Disclosed herein are detection methods that use magnetic nanoparticles (MNPs) to allow molecules to be identified. Embodiments of this disclosure include methods of using magnetic sensors (e.g., magnetoresistive sensors) to detect temperature-dependent magnetic fields (or changes in magnetic fields) emitted by MNPs, and, specifically to distinguish between the presence and absence of magnetic fields emitted, or not emitted, by MNPs at different temperatures selected to take advantage of knowledge of how the MNPs' magnetic properties change with temperature. Embodiments disclosed herein may be used for nucleic acid sequencing, such as deoxyribonucleic acid (DNA) sequencing.

Disclosed herein are detection methods that use magnetic nanoparticles (MNPs) to allow molecules to be identified. Embodiments of this disclosure include methods of using magnetic sensors (e.g., magnetoresistive sensors) to detect temperature-dependent magnetic fields (or changes in magnetic fields) emitted by MNPs, and, specifically to distinguish between the presence and absence of magnetic fields emitted, or not emitted, by MNPs at different temperatures selected to take advantage of knowledge of how the MNPs' magnetic properties change with temperature. Embodiments disclosed herein may be used for nucleic acid sequencing, such as deoxyribonucleic acid (DNA) sequencing.

The present disclosure provides, in various aspects and embodiments, methods, compositions, and devices for magnetic nanoparticle based assay of nucleic acid sequence targets using isothermal amplification. Uses of the disclosure include detection of bacterial and/or virus nucleic acid sequence targets.

The present disclosure provides, in various aspects and embodiments, methods, compositions, and devices for magnetic nanoparticle based assay of nucleic acid sequence targets using isothermal amplification. Uses of the disclosure include detection of bacterial and/or virus nucleic acid sequence targets.

The invention relates to an aggregate comprising metallic nanoparticles and nucleic acid molecules wherein each metallic nanoparticle is coated with a polycation. The invention also relates to a method for obtaining the aggregate of the invention and to the use of said aggregate in methods for detecting the presence of a nucleic acid in a sample, in methods for detecting the presence of a given nucleotide at a predetermined position in a target nucleic acid, in methods for detecting the presence of a modified nucleotide at a predetermined position in a target nucleic acid, methods for detecting the presence of a conjugate between a double stranded nucleic acid and a chemical in a sample comprising double stranded nucleic acid molecules, in methods for determining the content of modified nucleotides in a target nucleic acid and in a method for determining the content of modified nucleotides in a target nucleic acid.

The invention relates to an aggregate comprising metallic nanoparticles and nucleic acid molecules wherein each metallic nanoparticle is coated with a polycation. The invention also relates to a method for obtaining the aggregate of the invention and to the use of said aggregate in methods for detecting the presence of a nucleic acid in a sample, in methods for detecting the presence of a given nucleotide at a predetermined position in a target nucleic acid, in methods for detecting the presence of a modified nucleotide at a predetermined position in a target nucleic acid, methods for detecting the presence of a conjugate between a double stranded nucleic acid and a chemical in a sample comprising double stranded nucleic acid molecules, in methods for determining the content of modified nucleotides in a target nucleic acid and in a method for determining the content of modified nucleotides in a target nucleic acid.

Method for detecting the presence of nucleases in a sample, characterized in that it comprises the steps of: —incubating the sample to be tested for the presence of nucleases with at least one oligonucleotide linker constituting the substrate for the nuclease to be detected, for a sufficient time to cause degradation of said oligonucleotide linker by the nuclease possibly present in the sample, —adding to the sample, upon incubation, colloidal gold nanoparticles comprising gold nanoparticles functionalized with a first probe oligonucleotide and gold nanoparticles functionalized with a respective second probe oligonucleotide, said first and second probe oligonucleotides being complementary to a respective portion of the nucleotide sequence of the oligonucleotide linker, and—examining the possible colour change of the sample as a result of the addition of said nanoparticles, a colour change of the sample to the colour assumed by the colloidal gold particles when aggregated at a distance less than their size being indicative of the absence of the tested nuclease from the sample.

Various approaches for generating long-distance contiguity information to facilitate contig assembly and phase determination are disclosed. Nucleic acids are assembled into complexes using binding moieties such that, when the nucleic acid backbones are cleaved, the ensuing fragments remain bound. Exposed ends are tagged and ligated either to one another or to tagging moieties such as oligo labels. Ligated junctions are sequenced, and the sequence information is used to assemble contigs into common scaffolds or to assign phase information. Various approaches to tagging the exposed ends are presented.

Various approaches for generating long-distance contiguity information to facilitate contig assembly and phase determination are disclosed. Nucleic acids are assembled into complexes using binding moieties such that, when the nucleic acid backbones are cleaved, the ensuing fragments remain bound. Exposed ends are tagged and ligated either to one another or to tagging moieties such as oligo labels. Ligated junctions are sequenced, and the sequence information is used to assemble contigs into common scaffolds or to assign phase information. Various approaches to tagging the exposed ends are presented.

Certain aspects of the present disclosure relate generally to the detection of molecules, such as biomolecules, using functionalized particles, including microparticles. In one set of embodiments, a target molecule can be determined using magnetic particles and signaling particles that are able to bind to a portion of the target molecules. After allowing the magnetic and signaling particles to bind to the target molecule, e.g., to from a complex or an assembly, a magnetic field can be used to attract the magnetic particles, e.g., to a certain po sition. Determination of whether the signaling entity is present in the location, qualitatively or quantitatively, can then be used to determine the target molecule. Other embodiments are generally directed to systems for making or using such particles or assemblies, kits including these, or the like.