Nucleic acid ligand diagnostic Biochip

• US 6,242,246 B1
• Filed: 12/15/1997
• Issued: 06/05/2001
• Est. Priority Date: 12/15/1997
• Status: Expired due to Term

• Current Assignee: SomaLogic Operating Co., Inc. (Somalogic Incorporated)
• Original Assignee: Somalogic Incorporated
• Inventors: Gold, Larry, Drolet, Dan, Jayasena, Sumedha, Zichi, Dom, Gill, Stanley, Creighton, Steve
• Primary Examiner(s): Zitomer, Stephanie
• Assistant Examiner(s): FORMAN, BETTY J
• Application Number:
  US08/990,436
• Time in Patent Office: 1,268 Days
• Field of Search: 435/287.1, 435/287.2, 435/91.1, 435/6, 435/194, 436/94, 536/24.3, 536/23.1, 536/25.4
• US Class Current: 435/287.1
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6839 Triple helix formation or other higher order conformations in hybridisation assays
• CPC Class Codes: C12Q 2525/205 Aptamer
• CPC Class Codes: C12Q 2541/101 Selex
• CPC Class Codes: C12Q 2565/101 Interaction between at least two labels
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: C40B 40/00 Libraries per se, e.g. arrays, mixtures
• CPC Class Codes: Y10S 977/924 using nanostructure as support of dna analysis

Abstract

A Nucleic acid ligand “Biochip” is disclosed, consisting of a solid support to which one or more specific Nucleic acid ligands is attached in a spatially defined manner. Each Nucleic acid ligand binds specifically and avidly to a particular Target molecule contained within a Test mixture, such as a Bodily fluid The Target molecules include, but are not limited to, proteins (cellular, viral, bacterial, etc.) hormones, sugars, metabolic byproducts, cofactor, and intermediates, drugs, and toxins. Contacting the Test mixture with the Biochip leads to the binding of a Target molecule to its cognate Nucleic acid ligand. Binding of Target to the Nucleic acid ligand results in a detectable change at each specific location on the Biochip. The detectable change can include, but is not limited to, a change in fluorescence, or a change in a physical parameter, such as electrical conductance or refractive index, at each location on the Biochip. The Biochip will then be read by a device, such as a fluorescence scanner or a surface plasma resonance detector, that can measure the magnitude of the change at each location on the Biochip. The location of the change reveals what Target molecule has been detected, and the magnitude of the change indicates how much of it is present The combination of these two pieces of information will yield diagnostic and prognostic medical information when signal patterns are compared with those obtained from Bodily fluids of individuals with diagnosed disorders FIG. 1). In principle, the Biochip could be used to test any chemically complex mixture provided that Nucleic acid ligands to components suspected of being present in the mixture are attached to the Biochip. Thus, the Nucleic acid ligand Biochip will have a wider use in environmental testing, etc.

Claims

1. A method for making a biochip comprising a plurality of distinct nucleic acid ligands at spatially discrete locations on a solid support, the method comprising:

I. identifying each of said distinct nucleic acid ligands to a target molecule by the method;

(a) preparing a candidate mixture of nucleic acid sequences;

(b) contacting said candidate mixture of nucleic acids with a target molecule, wherein nucleic acids having an increased affinity to said target molecule relative to the candidate mixture are partitioned from the remainder of the candidate mixture;

(c) partitioning the increased affinity nucleic acids from the remainder of the candidate mixture;

(d) amplifying the increased affinity nucleic acids to yield a mixture of nucleic acids enriched for nucleic acid sequences with relatively higher affinity and specificity for binding to said target molecule; and

(e) repeating steps b), c) and d) until said nucleic acids possess the desired affinity for said target molecule, whereby a nucleic acid ligand of said target molecule may be identified;

II. attaching said distinct nucleic acid ligands to spatially discrete locations on a solid support.

2. The method of claim 1 wherein said nucleic acid ligands are attached to said solid support via covalent bonds.

3. The method of claim 1 wherein said nucleic acid ligands are attached to said solid support via non-covalent bonds.

4. A method for making a plurality of solid supports each having a distinct nucleic acid ligand attached to its surface, the method comprising:

I. Identifying each of said distinct nucleic acid ligands to a target molecule by the method;

(a) preparing a candidate mixture of nucleic acid sequences;

(b) contacting said candidate mixture of nucleic acids with a target molecule, wherein nucleic acids having an increased affinity to said target molecule relative to the candidate mixture are partitioned from the remainder of the candidate mixture;

(c) partitioning the increased affinity nucleic acids from the remainder of the candidate mixture;

(d) amplifying the increased affinity nucleic acids to yield a mixture of nucleic acids enriched for nucleic acid sequences with relatively higher affinity and specificity for binding to said target molecule; and

(e) repeating steps b), c) and d) until said nucleic acid ligands possess the desired affinity for said target molecule, whereby a nucleic acid ligand of said target molecule may be identified;

II. Attaching said distinct nucleic acid ligands to a plurality of solid supports.