Compositions and methods for detecting microorganisms

• US 10,538,771 B2
• Filed: 08/31/2018
• Issued: 01/21/2020
• Est. Priority Date: 02/18/2014
• Status: Active Grant

• Current Assignee: SomaLogic Operating Co., Inc. (Somalogic Incorporated)
• Original Assignee: Somalogic Incorporated
• Inventors: Ochsner, Urs A., Janjic, Nebojsa
• Primary Examiner(s): Bowman, Amy H
• Application Number:
  US16/118,596
• Publication Number:
  US 20180371462A1
• Time in Patent Office: 508 Days
• CPC Class Codes: C12N 15/1048 SELEX
• CPC Class Codes: C12N 15/115 Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
• CPC Class Codes: C12N 2310/16 Aptamers
• CPC Class Codes: C12Q 1/14 Streptococcus; Staphylococcus
• CPC Class Codes: G01N 2333/31 from Staphylococcus (G)
• CPC Class Codes: G01N 33/5308 for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
• CPC Class Codes: G01N 33/569 for microorganisms, e.g. protozoa, bacteria, viruses

Abstract

Described herein are compositions and methods for detecting the presence or absence of a microorganism in a sample comprising contacting the sample with an aptamer capable of binding to a cell-surface protein of the microorganism to form a complex, contacting the mixture with a second aptamer capable of binding to the first cell-surface protein or a second cell-surface protein of the microorganism; and performing an assay to detect the second aptamer, wherein detecting the second aptamer indicates that the microorganism is present in the sample, and wherein not detecting the second aptamer indicates that the microorganism is absent from the sample.

Claims

1. A nucleic acid molecule comprising the sequence of SEQ ID NOs:

10-12, wherein n is independently, for each occurrence, a C-5 modified pyrimidine selected from the group consisting of 5-(N-benzylcarboxyamide)-2′

-deoxycytidine (BndC);

5-(N-2-phenylethylcarboxyamide-2′

-deoxycytidine (PEdC);

5-(N-3-phenylpropylcarboxyamide)-2′

-deoxycytidine (PPdC);

5-(N-1-naphthylmethylcarboxyamide-2′

-deoxycytidine (NapdC);

5-(N-2-naphthylmethylcarboxyamide)-2′

-deoxycytidine (2NapdC);

5-(N-1-naphthyl-2-ethylcarboxyamide)-2′

-deoxycytidine (NEdC);

5-(N-2-naphthyl-2-naphthyl-2-ethylcarboxyamide)-2′

-deoxycytidine (2NEdC);

5-(N-benzylcarboxyamide)-2′

-deoxyuridine (BndU);

5-(N-isobutylcarboxyamide-2′

-deoxyuridine (iBudU);

5-(N-tryptaminocarboxyamide-2′

-deoxyuridine (TrpdU);

5-(N-[1-(3-trimethylamonium) propyl]carboxyamide)-2′

-deoxyuridine chloride and 5-(N-naphthylmethylcarboxyamide)-2′

-deoxyuridine (NapdU), wherein the nucleic acid molecule is from about 40 to about 100 nucleotides in length.

2. The nucleic acid molecule of claim 1, wherein C-5 modified pyrimidine is a 5-(N-benzylcarboxyamide)-2′

-deoxyuridine (BndU).

3. The nucleic acid molecule of claim 1, wherein the nucleic acid molecule has affinity for a ClfA protein.

4. A kit for detecting the presence or absence of a microorganism in a sample comprising a nucleic acid molecule of claim 1.