Abstract: Nanopore arrays are fabricated by controlled breakdown in solid-state membranes integrated within polydimethyl-siloxane (PDMS) microfluidic devices. This technique enables the scalable production of independently addressable nanopores. By confining the electric field within the microfluidic architecture, nanopore fabrication is precisely localized and electrical noise is significantly reduced during sensing.

Abstract: A device comprising a support part is disclosed. The support part is configured to receive a tip holder, a liquid waste container and a multiwell plate. The multiwell plate comprises at least one row of vessels which comprise a closed bottom and an open top. A method of removing liquid waste during magnetic separation using such a device is also disclosed.

Abstract: Methods and systems for extracting DNA from a sample are provided. A method includes: lysing red blood cells of the sample using a first solution; dissolving lipids of cellular membranes in the sample using a second solution; and releasing DNA of the sample into a buffer using a third solution.

Abstract: A method for enrichment and isolation of microbial cells and microbial nucleic acids from a biological sample is described. The method comprises (i) adding to an initial volume of biological sample a differential cell lysis solution to obtain a final concentration of 0.1 to 1% of SDS in the sample; (ii) mixing the solution obtained in step (i) for a period of time sufficient to lyse the host cells present in the biological sample, while preserving the integrity of cells; and (iii) separating the microbial cells from the lysed host cells components. Differential cell lysis solutions and kits for practicing the method of the present invention are also provided.

Abstract: The present invention provides, among other things, methods of purifying messenger RNA (mRNA) including the steps of subjecting an impure preparation comprising in vitro synthesized mRNA to a denaturing condition, and purifying the mRNA from the impure preparation from step (a) by tangential flow filtration, wherein the mRNA purified from step (b) is substantially free of prematurely aborted RNA sequences and/or enzyme reagents used in in vitro synthesis.

Abstract: The invention provides compositions and methods for preserving a biological material—such as a protein, a nucleic acid or a biological sample, or any combination thereof—in a substantially water-free, nonionic or ionic organic solvent. Improved preservation, including for example the stability and/or the solubility of the biological material in the substantially water-free fluid medium, is achieved with compositions comprising one or more substances (e.g., an antioxidant) described in the disclosure, and/or a metal salt. The biological material is soluble and stable, and retains its function and activity, when it is preserved in the substantially water-free fluid medium at ambient temperature or higher for extended periods of time. Therefore, the composition comprising the biological material does not need to be refrigerated or frozen during shipping or storage.

Abstract: The present invention concerns an improved method for the isolation of nucleic acids such as DNA and RNA from bacterial, plant, animal or human cells as well as from cell cultures and virus cultures, wherein the nucleic acid is immobilised on a matrix having a silicon-oxygen compound in the presence of a chaotropic agent and an alkanol, carried out in a temperature range of 36° to 75° C.

Abstract: Includes the following steps: (1) Mix organs and tissues with formamide and monovalent cation salt solution, homogenize them to obtain the dehydrated biological sample; (2) Mix the dehydrated biological sample with monovalent cation salt solution for incubation; (3) Add the monovalent cation salt solution with precipitation effect to the mixture, mix them and centrifuge, then pour the supernatant into another centrifuge tube; (4) Add isopropanol, mix it and centrifuge, and then discard the upper phase liquid, the lower phase liquid and the visible residual impurities between the upper and lower phases to get white RNA precipitate. This method proposed in the invention enables efficient isolation of protein from RNA in the biological samples.

Abstract: Disclosed herein are methods, compositions, and kits for isolating actively translated mRNA from heterogeneous cell populations. Also disclosed herein are methods, compositions, and kits for identifying cell types that respond to stimuli in heterogeneous cell populations.

Abstract: A set of paramagnetic particles synthesized by co-precipitation methods wherein an alkaline hydroxide solution is mixed with a metal salt solution. The alkaline hydroxide features ammonium hydroxide, potassium hydroxide, sodium hydroxide, or mixtures thereof. The metal salt solution features at least one ferrous salt and at least one tetravalent metal salt selected from Group 4 elements of the Periodic Table. The concentration of the ferrous salt is equal to or greater than the concentration of the tetravalent metal salt. The paramagnetic particles may be used for bioprocessing via magnetic fields. Bioprocessing, for example, may include purifying, concentrating, or detecting biomolecules of interest (e.g., nucleic acids, carbohydrates, peptides, proteins, other organic molecules, cells, organelles, microorganisms, viruses, etc.), or other magnetic field-based processes common to applications in separation science, diagnostics, molecular biology, protein chemistry, and clinical practice.

Abstract: Disclosed herein are processes for collecting nucleic acids from particulate samples. One embodiment disclosed herein relates to the use of ultrasonic energy to simultaneously shear large nucleic acid molecules and large particulates to very small sizes prior to or during a chemical binding step to a nucleic acid binding surface. Another embodiment involves crushing the nucleic acid binding surface prior to eluting the bound nucleic acid molecules to enable better wetting of the nucleic acid binding surface and easier diffusion of bound nucleic acid molecules out of the nucleic acid binding surface.

Abstract: A fluid sample extraction device is disclosed comprising a housing defining an internal fluid passage having a distal open end and a proximal open end and a porous medium within the fluid passage, between the distal open end and proximal open end. The porous medium, which may be glass, is configured to allow fluid flow in the fluid passage to flow around the porous medium, toward the proximal open end of the housing, when fluid is drawn from the distal open end toward the proximal open end, and to allow fluid in the fluid passage to flow toward the distal open end of the housing, through the porous medium when the fluid is forced toward the distal open end. The porous medium is also configured to capture nucleic acids in the porous medium from the fluid when fluid is forced through the porous medium. Devices and kits are also disclosed.

Abstract: Includes the following steps: (1) Mix organs and tissues with formamide and monovalent cation salt solution, homogenize them to obtain the dehydrated biological sample; (2) Mix the dehydrated biological sample with monovalent cation salt solution for incubation; (3) Add the monovalent cation salt solution with precipitation effect to the mixture, mix them and centrifuge, then pour the supernatant into another centrifuge tube; (4) Add isopropanol, mix it and centrifuge, and then discard the upper phase liquid, the lower phase liquid and the visible residual impurities between the upper and lower phases to get white RNA precipitate. This method proposed in the invention enables efficient isolation of protein from RNA in the biological samples.

Abstract: Methods, devices, and systems for integrating extraction and purification of bio-sample regions and materials with patient analysis, diagnosis, follow up, and treatment. The invention provides a means to insert disclosed substrates, cartridges, and cartridge-processing instrument or instruments into a standard clinic or pathology laboratory workflow. Specifically, we disclose methods, devices, and systems for inserting standard pathology slides into disclosed cartridges and cartridge-processing instruments, either manually, semi-automatically, automatically, or by robotic means.

Abstract: A simple and convenient method for concentrating a biomolecule, including protein or nucleic acid molecules, from a sample. Purified and isolated biomolecules obtained by this method. Methods for improving the specificity or sensitivity of detecting a biomolecule by concentration and/or purification or isolation of the biomolecule according to the method of the invention.

Abstract: Alkynyl-derivatized cap analogs, alkynyl-modified capped RNA, 1,4-disubstituted triazole-derivatized capped RNA, methods of preparation, methods of isolation, and uses thereof are provided. The “click” modification facilitates detection and isolation of capped RNAs and the 1,4-disubstituted triazole derivatives formed by the “click” reaction are useful for producing RNA transcripts and encoded protein.

Abstract: The method for isolating nucleic acids from a food sample comprising the following steps: a) obtaining a food enrichment culture; b) transferring a portion of the food enrichment culture into a reaction vessel thereby providing a food enrichment sample and providing a water-immiscible phase in contact with the food enrichment culture; c) lysing the food enrichment sample to provide a lysed sample; d) isolating nucleic acids from the lysed sample. Food enrichment culture samples are known to contain high concentrations of organic and/or liposoluble inhibitors. By contacting the enrichment culture sample with a water-immiscible phase before the actual DNA extraction procedure starts, part of the lipophilic inhibitors is expected to cross the phase interface due to an enhanced solubility in the organic phase and thereby become depleted.

Abstract: The present invention is directed to methods of isolating particles, such as nucleic acid-containing particles or microvesicles, from a biological sample and extracting nucleic acids therefrom, wherein the biological sample is cerebrospinal fluid. The present invention further provides methods for aiding diagnosis, prognosis, monitoring and evaluation of a disease or other medical condition in a subject by detecting a biomarker associated with a disease or medical condition thereof.

Abstract: The present invention relates to a novel protocol for making a hydrogel, which shows increased stability compared to hydrogels of the art, and can be reliably reproduced. The hydrogels produced by the methods of the present invention are preferably three dimensional, and particularly suitable for the culture of stem cells.

Abstract: Provided herein is a method for producing a population of oligonucleotides that has reduced synthesis errors. In certain embodiments, the method comprises: a) obtaining an initial population of hairpin oligonucleotide molecules that each comprise a double-stranded stem region and a loop region; b) contacting the double-stranded region of the hairpin oligonucleotide molecules with a mismatch binding protein; and c) eliminating any molecules that bind to the mismatch binding protein, thereby producing a population of oligonucleotides that has reduced synthesis errors. A kit and a composition for performing the method are also provided.

Abstract: The present invention relates to a method for recovering an aqueous phase comprising biomolecules dissolved therein from a multiphasic mixture, comprising at least said aqueous phase and a further liquid phase which is immiscible with said aqueous phase wherein said further liquid phase comprises at least one hydrocarbon compound. The invention further relates to the use of a hydrophilic filtering material, a device comprising such a filtering material or a kit comprising said device for recovering an aqueous phase comprising biomolecules dissolved therein from a mixture of said aqueous phase and at least one hydrocarbon compound comprising further liquid phase which is immiscible with said aqueous phase.

Abstract: The present invention concerns compositions and methods of extracting infectious pathogens from a volume of blood. In one embodiment, the method includes the steps of creating a fibrin aggregate confining the pathogens and introducing a fibrin lysis reagent to expose the pathogens for analysis. The present invention also concerns materials and methods for removing aurintricarboxylic acid (ATA) from a sample.

Abstract: Oligonucleotides with a novel sugar-phosphate backbone containing at least one internucleoside 3?-NHP(O)(S?)O-5? linkage, and methods of synthesizing and using the inventive oligonucleotides are provided. The inventive thiophosphoramidate oligonucleotides were found to retain the high RNA binding affinity of the parent oligonucleotide N3??P5? phosphoramidates and to exhibit a much higher acid stability.

Abstract: The invention is directed to a process for extracting materials from biological material, which process is characterized in that the naturally occurring biological material is treated with an extractant consisting of a deep eutectic solvent of natural origin or a an ionic liquid of natural origin to produce a biological extract of natural origin dissolved in the said solvent or ionic liquid.

Abstract: A nucleic acid purification device includes a housing and an adapter operatively attached to the housing. The adapter is configured to receive at least one well plate which includes a plurality of wells for receiving contents including at least a sample and a plurality of paramagnetic particles. The device also includes a motor disposed within the housing and configured to selectively move at least the adapter to thereby disrupt or shake the contents of the plurality of wells when the at least one well plate is received by the adapter. The device further includes at least one electromagnetic feature configured to selectively receive an electrical signal and thereby magnetize at least a portion of the plurality of paramagnetic particles when the plurality of paramagnetic particles are received by the plurality of wells and the at least one well plate is received by the adapter.

Abstract: A reagent for oligonucleotide synthesis or purification, wherein the reagent has a structure of: X—C—L—H??(Formula A) wherein X is a phosphoramidite group, an H-phosphonate group, an acetal group, or an isocyanate; C is a direct bond or a cleavable adaptor represented by —Ca—Cb—; L is a hydrocarbyl chain; and H is a terminal alkyne or an activated cyclooctyne. The reagent of Formula (A) can be used in the synthesis and purification of oligonucleotides.

Abstract: A process for the extraction of pDNA from cells is provided. In one aspect, the process comprises heating a liquid comprising the cells to an average temperature of from 95° C. to about 120° C. for a time of less than 10 seconds. In certain preferred aspects, the pDNA is extracted by the use of flow-through apparatus.

Abstract: The invention broadly relates to methods of fragmenting seed by use of mechanical devices such as crushing pins or other crushing devices with a preconditioned hard seed. Methods of preconditioning the seeds to soften the seed for more effective fragmentation which are adapted to enhance extracted DNA yields and/or DNA quality are shown. Extracted DNA yield from alkali-soaked seeds can be significantly increased by adding an osmoticum to a seed-softening alkali soaking solution used for pretreatment of the seeds prior to crushing them. The osmoticum inhibits and reduces liquid uptake by the seeds, but the seeds are weakened enough to be crushed with steel beads, without requiring the use of crushing pins or other crushing devices.

Abstract: There is provided a nucleic acid extraction method applicable to microbes in a relatively wide range, and capable of rapidly extracting nucleic acid. The nucleic acid extraction method comprises the steps of introducing a cell suspension into a vessel, sealing the vessel, and preheating a heater up to a set temperature not lower than 100° C. Further, the method comprises the step of bringing the vessel into contact with the heater heated up to the set temperature, thereby heating the cell suspension housed in the vessel up to a prescribed highest temperature at not lower than 100° C. with the vessel held in a sealed state.

Abstract: The present disclosure relates to systems and methods for nucleic acid isolation. In particular, the present disclosure provides systems and methods for isolating nucleic acids from aqueous samples (e.g., blood or urine).

Abstract: Methods for processing polynucleotide-containing biological samples, and materials for capturing polynucleotide molecules such as RNA and/or DNA from such samples. The RNA and/or DNA is captured by polyamindoamine (PAMAM (Generation 0)) bound to a surface, such as the surface of magnetic particles. The methods and materials have high efficiency of binding RNA and of DNA, and of release, and thereby permit quantitative determinations.

Abstract: A rapid one-pass liquid filtration system efficiently concentrates biological particles that are suspended in liquid from a dilute feed suspension. A sample concentrate or retentate suspension is retained while eliminating the separated fluid in a separate flow stream. Suspended biological particles include such materials as proteins/toxins, viruses, DNA, and/or bacteria in the size range of approximately 0.001 micron to 20 microns diameter. Concentration of these particles is advantageous for detection of target particles in a dilute suspension, because concentrating them into a small volume makes them easier to detect. Additional concentration stages may be added in “cascade” fashion, in order to concentrate particles below the size cut of each preceding stage remaining in the separated fluid in a concentrated sample suspension. This process can also be used to create a “band-pass” concentration for concentration of a particular target size particle within a narrow range.

Abstract: The present invention relates to a method of ensuring the effectiveness of the extraction workup from a biological sample of nucleic acid. The inventive method is able to distinguish between possible defects in the extraction of nucleic acid from a sample and possible defects in a subsequent amplification step. The present invention also relates to a packaged array for extracting nucleic acid from a biological sample.

Abstract: The invention relates to a method for filtering nucleic acids, to a kit for carrying out the method according to the invention and to a novel use of magnetic particles for filtering a biological sample. The method according to the invention comprises the following steps: a) the sample is held in an aqueous solution; b) lysing of the sample; c) separation of cellular debris; and d) the nucleic acids are isolated from the solution, steps (a) to (c) taking place under non-chaotropic conditions.

Abstract: Compositions and methods for the efficient extraction, enrichment and isolation of nucleic acids from fresh, fixed or fixed and embedded cells, tissues, biological materials and cellular source material.

Abstract: The present invention is a new and non-obvious method for the improved and simplified purification of nucleic acids.

Abstract: The present invention discloses small plant virus RNA molecules involved in modulating a plant defence response, particularly non-translated, plant viral microRNA molecules. The present invention also provides methods of their production and uses of these microRNA molecules for reducing a susceptibility of a plant to a pathogen.

Abstract: An RNA extraction buffer, an RNA extraction method, and an RNA extraction kit are described which enable functional, rapid, efficient, and high-quality RNA isolation from samples containing high concentrations of aqueous metal cations, clays, silica, or silicate minerals

Abstract: Removable cartridges are used on automated flow-through systems for the purpose of extracting and purifying genetic material from complex matrices. Different types of cartridges are paired with specific automated protocols to concentrate, extract, and purifying pathogenic or human genetic material. Their flow-through nature allows large quantities sample to be processed. Matrices may be filtered using size exclusion and/or affinity filters to concentrate the pathogen of interest. Lysed material is ultimately passed through a filter to remove the insoluble material before the soluble genetic material is delivered past a silica-like membrane that binds the genetic material, where it is washed, dried, and eluted. Cartridges are inserted into the housing areas of flow-through automated instruments, which are equipped with sensors to ensure proper placement and usage of the cartridges. Properly inserted cartridges create fluid- and air-tight seals with the flow lines of an automated instrument.

Abstract: An apparatus and a method for obtaining a (poly)nucleotide sequence of interest include steps of cultivating hosts cells to produce a nucleotide sequence of interest and harvesting these cells, introducing these cells in a passageway and disintegrating them in a continuous process. In the continuous process, performing in the passageway a precipitation of contaminants by a mixing of the disintegrated cells with a solution containing one or more salt(s) and obtaining a mixture and allowing a precipitate to separate from the solution of this mixture, preferably to float and/or to sediment from the solution of this mixture for 1-48 hours and pumping out a soluble material from this solution, while excluding recovering the precipitate.

Abstract: In some embodiments, the present teachings provide compositions, systems, methods and kits for reducing the complexity of nucleotide sequences in a nucleic acid sample comprising the steps: hybridizing a plurality of polynucleotide constructs to at least one blocker oligonucleotide and to at least one capture oligonucleotide, wherein the plurality of polynucleotide constructs include a plurality of polynucleotides each joined to at least one nucleic acid adaptor, wherein the at least one nucleic acid adaptor can hybridize to the at least one blocker oligonucleotide, and wherein the at least one capture oligonucleotide can hybridize to at least a portion of target polynucleotides that are a sub-population of the plurality of polynucleotides, so as to produce a capture duplex.

Abstract: The present invention relates to a method for purifying a defined amount of nucleic acids from a nucleic acid-containing sample, which has at least the following steps: (a.) contacting the nucleic acid-containing sample with a defined amount of a nucleic acid binding phase with the following features: (i) the nucleic acid binding phase has nucleic acid binding ligands that have at least one protonatable group; (ii) the nucleic acid binding ligands are bound to a carrier; (iii) the nucleic acid binding phase has a surface with a low charge density, wherein the amount of nucleic acids in the sample exceeds the binding capacity of the amount of nucleic acid binding phase used; (b.) binding of the nucleic acids to the nucleic acid binding phase at a pH (binding pH) that is below the pKs value of at least one of the protonatable groups; (c.) elution of the nucleic acids at a pH that is above the binding pH, wherein a defined amount of nucleic acids is obtained.

Abstract: The present invention solves the problem of isolating nucleic acids from cells in the presence of the growth medium. The invention is particularly useful for isolating extrachromosomal replicons such as plasmids. Cells are lysed in the presence of the medium in which they were grown and nucleic acids are isolated using a pipette tip column. A liquid handling robot can be used to isolate nucleic acids from multiple samples simultaneously without the need for human intervention.

Abstract: A solid substrate for the extraction, stabilization, and storage of proteins is provided. The substrate includes: a polysaccharide, such as melezitose under a substantially dry state. The substrate is configured to extract proteins from a sample and stabilize the extracted proteins in a dry format under ambient conditions for a prolonged period of time. Methods for collecting and recovering the proteins stored in the dry solid substrate are also described.

Abstract: The present invention provides methods for selectively enriching a biological sample for short nucleic acids, such as fetal DNA in a maternal sample or apoptic DNA in a biological sample from a cancer patient and for subsequently analyzing the short nucleic acids for genotype, mutation, and/or aneuploidy.

Abstract: Collection devices and kits for biological sample collection include a biologic sample collection device having a hydrophilic swab matrix that includes a modified polycaprolactone (PCL). Methods of production and use thereof are also described herein. The biologic sample collection devices, kits and methods described herein are used to collect a biologic sample (e.g., blood, buccal cells, etc.) and to enable extraction of nucleic acids (e.g., DNA) from that biologic sample so that the nucleic acids can be analyzed (e.g., sequencing and subsequent analyses of DNA).

Abstract: Methods for extracting high quality nucleic acids from a heterogenous collection of nucleic acid-containing materials from a biological sample are disclosed. The heterogenous collection of nucleic-acid containing materials may contain cells or microvesicles, or both. The extractions obtained by the methods described herein are characterized by high yield and high integrity, making the extracted nucleic acids useful for various applications in which high quality nucleic acid extractions are preferred, e.g., a diagnosis, prognosis, or therapy evaluation for a medical condition.

Abstract: The presently disclosed subject matter is directed to methods of aiding diagnosis, prognosis, monitoring and evaluation of a disease or other medical condition in a subject by detecting a biomarker in microvesicles isolated from a biological sample from the subject.

Abstract: The present invention relates to a microfluidic device for extracting and isolating DNA from cells. The device includes a support having an inlet port for receiving a sample containing a cell, an outlet port for dispensing DNA isolated from the cell, and a microfluidic channel disposed within the support and extending from the inlet port to the outlet port. The microfluidic channel includes a micropillar array, an inflow channel disposed between the inlet port and the micropillar array, and an outflow channel disposed between the micropillar array and the outlet port. The micropillar array includes micropillars spatially configured to entrap, by size exclusion, the cell, to immobilize DNA released from the cell, and to maintain the immobilized DNA in elongated or non-elongated form when hydrodynamic force is applied to the microfluidic channel. Systems and methods of making and using the device are also provided herein.

Abstract: Various embodiments of the present disclosure generally relate to molecular biological protocols, equipment and reagents for the extraction and fractionation of DNA molecules, from whole or lysed samples, in a single flow-through device.