The present invention relates to, inter alia, a microfluidic device for capturing target cells and analyzing genomic DNA isolated from the target cells while under flow conditions. The microfluidic device includes a cell microchannel and a nucleic acid microchannel that intersect in an orthogonal manner, thereby forming a cell capture intersection region. The microfluidic device also includes a cell capture array and a nucleic acid entanglement array. The cell capture array includes a plurality of cell capturing micropillars and is located in the cell capture intersection region. The nucleic acid entanglement array includes a plurality of nucleic acid entanglement micropillars that function to physically entangle and maintain thereon genomic DNA isolated from the one or more target cell, and is located in a portion of the nucleic acid microchannel that is adjacent to and downstream of the cell capture intersection region. Methods of using the microfluidic device are also disclosed.

Systems and methods for trapping a polynucleotide strand at a surface of a channel. Methods may include providing a polymer to the surface of the channel and physically interacting the polymer with the surface of the channel. Methods may also include providing a sample including the polynucleotide strand to the polymer interacting with the surface of the channel and applying an electric field to the polynucleotide strand to promote a physical interaction between the polynucleotide strand and the polymer to trap the polynucleotide strand at the surface of the channel.

Systems and methods for trapping and detecting a polynucleotide strand in a channel. Methods may include labeling at least one subsequence within a polynucleotide strand to obtain a labeled polynucleotide strand having at least one label. Methods may additionally include providing a polymer to a surface of a channel and physically interacting the polymer with the surface of the channel. Methods may also include providing a sample including the labeled polynucleotide strand to the channel, applying an electric field to the labeled polynucleotide strand to promote a physical interaction between the labeled polynucleotide strand and the polymer at the surface of the channel to trap the labeled polynucleotide strand at the surface of the channel, and detecting the at least one label within the labeled polynucleotide strand.

The disclosure describes apparatus and methods for multiplexed amplification and detection of nucleic acid targets in a sample. Embodiments of the present disclosure include a mechanical system configured to provide loading, vertical positioning and clamping of a chip; a thermal control system configured to maintain distinct temperatures of the chip, and an optical fluorescence imaging system.

A flow channel structure for removing a foreign substance includes a first flow channel, where the first flow channel has a first region having a depth shallower than a depth of another region. A method for removing a foreign substance in a fluid includes flowing the fluid to the first flow channel of the flow channel structure for removing a foreign substance.

Systems and methods for presenting nucleic acid molecules for analysis are provided. The nucleic acid molecules have a central portion that is contained within a nanoslit. The nanoslit contains an ionic buffer. The nucleic acid molecule has a contour length that is greater than a nanoslit length of the nanoslit. An ionic strength of the ionic buffer and electrostatic or hydrodynamic properties of the nanoslit and the nucleic acid molecule combining to provide a summed Debye length that is greater than or equal to the smallest physical dimension of the nanoslit.