Disclosed is a method of facilitating detection of a nucleic acid target sequence. The method may include utilizing a toehold-mediated DNA strand displacement apparatus comprising a portion complementary to the nucleic acid target sequence. The method may further include utilizing a RNA toehold switch comprising a RNA sequence. Further, the toehold portion of the RNA sequence may be complementary to a portion of the toehold-mediated DNA strand displacement apparatus. The method may further include combining the toehold-mediated DNA strand displacement apparatus and the RNA toehold switch in an assay, such that the two are never in direct physical contact with each other. Accordingly, a sample containing the nucleic acid target sequence on the substrate may displace a nucleic acid strand from the toehold-mediated DNA strand displacement apparatus and bind a portion of it to the RNA toehold switch resulting in expression of the reporter protein.

Disclosed is a method of facilitating detection of a nucleic acid target sequence. The method may include utilizing a toehold-mediated DNA strand displacement apparatus comprising a portion complementary to the nucleic acid target sequence. The method may further include utilizing a RNA toehold switch comprising a RNA sequence. Further, the toehold portion of the RNA sequence may be complementary to a portion of the toehold-mediated DNA strand displacement apparatus. The method may further include combining the toehold-mediated DNA strand displacement apparatus and the RNA toehold switch in an assay, such that the two are never in direct physical contact with each other. Accordingly, a sample containing the nucleic acid target sequence on the substrate may displace a nucleic acid strand from the toehold-mediated DNA strand displacement apparatus and bind a portion of it to the RNA toehold switch resulting in expression of the reporter protein.

Disclosed is a system and method for the controlled clustering of gene regulatory proteins at the specific target genomic loci. The technology enables formation of liquid-like droplets closely interfaced with genome organization. This technology can be utilized for perturbing endogenous nuclear structures as well as nucleating synthetic membrane-less assemblies. The technology can also be utilized for inducing or detecting mechanical stresses within the genome.

Disclosed is a system and method for the controlled clustering of gene regulatory proteins at the specific target genomic loci. The technology enables formation of liquid-like droplets closely interfaced with genome organization. This technology can be utilized for perturbing endogenous nuclear structures as well as nucleating synthetic membrane-less assemblies. The technology can also be utilized for inducing or detecting mechanical stresses within the genome.

The present invention refers to methods for selectively recognizing a base pair in a DNA sequence by a polypeptide, to modified polypeptides which specifically recognize one or more base pairs in a DNA sequence and, to DNA which is modified so that it can be specifically recognized by a polypeptide and to uses of the polypeptide and DNA in specific DNA targeting as well as to methods of modulating expression of target genes in a cell.

The present invention refers to methods for selectively recognizing a base pair in a DNA sequence by a polypeptide, to modified polypeptides which specifically recognize one or more base pairs in a DNA sequence and, to DNA which is modified so that it can be specifically recognized by a polypeptide and to uses of the polypeptide and DNA in specific DNA targeting as well as to methods of modulating expression of target genes in a cell.

The technology as disclosed herein relates to methods, compositions and kits for multiplex measuring levels of expression of target RNA species (e.g., mRNA and non-coding RNAs) in single, living cells. Aspects of the invention relate to, in part, a duplex-binding protein which is labeled with a FRET dye, and a RNA-binding probe, which comprises a spectrally paired FRET dye and specifically hybridizes to a target RNA. When the RNA-binding probe binds to a target RNA, a duplex is formed, which is allows binding of the duplex-binding protein bringing the two FRET dyes into close proximity and allowing fluorescence resonance energy transfer (FRET) reaction and a detectable change in fluorescence, which determines the amount of target RNA species in the living cell. Aspects of the invention also include, kits, vectors and polynucleic acid sequences of the duplex-binding protein and RNA-binding probes disclosed herein, and cell and cell lines comprising the same.

The technology as disclosed herein relates to methods, compositions and kits for multiplex measuring levels of expression of target RNA species (e.g., mRNA and non-coding RNAs) in single, living cells. Aspects of the invention relate to, in part, a duplex-binding protein which is labeled with a FRET dye, and a RNA-binding probe, which comprises a spectrally paired FRET dye and specifically hybridizes to a target RNA. When the RNA-binding probe binds to a target RNA, a duplex is formed, which is allows binding of the duplex-binding protein bringing the two FRET dyes into close proximity and allowing fluorescence resonance energy transfer (FRET) reaction and a detectable change in fluorescence, which determines the amount of target RNA species in the living cell. Aspects of the invention also include, kits, vectors and polynucleic acid sequences of the duplex-binding protein and RNA-binding probes disclosed herein, and cell and cell lines comprising the same.

Described herein relates to methods of accurately determining DNA barcodes using a cylindrical nanopore system. The system and method may include the steps of leveraging the average velocity of a double-stranded DNA segment passing through a single cylindrical nanopore that may be measured through repeated scanning to accurately determine protein tag locations on the double-stranded DNA segment. As such, the system and methods may provide for the accurate calculation of a barcode for the double-stranded DNA segment based on protein tag locations without underestimation or overestimate issues. Additionally, the underlying concept and/or the system and/or the methods may be equally applicable to other multi-nanopore systems which use the dwell time and/or time of flight velocities to measure the barcodes.

Described herein relates to methods of accurately determining DNA barcodes using a cylindrical nanopore system. The system and method may include the steps of leveraging the average velocity of a double-stranded DNA segment passing through a single cylindrical nanopore that may be measured through repeated scanning to accurately determine protein tag locations on the double-stranded DNA segment. As such, the system and methods may provide for the accurate calculation of a barcode for the double-stranded DNA segment based on protein tag locations without underestimation or overestimate issues. Additionally, the underlying concept and/or the system and/or the methods may be equally applicable to other multi-nanopore systems which use the dwell time and/or time of flight velocities to measure the barcodes.