in sequence in the same reaction mixture or vessel. The invention further relates to reagents and methods for improving multistep nucleic acid amplification reactions by controlling the output of the first amplification reaction. In particular, primers are provided that minimise the formation of aberrant amplification products. Such primers are particularly useful where first and second amplification reactions take place in a single reaction mixture or vessel.

Abstract: This disclosure provides for methods and reagents for rapid multiplex RPA reactions and improved methods for detection of multiplex RPA reaction products. In addition, the disclosure provides new methods for eliminating carryover contamination between RPA processes.

Abstract: An analysis apparatus including a stage, an analysis device placed on the stage and including receiving sections which accommodate a sample and a reagent for biochemical reaction, and are communicated with one another through a flow path having an inlet and an outlet, a liquid introduction section which is connected to the inlet and supplies into the flow path the sample, the reagent, and an sealing liquid for sealing each of the receiving sections, and a waste liquid storage section which is connected to the outlet and stores as waste liquid an excess of the sample and the reagent and a part of the sealing liquid supplied to the flow path, an optical system which includes an objective lens, emits excitation light to the receiving sections and allows observation of fluorescence generated in the receiving sections by the excitation light, and a control unit that controls such that the sealing liquid and the excess of the sample and the reagent form an interface in the waste liquid storage section, and that the

Abstract: Systems and methods are provided for sample processing. A device may be provided, capable of receiving the sample, and performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing multiple assays. The device may comprise one or more modules that may be capable of performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing the steps using a small volume of sample.

Abstract: The present invention features compositions and methods for amplifying a target oligonucleotide in a sample, including detection of the target oligonucleotide in real time.

Abstract: Systems and methods for handling a variety of sample and preparatory fluids in a rack specifically configured for compatibility with predetermined liquid handlers such as automated pipettors or multi-channel manual pipettors and set up for magnetic based sample preparation. The rack can hold all of the necessary sample and reagent vials, and present them to the pipettor in some embodiments in a way that allows for parallel operation. The rack includes slidable magnets that in some embodiments are actuatable directly by the pipettor, eliminating a layer of complexity. Combined with a suitable pipettor the magnet enabled rack supports a multistep magnetic based sample preparation capability in a high throughput manner at one station that enhances sample purity throughout magnetic separation processes.

Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by exonuclease treatment and optionally blocking the 3? ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing.

Abstract: Methods for amplifying a target nucleic acid by self-sustained amplification methods are described. The methods are designed, in particular, to be carried out without use of specialised lab facilities or instruments. Compositions, lyophilised formulations, and kits for carrying out the methods are also described.

Abstract: Ultraspecific, programmable nucleic acid sensors capable of detecting and preferentially amplifying target DNA molecules comprising a particular SNP or mutation are provided. In some cases, the ultraspecific programmable nucleic acid sensors are useful for detecting SNP-containing DNA molecules indicative of cancer such as cell-free DNA circulating in the blood or indicative of organ transplant rejection Also provided are methods for construction of such ultraspecific nucleic acid sensors and methods for preferential amplification of target DNA molecules containing a mutation of interest, as well as testing systems for early cancer screening and routine monitoring of circulating cancer DNA using liquid biological samples such as serum, plasma, or saliva.

Abstract: The present invention features compositions and methods for quantifying detection of a target oligonucleotide in a sample in real time. These methods are compatible with target oligonucleotides amplified using a NEAR reaction.

Abstract: Methods for in vitro transcription and translation from an RCA product are provided. The methods comprise providing a double-stranded RCA product, wherein the double-stranded RCA product consists essentially of tandem repeats of a minimalistic expression sequence. The methods further comprise expressing a protein from the double-stranded RCA product in a cell-free expression system.

Abstract: The present invention relates to a method for introducing mutations into at least one target nucleic acid molecule comprising (a) providing at least one sample comprising at least one target nucleic acid molecule; and (b) amplifying the at least one target nucleic acid molecule using a low bias DNA polymerase. The present further relates to a use of a low bias DNA polymerase in a method for introducing mutations into one or more nucleic acid molecule(s), a group of sample tags, a method for designing the group of sample tags, a computer readable medium, and a method for preferentially amplifying target nucleic acid molecules.

Abstract: The present disclosure provides methods, compositions, and systems employing blocked primers. Aspects of the disclosure include providing a blocked primer reaction mixture that includes a blocked primer and a template nucleic acid component from a single cell; unblocking the blocked primer to produce an active primer reaction mixture and subjecting the activated primer reaction mixture to primer extension conditions, such as nucleic acid amplification conditions.

Abstract: The invention provides a method and kit for preventing inhibition of a thermal cycling reaction by protein coagulation in a sample.

Abstract: The present disclosure provides a digital PCR system. The system includes a droplet formation assembly and a droplet orifice assembly. The droplet formation assembly includes a heat conducting plate and a cover plate, at least one inverted U-shaped step is placed on a side surface of the cover plate, the heat conducting plate, the cover plate and the inverted U-shaped step together form a droplet formation chamber having an opening at a bottom. The droplet orifice assembly is connected below the droplet formation assembly, and includes a plurality of droplet orifices, the droplet orifice is connected with the droplet formation chamber, and a vaporization component is placed in the droplet orifice, the vaporization component vaporizes a digital PCR solution in the droplet orifice and rapidly pushes the digital PCR solution into a droplet forming oil in the droplet formation chamber, to form a digital PCR droplet.

Abstract: The present disclosure provides a solid phase method of making oligonucleotides via sequential coupling cycles including at least one coupling of a dinucleotide dimer subunit to a free 3?-terminal group of a growing chain. The oligonucleotides include at least two nucleoside subunits joined by a N3??P5? phosphoramidate linkage. The method may include the steps of (a) deprotecting the protected 3? amino group of a terminal nucleoside attached to a solid phase support, said deprotecting forming a free 3? amino group; (b) contacting the free 3? amino group with a 3?-protected amino-dinucleotide-5?-phosphoramidite dimer in the presence of a nucleophilic catalyst to form an internucleoside N3??P5? phosphoramidite linkage; and (c) oxidizing (e.g., sulfurizing) the linkage. The compositions produced by the subject methods may include a reduced amount of one or more (N?x) oligonucleotide products. Also provided are pharmaceutical compositions including the subject oligonucleotide compositions.

Abstract: The present invention is directed to methods for replicating, amplifying, and sequencing of nucleic acids using the thermostable, bifunctional replicase “TthPrimPol” from Thermus thermophilus HB27. The TthPrimPol enzyme is extremely tolerant to alterations of the nucleotides of the template nucleic acid. Therefore, in one aspect the invention discloses methods for replicating, amplifying and sequencing of damaged polynucleotide templates.

Abstract: Provided herein, among other things, is an automatable procedure that employs in vitro directed evolution to create DNA sequences that encode a ligand-responsive ribozyme and which, when transcribed, can control expression of genes they are coupled to. The method also allows creation of functional RNA sequences that bind target molecules, without requiring any modification or immobilization of the target.

Abstract: Compositions, methods and kits are disclosed for synthesizing and amplifying pools of probes using precursor oligonucleotides. In some aspects the precursor is amplified and nicking enzymes are used to separate the full length probes from the amplification products. The methods enable the preparation of single stranded DNA probes of defined sequence and length that are suitable for use in target detection assays.

Abstract: A hand-held molecular diagnostic test device includes a housing, an amplification (or PCR) module, and a detection module. The amplification module is configured to receive an input sample, and defines a reaction volume. The amplification module includes a heater such that the amplification module can perform a polymerase chain reaction (PCR) on the input sample. The detection module is configured to receive an output from the amplification module and a reagent formulated to produce a signal that indicates a presence of a target amplicon within the input sample. The amplification module and the detection module are integrated within the housing.

Abstract: Provided is a nucleic acid isothermal self-amplification method comprising, adding suitable palindrome complementary sequences at both ends of a target template to form a stem-loop structure spontaneously, and providing reagents and conditions as needed to perform self-amplification. The method does not require addition of additional amplification primers. The reagent comprises a DNA polymerase having a strand displacement activity. The method does not rely on exogenous amplification primers for amplification, has a constant amplification temperature without a complex temperature control equipment, and achieves rapid amplification. The amplification product is a long single-stranded DNA of a continuous complementary sequence and can be applied to special occasions. In addition, the amplification has no GC bias.

Abstract: Systems and methods are described for heating sample transfer lines between a source of a sample and a detection system to detect analytes of interest in the sample, where the sample is maintained in a heated state to maintain dissolved analytes of interest in solution.

Abstract: Techniques, systems, and devices are disclosed for non-thermal cycling of polymerase chain reaction (PCR). In one aspect, a method for cycling PCR includes receiving an electrolytic fluid including ions, primers, polymerase enzymes, nucleotides, and a double-stranded nucleic acid in a fluid chamber having a first electrode and a second electrode, applying an electric field across the first and the second electrodes to generate a first pH level of the electrolytic fluid to denature the double-stranded nucleic acid to at least partial single strands, and applying a second electric field across the first and second electrodes to produce a second pH level of the electrolytic fluid, in which the second pH level enables binding of a polymerase enzyme and a primer with a corresponding segment of the single strands.

Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.

Abstract: Methods, compositions, and kits are provided for quantification of genome editing.

Abstract: The invention relates to methods of RNA amplification, including methods for the reverse transcription of cDNA from RNA using a thermostable reverse transcriptase. In a particular aspect, the methods are capable of linear amplification of an RNA template through multiple cycles of cDNA synthesis.

Abstract: A reagent solution includes water, a nucleotide, and tris(2-carboxyethyl)phosphine in a range of 0.5 ?M to 1000 ?M. The reagent solution can further include a non-ionic surfactant in an amount of 0.001% to 1% or a biocidal agent in an amount of 0.001% to 1%. The reagent solution can include salts, such as sodium chloride or magnesium sulfate.

Abstract: Compositions and methods, systems, and kits for detecting and quantifying variations in numbers of molecules, particularly variations in gene dosage, e.g., due to gene duplication, or to variations from the normal euploid complement of chromosomes, e.g., trisomy of one or more chromosomes that are normally found in diploid pairs, without digital sequencing.

Abstract: The present invention provides detection systems and methods for detection of loci and genomic regions in a sample, including mixed samples, using hybridization to an array.

Abstract: The present disclosure provides, in some embodiments, methods and compositions for exponential amplification of single- and double-stranded DNA under isothermal conditions.

Abstract: Improved multiple displacement amplification (MDA) reagents and methods are provided.

Abstract: The present disclosure relates to multifunctional molecules, including molecules according to formula (I): ([(B1)M-D-L1]Y-H1)O-G-(H2-[L2-E-(B2)K]W)P, ??(I) wherein G, H1, H2, D, E, B1, B2, M, K, L1, L2, O, P, Y, and W are defined herein. The present disclosure also relates to methods of preparing and using such multifunctional molecules to identify encoded molecules capable of binding target molecules.

Abstract: Techniques regarding screening for mutations using nanoscale deterministic arrays are provided. For example, one or more embodiments described herein can comprise a method, which can comprise cleaving a deoxyribonucleic acid segment hybridized with a molecular probe to form a sample fluid. The cleaving can occur at a first end and a second end of the molecular probe. Also, the cleaving can comprise a cleaving agent that targets base pair mismatches. The method can also comprise supplying the sample fluid to a nanoscale deterministic lateral displacement array to screen for a single nucleotide polymorphism.

Abstract: Methods for amplification of a target nucleic acid sequence comprising strand invasion are provided in which strand invasion occurs both at upstream and downstream regions of the target nucleic acid sequence. Further provided are kits and compositions suitable for use in such methods. The methods may comprise amplifying a target nucleic acid sequence comprising a region of unknown sequence, or determining the sequence of a target nucleic acid comprising a region of unknown sequence.