The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address issues associated with the heterogeneity of analyte abundance (e.g., gene expression levels) and variations among reactions at different locations of a sample (e.g., amplification reaction starting earlier at one location than another location). In some aspects, a method disclosed herein provides a tighter distribution of signal spot size and intensity in a sample, as compared to methods that result in a wide and heterogeneous size and intensity distribution of signal spots.

The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address issues associated with the heterogeneity of analyte abundance (e.g., gene expression levels) and variations among reactions at different locations of a sample (e.g., amplification reaction starting earlier at one location than another location). In some aspects, a method disclosed herein provides a tighter distribution of signal spot size and intensity in a sample, as compared to methods that result in a wide and heterogeneous size and intensity distribution of signal spots.

Provided herein, in some aspects, are methods of imaging molecules without a microscope or other specialized equipment, referred to herein as “microscope-free imaging (MFI).” Herein, “molecular instruments” (e.g., DNA-based and protein-based molecules) are used, instead of microscopes, in a “bottom-up” approach for inspecting molecular targets.

Provided herein, in some aspects, are methods of imaging molecules without a microscope or other specialized equipment, referred to herein as “microscope-free imaging (MFI).” Herein, “molecular instruments” (e.g., DNA-based and protein-based molecules) are used, instead of microscopes, in a “bottom-up” approach for inspecting molecular targets.

Provided herein is a method of moving a double-stranded polynucleotide with respect to a nanopore using a motor protein. The method allows a portion of the polynucleotide to be interrogated by the pore multiple times. Also provided are polynucleotide adapters and kits comprising such adapters. The methods find use in characterising polynucleotides, for example in sequencing.

Provided herein is a method of moving a double-stranded polynucleotide with respect to a nanopore using a motor protein. The method allows a portion of the polynucleotide to be interrogated by the pore multiple times. Also provided are polynucleotide adapters and kits comprising such adapters. The methods find use in characterising polynucleotides, for example in sequencing.

The relative abundance of bacterial species in a patient’s microbiome is quantified using DNA nanostructures that fluoresce multiple colors. Immobilizing binders have binding sites with nucleotide sequences complementary to those at a primary site on rRNA subunits of each selected bacterial species. Fluorophore binders have binding sites with nucleotide sequences complementary to those at a secondary site on the rRNA subunits. The fluorophore binders for each bacterial species are attached to nanostructures that fluoresce a particular color for each bacteria. The immobilizing binders are attached to the surface of a microscopy chamber. RNA subunits are extracted from a microbiome sample of the patient and are attached to the corresponding immobilizing binders and fluorophore binders such that the RNA subunits of each bacterial species fluoresce a color unique to the species. DNA nanostructures emitting the same color are counted to determine the relative concentration of the bacterial species in the sample.

The relative abundance of bacterial species in a patient’s microbiome is quantified using DNA nanostructures that fluoresce multiple colors. Immobilizing binders have binding sites with nucleotide sequences complementary to those at a primary site on rRNA subunits of each selected bacterial species. Fluorophore binders have binding sites with nucleotide sequences complementary to those at a secondary site on the rRNA subunits. The fluorophore binders for each bacterial species are attached to nanostructures that fluoresce a particular color for each bacteria. The immobilizing binders are attached to the surface of a microscopy chamber. RNA subunits are extracted from a microbiome sample of the patient and are attached to the corresponding immobilizing binders and fluorophore binders such that the RNA subunits of each bacterial species fluoresce a color unique to the species. DNA nanostructures emitting the same color are counted to determine the relative concentration of the bacterial species in the sample.

The invention provides a method for optimizing isHCR for multiplexed labeling, which combines binder-biomolecule interactions with hybridization Chain Reaction (HCR).

The invention provides a method for optimizing isHCR for multiplexed labeling, which combines binder-biomolecule interactions with hybridization Chain Reaction (HCR).