A method of sequencing a polynucleotide strand can include providing the polynucleotide strand with a primer annealed thereto and a polymerase operably bound to the polynucleotide strand; successively exposing the polynucleotide strand to the flow of four different dNTPs according to a first predetermined ordering; and successively exposing the polynucleotide strand to the flow of four different dNTPs according to a second predetermined ordering, wherein the second predetermined ordering is different from the first predetermined ordering.

A method of sequencing a polynucleotide strand can include providing the polynucleotide strand with a primer annealed thereto and a polymerase operably bound to the polynucleotide strand; successively exposing the polynucleotide strand to the flow of four different dNTPs according to a first predetermined ordering; and successively exposing the polynucleotide strand to the flow of four different dNTPs according to a second predetermined ordering, wherein the second predetermined ordering is different from the first predetermined ordering.

Polynucleotide sequencing methods include incubating unlabeled nucleotides with a cluster of template polynucleotide strands having the same sequence when the identity of the previously added labeled nucleotide is being detected. The detection step provides time for the addition of the unlabeled nucleotides to be incorporated into the copy strands in which the previously added labeled nucleotide did not get incorporated. Thus, at the end of the detection step, all or most of the copy strands will be in phase and ready to incorporate the appropriate labeled nucleotide in the subsequence incorporate step.

Polynucleotide sequencing methods include incubating unlabeled nucleotides with a cluster of template polynucleotide strands having the same sequence when the identity of the previously added labeled nucleotide is being detected. The detection step provides time for the addition of the unlabeled nucleotides to be incorporated into the copy strands in which the previously added labeled nucleotide did not get incorporated. Thus, at the end of the detection step, all or most of the copy strands will be in phase and ready to incorporate the appropriate labeled nucleotide in the subsequence incorporate step.

The present invention proposes a method of using oligonucleotide aptamers binding with certain specific biomolecules associated with a disease to purify the specific biomolecules from disease patient's samples and to identify biomarkers for the particular disease. The present invention describes a method using the magnetic assisted rapid aptamer selection (MARAS) to select aptamers having high binding affinity for certain disease-related biomolecules and not for other non-disease-related biomolecules from nucleic acid libraries. Meanwhile, the present invention also proposes a method of using the aptamer obtained above as a capture ligand to purify certain specific biomolecules related to a disease from disease patients' samples. Further, the present invention describes the use of the obtained aptamer as the capture ligand to purify biomolecules with a specific binding affinity range by applying an oscillating magnetic field range as a virtual filter.

The present invention proposes a method of using oligonucleotide aptamers binding with certain specific biomolecules associated with a disease to purify the specific biomolecules from disease patient's samples and to identify biomarkers for the particular disease. The present invention describes a method using the magnetic assisted rapid aptamer selection (MARAS) to select aptamers having high binding affinity for certain disease-related biomolecules and not for other non-disease-related biomolecules from nucleic acid libraries. Meanwhile, the present invention also proposes a method of using the aptamer obtained above as a capture ligand to purify certain specific biomolecules related to a disease from disease patients' samples. Further, the present invention describes the use of the obtained aptamer as the capture ligand to purify biomolecules with a specific binding affinity range by applying an oscillating magnetic field range as a virtual filter.

The disclosure provides a method for detecting a target analyte in a biological sample including contacting the sample with one or more probe sets each comprising a primary probe and a linker, contacting the sample with an initiator sequence, contacting the sample with a plurality of fluorescent DNA hairpins, wherein the probe binds the target molecule, the linker connects the probe to the initiator sequence, and wherein the initiator sequence nucleates with the cognate hairpin and triggers self-assembly of tethered fluorescent amplification polymers, and detecting the target molecule by measuring fluorescent signal of the sample.

The disclosure provides a method for detecting a target analyte in a biological sample including contacting the sample with one or more probe sets each comprising a primary probe and a linker, contacting the sample with an initiator sequence, contacting the sample with a plurality of fluorescent DNA hairpins, wherein the probe binds the target molecule, the linker connects the probe to the initiator sequence, and wherein the initiator sequence nucleates with the cognate hairpin and triggers self-assembly of tethered fluorescent amplification polymers, and detecting the target molecule by measuring fluorescent signal of the sample.

Materials and methods for the diagnosis of traumatic brain injury using miRNA biomarkers are disclosed. Amplification nucleotide chains amplify a detectable signal indicating the expression and/or upregulation of the biomarkers. Detection of the amplified signal is accomplished with capture nucleotide chains in a stem-loop conformation. The loop sequence of the capture nucleotide chains binds with the biomarkers and/or an indicator nucleotide chain released in the presence of one or more of the biomarkers. Binding is detected with indicators on one or more of indicator nucleotide chains released during amplification, the capture nucleotide chains, and signal nucleotide chains capable of complementary base-pair binding to the capture nucleotide chains. Incorporating the foregoing into a lateral flow assay permits point of care diagnosis.

Materials and methods for the diagnosis of traumatic brain injury using miRNA biomarkers are disclosed. Amplification nucleotide chains amplify a detectable signal indicating the expression and/or upregulation of the biomarkers. Detection of the amplified signal is accomplished with capture nucleotide chains in a stem-loop conformation. The loop sequence of the capture nucleotide chains binds with the biomarkers and/or an indicator nucleotide chain released in the presence of one or more of the biomarkers. Binding is detected with indicators on one or more of indicator nucleotide chains released during amplification, the capture nucleotide chains, and signal nucleotide chains capable of complementary base-pair binding to the capture nucleotide chains. Incorporating the foregoing into a lateral flow assay permits point of care diagnosis.