The present disclosure provides materials and methods to link imaging and sequencing measurements of a single cell. Sequencing information can be linked with phenotypic measurements that are not directly encoded in the genome such as morphological features, protein expression & localization, organelle dynamics, or the metabolic composition of a cell.

The present disclosure provides materials and methods to link imaging and sequencing measurements of a single cell. Sequencing information can be linked with phenotypic measurements that are not directly encoded in the genome such as morphological features, protein expression & localization, organelle dynamics, or the metabolic composition of a cell.

A method of distinguishing nucleotide sequences for different nucleic acid molecules including the steps of (a) mixing a plurality of different nucleic acid molecules with polymerase molecules and nucleotide molecules, wherein the different nucleic acid molecules are attached to a surface in the form of an array of nucleic acid features; (b) determining a transient state of the polymerase molecules at the nucleic acid features; and (c) identifying a subset of nucleic acid features that correctly incorporate the nucleotide molecules based on the transient state of the polymerase molecules at the nucleic acid features, thereby distinguishing the nucleotide sequences for the different nucleic acid molecules.

The present disclosure is directed to designing dyes and methods to alter the parameters controlling the dipole-dipole coupling of dyes bound to a nucleotide oligomer architecture, which are used to propagate excitons for use in next generation room temperature quantum information systems. The disclosed dyes and methods are directed to changing the dye stability, symmetry, overlap, and steric hindrance of the dyes to fine tune aggregate systems.

The present disclosure is directed to designing dyes and methods to alter the parameters controlling the dipole-dipole coupling of dyes bound to a nucleotide oligomer architecture, which are used to propagate excitons for use in next generation room temperature quantum information systems. The disclosed dyes and methods are directed to changing the dye stability, symmetry, overlap, and steric hindrance of the dyes to fine tune aggregate systems.

Disclosed are nucleic acid-chromophores and nucleic acid assembly containing the nucleic acid-chromophores. The nucleic acid-chromophore contains a nucleic acid strand and two or more adjacent chromophores. The two or more adjacent chromophores can be covalently incorporated in the backbone of the nucleic acid strand. One or more photophysical properties of the adjacent chromophores can be altered by a change in the nucleic acid assembly. In some forms, the nucleic acid assembly can contain a nucleic acid scaffold. In these forms, the change in the nucleic acid assembly can be a change in the length of a nucleic acid hybrid in the nucleic acid scaffold that is opposite the adjacent chromophores. Typically, the nucleic acid hybrid does not contain any chromophore. The nucleic acid-chromophores can serve as molecular fluorophores with emission properties that are highly sensitive to local geometry and the chemical environment.

Disclosed are nucleic acid-chromophores and nucleic acid assembly containing the nucleic acid-chromophores. The nucleic acid-chromophore contains a nucleic acid strand and two or more adjacent chromophores. The two or more adjacent chromophores can be covalently incorporated in the backbone of the nucleic acid strand. One or more photophysical properties of the adjacent chromophores can be altered by a change in the nucleic acid assembly. In some forms, the nucleic acid assembly can contain a nucleic acid scaffold. In these forms, the change in the nucleic acid assembly can be a change in the length of a nucleic acid hybrid in the nucleic acid scaffold that is opposite the adjacent chromophores. Typically, the nucleic acid hybrid does not contain any chromophore. The nucleic acid-chromophores can serve as molecular fluorophores with emission properties that are highly sensitive to local geometry and the chemical environment.

The present invention relates to an ultrasensitive assay platform for the detection of nucleic acids such as microRNAs (miRNAs), which are important biomarker for diseases including cancer. The platform allows high throughput detection of multiple nucleic acid sequences miRNAs on the single-molecule level using fluorescence labeling, molecular barcoding, and flow based detection and multiparametric data analysis.

The present invention discloses a method of detecting the presence of mutated genes, mRNAs or microRNAs in a subject. The method comprises the following steps: (1) Provide a body fluid sample containing cells, circulating tumor cells (CTCs), and/or extracellular vesicles (EVs); and use an analyzer having overhang molecular beacons to measure fluorescence signals generated by interactions between the body fluid sample and the overhang molecular beacons, so as to detect the presence of the mutated genes, mRNAs or microRNA. Furthermore, a biochip comprising a gold coating substrate and tethered lipoplex nanoparticles encapsulating the overhang molecular beacons is also provided in the invention.

The present invention discloses a method of detecting the presence of mutated genes, mRNAs or microRNAs in a subject. The method comprises the following steps: (1) Provide a body fluid sample containing cells, circulating tumor cells (CTCs), and/or extracellular vesicles (EVs); and use an analyzer having overhang molecular beacons to measure fluorescence signals generated by interactions between the body fluid sample and the overhang molecular beacons, so as to detect the presence of the mutated genes, mRNAs or microRNA. Furthermore, a biochip comprising a gold coating substrate and tethered lipoplex nanoparticles encapsulating the overhang molecular beacons is also provided in the invention.