Fluorous oligonucleotide microarray

• US 10,443,093 B2
• Filed: 11/23/2016
• Issued: 10/15/2019
• Est. Priority Date: 10/14/2014
• Status: Active Grant

• Current Assignee: MS2 Array, LLC
• Original Assignee: MS2 Array, LLC
• Inventors: Yu, Marvin
• Primary Examiner(s): Leavitt, Maria G
• Application Number:
  US15/360,066
• Publication Number:
  US 20170073743A1
• Time in Patent Office: 1,056 Days
• Field of Search: None
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00454 by chemical cleavage from the solid support
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00632 Introduction of reactive groups to the surface
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C40B 50/18 using a particular method of attachment to the solid support

Abstract

A fluorous-modified composition, a fluorous nucleoside, nucleotide, or oligonucleotide microarray, a compositional detection process, a process of forming a fluorous nucleoside, nucleotide, or oligonucleotide microarray, and fluorous nucleoside, nucleotide, or oligonucleotide microarray processes are disclosed. The fluorous-modified composition includes a linker, a nucleoside, nucleotide, or oligonucleotide connected to the linker, and a fluorous domain connected to the linker. The fluorous-modified composition includes at least one terminal perfluoroalkyl group in the fluorous domain, a solid-phase attachment group connected to the linker, or a combination thereof. The compositional detection process includes using the fluorous microarray for compositional detection. The processes of forming a fluorous microarray include transfer blotting the fluorous-modified composition to form a fluorous microarray and the spotting of reaction mixtures containing a fluorous-modified nucleoside, nucleotide, or oligonucleotide. The fluorous microarray includes a fluorous-modified conductive surface and fluorous nucleoside, nucleotide, or oligonucleotides positioned on the fluorous-modified surface. The fluorous microarray process includes using information corresponding to a compositional detection process.

Claims

1. A microarray for detecting targets and biomolecule interactions, comprising:

(a) a covalently-modified electrically conductive fluorous surface comprising a compositional grid,

(i) wherein the surface is electrically conductive with a sheet resistivity of less than 50 ohms/square, and

(ii) wherein the electrically conductive surface is perfluorocarbon modified;

(b) a plurality of fluorous-modified oligonucleotide compositions, wherein each fluorous-modified oligonucleotide composition in the plurality of fluorous-modified oligonucleotide compositions includes;

(i) a terminal fluorous domain or tag comprising at least one perfluoroalkyl group in the fluorous domain or tag, wherein the terminal fluorous domain or tag immobilizes each fluorous-modified oligonucleotide composition on the perfluorocarbon covalently-modified electrically conductive surface by non-covalently interacting with the perfluorocarbon modified surface through fluorous partitioning, wherein a fluorous-modified oligonucleotide composition occupies a defined location within the grid;

(ii) a linker connected to the terminal fluorous domain or tag, wherein the linker is a diamine linker, a phosphonic acid-hydroxyl linker, or an alkynyl amine linker; and

(iii) an oligonucleotide connected to the linker, wherein the oligonucleotide is configured to bind targets and interact with biomolecules of interest;

(c) wherein the presence of a target bound to the oligonucleotide in the fluorous-modified oligonucleotide composition or biomolecule interaction with the oligonucleotide in the fluorous-modified oligonucleotide composition is detectable by mass spectrometry through individual laser ionization of the oligonucleotide fluorous-modified composition immobilized on the perfluorocarbon covalently-modified electrically conductive surface.

2. The microarray of claim 1, wherein the covalently-modified electrically conductive fluorous surface is selected from the group consisting of a fluorous-modified indium tin oxide, fluorous-modified metal oxide, fluorous-modified silicon, a fluorinated nano-structured surface, fluorous-modified graphene surface, fluorous-modified graphene oxide surface, and combinations thereof.

3. The microarray of claim 1, wherein the fluorous-modified oligonucleotide compositions are substrates for kinases, transcriptases, reverse transcriptases, proteases, glycosyl transferases, phosphatases, methyltransferases, ligases, RNAses, DNAses, or other oligonucleotide modifying enzyme.

4. The microarray of claim 1, wherein a subset of the target bound to the oligonucleotide is a reversible or irreversible binding partner for transcription factors, proteins or protein complexes, peptides, or oligonucleotides of biological interest.

5. The microarray of claim 1, wherein the fluorous-modified oligonucleotide compositions are a component of a mixture of compounds used in an enzymatic, protein binding, or ligand binding reaction prior to positioning on the fluorous-modified conductive surface.