A filter for isolating nucleic acid from a sample and methods of isolating and purifying nucleic acid from a sample are described. The filter has a first porous region and a second porous region. The first porous region is arranged to be contacted in use by the sample before the second porous region, and the first porous region has a nominal pore size that is greater than the second porous region.

Methods, systems and apparatus for automated extraction, purification, and processing of nucleic acids from biological samples are presented. In some embodiments, hydrogel supports are used to immobilize particulate biological input samples and extract nucleic acids during operations. The use of hydrogel facilitates automated sample processing on robotic liquid handling systems. Devices, methods, and systems are also provided for electrophoretic sample preparation.

A syringe device having a plunger beneath which is disposed a rupturable capsule containing a nucleic acid wash buffer and a rupturing mechanism for rupturing the capsule, wherein the capsule, syringe, plunger, and rupturing mechanism are so configured as to first apply pneumatic pressure to force a nucleic acid solution through a membrane and to thereafter rupture the capsule and force a first volume of the wash buffer through the membrane.

A system, methods, and apparatus are described to collect and prepare single cells and groups of cells from microsamples of specimens and encode spatial information of the physical position of the cells in the specimen. In some embodiment, beads or surfaces with oligonucleotides containing spatial barcodes are used to analyze DNA or RNA. The spatial barcodes allow the position of the cell to be defined and the nucleic acid sequencing information, such as target sequencing, whole genome, gene expression, used to analyze the cells in a microsample for cell type, expression pattern, DNA sequence, and other information, in the context of the cell's physical position in the specimen. In other embodiment, markers such as isotopes are added to a microsample to encode spatial position with mass spectoscopy or other analysis. The spatial encoded information is then readout by analysis such as DNA sequencing, mass spectrometry, fluorescence, or other methods.

The invention provides columns (including pipette tip columns) and automated methods for the purification of nucleic acids including plasmids. Nucleic acids can be purified from unclarified, clarified or partially-clarified cell lysates that contain cell debris. The columns typically include a bed of medium positioned above a bottom frit and with an optional top frit. Plasmid preparation scales include miniprep, midiprep, maxiprep, megaprep and gigaprep.

General methods and strains of bacteria are described that dramatically simplify and streamline plasmid DNA production. In one preferred embodiment, endolysin mediated plasmid extraction combined with flocculation mediated removal of cell debris and host nucleic acids achieves increased yield and purity with simplified downstream purification and reduced waste streams, thus reducing production costs.

Large scale processes for producing high purity samples of biologically active molecules of interest from bacterial cells are disclosed. The methods comprise the steps of producing a lysate solution by contacting a cell suspension of said plurality of cells with lysis solution; neutralizing said lysate solution with a neutralizing solution to produce a dispersion that comprises neutralized lysate solution and debris; filtering the dispersion through at least one filter; performing ion exchange separation on said neutralized lysate solution to produce an ion exchange eluate; and performing hydrophobic interaction separation on said ion exchange eluate to produce a hydrophobic interaction solution. Further, provided are compositions comprising large scale amounts of plasmid DNA produced by the disclosed large scale processes.

Presented herein are methods and compositions surface-based tagmentation. In particular embodiments, methods of preparing an immobilized library of fragmented and tagged DNA molecules on a solid surface are presented. In particular embodiments, the solid surface comprises immobilized transposomes in a dried format, suitable for reconstitution upon contact with liquid, such as a liquid sample.

Various embodiments relate to a syringe for separating nucleic acids from a blood sample and systems that include the syringe and a portable PGR device. The syringe may include a shell defining a central aperture extending through a longitudinal axis of the syringe, a plunger disposed within the central aperture of the shell, and a core rotatably disposed within the central aperture. The syringe may further include a needle fluidically connectable to the inlet of the shell. Various embodiments relate to a method for separating nucleic acids from a blood sample, the method comprising drawing the blood sample from a patient using the syringe according to any of the embodiments described herein.

The present invention provides, among other things, methods for purifying high quality messenger RNA (mRNA) suitable for clinical use, without using any caustic or flammable solvents. The present invention is, in part, based on surprising discovery that mRNA can be successfully purified by selective precipitation and washing without using ethanol while maintaining integrity and high purity of mRNA. Thus, the present invention provides an effective, reliable, and safer method of purifying RNA from large scale manufacturing process therapeutic applications without using any caustic or inflammable solvents.