Described are methods for developing treatment plans for patients with cancer and other diseases based on drug binding interactions of kinase inhibitors. Also described are methods for determining the mutational status of a kinase and kinase occupancy.

The present invention provides a method for controlling a speed of a polypeptide passing through a nanopore and use thereof in determining an amino acid sequence of a polypeptide. Specifically, the method comprises: conjugating a polynucleotide to the polypeptide to give a polynucleotide-polypeptide conjugate, and applying a voltage across the nanopore in the presence of a polynucleotide binding enzyme to move the conjugate through the nanopore. The polynucleotide binding enzyme controls the movement of the polynucleotide and thereby controls the movement of the conjugated polypeptide in the nanopore, thus controlling the speed of the polypeptide passing through the nanopore. While controlling the speed of the polypeptide, the present invention reads a nanopore current signal during the process of the polypeptide passing through the nanopore to give an electrical signal of the polypeptide. The electrical signal can be further used to acquire an amino acid sequence of the polypeptide, to identify the polypeptide or a part thereof, or to establish a library of polypeptide electrical signals.

The present invention includes method and system for detecting kinase activity in vivo, comprising: providing a cell that comprises one or more mutated kinases, wherein the one or more mutated kinases comprise a mutation that enlarges an ATP binding pocket of the kinase; contacting the cell with an ATP analog-nanoparticle conjugate capable of intracellular delivery of the ATP analog-nanoparticle conjugate, wherein the ATP analog comprises a detectable label; culturing the cells under conditions in which the ATP analog-nanoparticle conjugate contacts the one or more mutated kinases in cellulo, wherein the detectable label is transferred from the ATP analog-nanoparticle conjugate to a substrate of the one or more mutated kinases, wherein the one or more kinases react to transfer the detectable label to the substrate.

Compositions and methods for the treatment of malignancy are disclosed.

Compositions and methods for the treatment of malignancy are disclosed.

The invention is directed to methods for synthesizing a plurality of oligonucleotides in the same reaction vessel, and in some embodiments, using the synthesized oligonucleotides in an oligonucleotide-based assay in such reaction vessel. In some embodiments, methods of the invention are implemented by steps of (a) providing a plurality of different initiators attached to one or more supports, each different initiator having a terminal nucleotide with a different 3-O-blocking group; (b) for each different initiator, synthesizing a polynucleotide by repeated cycles of template-free enzymatic additions of 3′-O-blocked nucleoside triphosphates, wherein the blocking group of the 3-O-blocked nucleoside triphosphate is removable under deblocking conditions orthogonal to the deblocking conditions for removing blocking groups of the other initiators; and (c) releasing the oligonucleotides from the polynucleotides and the one or more solid supports.

The invention is directed to methods for synthesizing a plurality of oligonucleotides in the same reaction vessel, and in some embodiments, using the synthesized oligonucleotides in an oligonucleotide-based assay in such reaction vessel. In some embodiments, methods of the invention are implemented by steps of (a) providing a plurality of different initiators attached to one or more supports, each different initiator having a terminal nucleotide with a different 3-O-blocking group; (b) for each different initiator, synthesizing a polynucleotide by repeated cycles of template-free enzymatic additions of 3′-O-blocked nucleoside triphosphates, wherein the blocking group of the 3-O-blocked nucleoside triphosphate is removable under deblocking conditions orthogonal to the deblocking conditions for removing blocking groups of the other initiators; and (c) releasing the oligonucleotides from the polynucleotides and the one or more solid supports.

Disclosed is a method of measuring protein kinase activity, including a) attaching GMBS (N-[γ-maleimidobutyryloxy]sulfosuccinimide ester) to a base plate, b) attaching a substrate that reacts with a protein kinase to the base plate having GMBS attached thereto, thus manufacturing a kit for measuring protein kinase activity, c) introducing, to the kit, a mixture of a sample to be analyzed and a buffer including triton X-100, and d) probing phosphorylation of the substrate caused by the protein kinase contained in the sample, thereby measuring the activity of the protein kinase.

The invention relates to assays for nucleosome remodeling activity using functionalized recombinant mononucleosomes. The functionalized recombinant mononucleosomes comprise a histone octamer comprising recombinant histone H2A, H2B, H3 and H4 proteins and a DNA template comprising a nucleosome positioning sequence that effectively positions the histone octamer and a signal site. The invention further relates to methods of using the assay to quantify enzymatic activity of remodeling enzymes and identifying modulators of remodeling enzyme activity.

The invention relates to assays for nucleosome remodeling activity using functionalized recombinant mononucleosomes. The functionalized recombinant mononucleosomes comprise a histone octamer comprising recombinant histone H2A, H2B, H3 and H4 proteins and a DNA template comprising a nucleosome positioning sequence that effectively positions the histone octamer and a signal site. The invention further relates to methods of using the assay to quantify enzymatic activity of remodeling enzymes and identifying modulators of remodeling enzyme activity.