Disclosed herein is a more sensitive and accurate method of monitoring the pH of a solution, wherein the pH of the solution is quantified as a function of the electrochemical response of the solution in a two or three-electrode electrochemical cell, wherein the solution comprises a compound capable of undergoing a change in its oxidation state and/or structural conformation as a function of the pH of the solution. Also disclosed are highly accelerated methods and processes enabling analysis of specific polynucleotide sequences in a sample, e.g. a biological sample. The methods disclosed herein are, for example, useful for rapid screening of a large amount of samples in a point-of-care setting.

Mathematical models for the analysis of signal data generated by sequencing of a polynucleotide strand using a pH-based method of detecting nucleotide incorporation(s). In an embodiment, the measured output signal from the reaction confinement region of a reactor array is mathematically modeled. The output signal may be modeled as a linear combination of one or more signal components, including a background signal component. This model is solved to determine the nucleotide incorporation signal. In another embodiment, the incorporation signal from the reaction confinement region of a reactor array is mathematically modeled.

Mathematical models for the analysis of signal data generated by sequencing of a polynucleotide strand using a pH-based method of detecting nucleotide incorporation(s). In an embodiment, the measured output signal from the reaction confinement region of a reactor array is mathematically modeled. The output signal may be modeled as a linear combination of one or more signal components, including a background signal component. This model is solved to determine the nucleotide incorporation signal. In another embodiment, the incorporation signal from the reaction confinement region of a reactor array is mathematically modeled.

An object of the invention is to obtain a biotinylated nucleic acid efficiently, by enhancing dissociation efficiency of biotin in the biotinylated nucleic acid and tamavidin 2 in a tamavidin 2-immobilized insoluble carrier. The inventive method for separating a biotinylated nucleic acid includes (1) contacting a sample containing a biotinylated nucleic acid wherein the biotin is bound to the nucleic acid with a insoluble carrier on which tamavidin is immobilized (a tamavidin-immobilized insoluble carrier) to form a complex of the biotinylated nucleic acid and the tamavidin-immobilized insoluble carrier, and (2) separating the biotinylated nucleic acid from the complex in a solution having pH of 7.8 to 9.5 and in the presence of free biotin. The invention also provides a method for separating the biotinylated nucleic acid to which the nucleic acid-binding protein is bound, a method for separating the nucleic acid-binding protein, and a kit for separating the nucleic acid.

An object of the invention is to obtain a biotinylated nucleic acid efficiently, by enhancing dissociation efficiency of biotin in the biotinylated nucleic acid and tamavidin 2 in a tamavidin 2-immobilized insoluble carrier. The inventive method for separating a biotinylated nucleic acid includes (1) contacting a sample containing a biotinylated nucleic acid wherein the biotin is bound to the nucleic acid with a insoluble carrier on which tamavidin is immobilized (a tamavidin-immobilized insoluble carrier) to form a complex of the biotinylated nucleic acid and the tamavidin-immobilized insoluble carrier, and (2) separating the biotinylated nucleic acid from the complex in a solution having pH of 7.8 to 9.5 and in the presence of free biotin. The invention also provides a method for separating the biotinylated nucleic acid to which the nucleic acid-binding protein is bound, a method for separating the nucleic acid-binding protein, and a kit for separating the nucleic acid.

Provided herein includes a method for characterizing a target cell-free nucleic acid (cfNA) molecule present in a biological sample such as a urine sample. It comprises isolating total cfNAs from the biological sample without prior preprocessing such as centrifugation to remove cell debris, and characterizing the target cfNA molecule based on the isolated total cfNAs. When the target cfNA is a low molecular weight (LMW) molecule, the method additionally comprises a fractionation step to obtain LMW nucleic acids from the total cfNAs before characterization. The method can detect significantly more copies of the target cfNA molecule compared with existing methods which typically discard the cell debris from the biological sample. Another method is also provided, which substantially recovers cfNAs from the usually discarded cell debris, thus also capable of detecting significantly more copies of the target cfNA molecule.

Provided herein includes a method for characterizing a target cell-free nucleic acid (cfNA) molecule present in a biological sample such as a urine sample. It comprises isolating total cfNAs from the biological sample without prior preprocessing such as centrifugation to remove cell debris, and characterizing the target cfNA molecule based on the isolated total cfNAs. When the target cfNA is a low molecular weight (LMW) molecule, the method additionally comprises a fractionation step to obtain LMW nucleic acids from the total cfNAs before characterization. The method can detect significantly more copies of the target cfNA molecule compared with existing methods which typically discard the cell debris from the biological sample. Another method is also provided, which substantially recovers cfNAs from the usually discarded cell debris, thus also capable of detecting significantly more copies of the target cfNA molecule.

A method of forming a polymer matrix array includes applying an aqueous solution into wells of a well array. The aqueous solution includes polymer precursors. The method further includes applying an immiscible fluid over the well array to isolate the aqueous solution within the wells of the well array and polymerizing the polymer precursors isolated in the wells of the well array to form the polymer matrix array. An apparatus includes a sensor array, a well array corresponding to the sensor array, and an array of polymer matrices disposed in the well array.

A method of forming a polymer matrix array includes applying an aqueous solution into wells of a well array. The aqueous solution includes polymer precursors. The method further includes applying an immiscible fluid over the well array to isolate the aqueous solution within the wells of the well array and polymerizing the polymer precursors isolated in the wells of the well array to form the polymer matrix array. An apparatus includes a sensor array, a well array corresponding to the sensor array, and an array of polymer matrices disposed in the well array.

Disclosed are new and improved methods and systems for nucleic acid sequence analysis that can analyze data indicative of natural by-products of nucleotide incorporation events without the need for exogenous labels or dyes to identify nucleic acid sequences of interest. In particular, the methods and systems of the present teachings can process such data and various forms thereof to align fragments of the nucleic acid(s) of interest, particularly those analyzed using an addition sequencing technique, for example, as occurs with the use of nucleotide flows.