A method for sequencing a target polynucleotide includes detecting a first series of nucleotide incorporations complementary to at least a portion of the target polynucleotide. The first series of nucleotide incorporations forms a first complementary polynucleotide. The target nucleotide is secured to a substrate disposed in a sequencing zone of an assembly. The method further includes moving the substrate to which the target nucleotide is secured to a templating zone of the assembly; removing the first complementary polynucleotide when the substrate is disposed at the templating zone of the assembly, the target polynucleotide remaining secured to the substrate; following the removing, moving the substrate to which the target polynucleotide is secured to the sequencing zone; and detecting a second series of nucleotide incorporations complementary to at least a portion of the target polynucleotide, the second series of nucleotide incorporations forming a second complementary polynucleotide.

Disclosed herein are methods for the detection of the presence of sperm DNA fragmentation in a semen sample. The methods include embedding of sperm cells of the semen sample in a gel, denaturing DNA of the sperm cells, and lysing the nuclear proteins of the sperm cells. The present method includes an ionic surfactant sodium dodycyl sulfate (SDS) and a chaotropic agent urea in the lysis solution for releasing DNA from protamine of chromosome, which significantly reduces the time required for lysis. A kit for detecting sperm DNA fragmentation in a semen sample is also disclosed.

Disclosed herein are methods for the detection of the presence of sperm DNA fragmentation in a semen sample. The methods include embedding of sperm cells of the semen sample in a gel, denaturing DNA of the sperm cells, and lysing the nuclear proteins of the sperm cells. The present method includes an ionic surfactant sodium dodycyl sulfate (SDS) and a chaotropic agent urea in the lysis solution for releasing DNA from protamine of chromosome, which significantly reduces the time required for lysis. A kit for detecting sperm DNA fragmentation in a semen sample is also disclosed.

Provided herein, in some embodiments, are methods, compositions and kits for large-scale production of long single-stranded DNA in solution.

Provided herein, in some embodiments, are methods, compositions and kits for large-scale production of long single-stranded DNA in solution.

Methods, devices and kits for sampling, releasing and stabilizing nucleic acid, including RNA and DNA, from virus, bacteria yeast and other cells is described. The released and stabilized nucleic acid may be analyzed and quantified without further sample preparation at the point of care or may be transported to a testing laboratory by shipment and analyzed directly. The nucleic acid, which can be RNA, remains safe and stable so that shipping by normal means including government postal service may be used. In addition, the RNA sample remains stable so that analysis can be performed immediately after receipt of sample or after storage for days, weeks or months. Storage may be at room or ambient temperature or cooler temperatures. The sampling apparatus used to acquire samples can interface with nucleic detection and measurement instrumentation including high throughput, parallel processing instruments.

Methods, devices and kits for sampling, releasing and stabilizing nucleic acid, including RNA and DNA, from virus, bacteria yeast and other cells is described. The released and stabilized nucleic acid may be analyzed and quantified without further sample preparation at the point of care or may be transported to a testing laboratory by shipment and analyzed directly. The nucleic acid, which can be RNA, remains safe and stable so that shipping by normal means including government postal service may be used. In addition, the RNA sample remains stable so that analysis can be performed immediately after receipt of sample or after storage for days, weeks or months. Storage may be at room or ambient temperature or cooler temperatures. The sampling apparatus used to acquire samples can interface with nucleic detection and measurement instrumentation including high throughput, parallel processing instruments.

The present disclosure provides compositions and methods for sample processing, particularly for oligonucleotide analysis e.g. analysis of formulated nucleic acid drugs. A composition for pretreating at least one target nucleic acid in a biological mixture provided herein includes a chaotropic agent selected from a substituted guanidine, a substituted amidine, a substituted quaternary amine, or a combination thereof, an optional protease, and/or an optional disulfide-reducing agent. Methods of analyzing at least one target nucleic acid in a biological mixture is also provided herein. Furthermore, the present disclosure provides methods for quantifying at least one target cationic lipid interacting with a nucleic acid.

The present disclosure provides compositions and methods for sample processing, particularly for oligonucleotide analysis e.g. analysis of formulated nucleic acid drugs. A composition for pretreating at least one target nucleic acid in a biological mixture provided herein includes a chaotropic agent selected from a substituted guanidine, a substituted amidine, a substituted quaternary amine, or a combination thereof, an optional protease, and/or an optional disulfide-reducing agent. Methods of analyzing at least one target nucleic acid in a biological mixture is also provided herein. Furthermore, the present disclosure provides methods for quantifying at least one target cationic lipid interacting with a nucleic acid.

The present disclosure is related to methods and materials for depleting unwanted RNA species from a nucleic acid sample. In particular, the present disclosure describes how to remove unwanted rRNA, tRNA, mRNA or other RNA species that could interfere with the analysis, manipulation and study of target RNA molecules in a sample.