Materials and Methods Relating to Nano-Tags and Nano-Brands

• US 20090246879A1
• Filed: 03/30/2009
• Published: 10/01/2009
• Est. Priority Date: 12/20/2002
• Status: Abandoned Application

• Current Assignee: Callida Genomics, Inc. (SBH Genomics, Inc.)
• Original Assignee: Callida Genomics, Inc. (SBH Genomics, Inc.)
• Inventors: Hauser, Brian, Komoski, Joseph, Drmanac, Radoje T.
• Application Number:
  US12/414,208
• Publication Number:
  US 20090246879A1
• Time in Patent Office: Days
• US Class Current: 436/89
• 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 2219/00479 Means for mixing reactants or products in the reaction vessels
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00572 Chemical means
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00592 Split-and-pool, mix-and-divide processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B82Y 15/00 Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C40B 20/04 Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
• CPC Class Codes: C40B 50/16 involving encoding steps
• CPC Class Codes: C40B 70/00 Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G01N 33/54346 Nanoparticles
• CPC Class Codes: G01N 33/68 involving proteins, peptides or amino acids involving lipoproteins G01N33/92
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The invention relates to novel methods and materials for encoding and decoding information on individual molecules through the use of nano-tags, nano-barcodes, or modifications of a native molecule.

Claims

1. A method of analyzing a polymer comprising the steps of:

a) modifying a monomer in a polymer consisting of two or more monomer types; and

b) detecting the position of the modified monomer in a single intact polymer.

2. The method of claim 1, wherein two or more monomers of a particular type are modified.

3. The method of claim 1, wherein two or more monomers of a particular type are detected.

4. The method of claim 1, wherein different monomer types are modified.

5. The method of claim 1, wherein two or more types of monomer in a polymer are modified and detected.

6. The method of claim 1, wherein the modification is selected from the group consisting of adding at least one atom, removing at least one atom, and replacing at least one atom.

7. The method of claim 1, wherein the polymer is an oligomer.

8. The method of claim 1, wherein the polymer comprises nucleic acids.

9. The method of claim 1, wherein the polymer comprises amino acids.

10. The method of claim 1, wherein the polymer comprises saccharides.

11. The method of claim 1, wherein the detection step comprises detecting properties selected from the group consisting of charge, shape, mass, electron flow, and combinations thereof.

13. The method of claim 1 or 12, wherein the detection step comprises an imaging process selected from the group consisting of atomic force microscopy, transmission electron microscopy, scanning tunneling electron microscopy, and combinations thereof.

12. A method of detecting nano-tags comprising the steps of:

a) passing a nano-tag into a confined space which causes a conformational change in the structure of the nano-tag; and

b) detecting the conformational change of the nano-tag.

14. A method of nucleic acid sequencing comprising the steps of:

a) specifically modifying one or more base types in a nucleic acid molecule; and

b) identifying the base type at two or more consecutive positions in an individual nucleic acid molecule.

15. The method of claim 14, wherein the modifications are mediated by a base-specific ligand.

16. The method of claim 15, wherein the base-specific ligand is selected from the group consisting of a peptide or an aptamer.

17. The method of claim 14, wherein the modifications are mediated by a method selected from the group consisting of

a) direct chemical modification by addition of a polymer subunit type,

b) direct chemical modification by partial or complete removal of a polymer subunit type,

c) chemical modification by partial or complete replacement of a polymer subunit type, and

d) indirect chemical modification by addition, replacement, or removal of a polymer subunit type.

18-34. -34. (canceled)