Multisignal labeling reagents and processes and uses therefor

• US 10,647,740 B2
• Filed: 12/21/2017
• Issued: 05/12/2020
• Est. Priority Date: 04/03/2003
• Status: Expired due to Term

• Current Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Original Assignee: Enzo Life Science, Inc.
• Inventors: Coleman, Jack, Rabbani, Elazar, Stavrianopoulos, Jannis, Pande, Praveen
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US15/850,028
• Publication Number:
  US 20180127456A1
• Time in Patent Office: 873 Days
• Field of Search: 536 266
• CPC Class Codes: C07D 219/08 Nitrogen atoms
• CPC Class Codes: C07D 405/14 containing three or more hetero rings
• CPC Class Codes: C07D 491/22 in which the condensed system contains four or more hetero rings
• 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: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C09B 11/00 Diaryl- or thriarylmethane dyes
• CPC Class Codes: C09B 11/08 Phthaleins; Phenolphthaleins; Fluorescein
• CPC Class Codes: C09B 11/24 Phthaleins containing amino groups ; Phthalanes; Fluoranes; Phthalides; Rhodamine dyes; Phthaleins having heterocyclic aryl rings; Lactone or lactame forms of triarylmethane dyes
• CPC Class Codes: C09B 57/02 Coumarine dyes
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: G01N 33/533 with fluorescent label
• CPC Class Codes: G01N 33/582 with fluorescent label

Abstract

Provided are compounds comprising two DNA supramolecular binding molecules covalently joined by a linker group. Also provided are multisignal labeling reagents comprising (i) an oligomer of nucleotides or nucleotide analogs; (ii) a DNA supramolecular binding molecule noncovalently bound to the oligomer; and (iii) a first reactive group or a first partner of a first binding pair covalently bound to the oligomer. Additionally provided are methods of producing multisignal labeling reagents.

Claims

1. A method of producing a multisignal labeling reagent, the method comprising

(a) obtaining

(i) a primer comprising an oligonucleotide;

(ii) a template comprising a nucleic acid comprising a first sequence that is complementary to the oligonucleotide and a second sequence that extends in the 5′

direction from the first sequence;

(iii) a polymerase capable of extending the oligonucleotide along the template nucleic acid when the template nucleic acid is hybridized to the oligonucleotide at the first sequence;

(iv) nucleotide triphosphates (NTPs) or analogs thereof that are capable of being incorporated into the extended oligonucleotide, wherein at least one of the NTPs or analogs comprises a non-radioactive detectable label, a second reactive group or a first partner of a second binding pair; and

(v) a polymer capable of binding to more than one of the extended oligonucleotide, wherein the polymer comprises a first reactive group or a first partner of a first binding pair;

(b) combining the primer, template, polymerase and NTPs or analogs under conditions such that the oligonucleotide hybridizes to the first sequence and is extended along the second sequence, where the extended oligonucleotide comprises at least two NTPs or analogs incorporated therein that comprise a non-radioactive detectable label, a second reactive group or a first partner of a second binding pair; and

(c) combining the extended oligonucleotide with the polymer under conditions such that at least two of the extended oligonucleotides bind to the polymer,

wherein,

(A) if at least one of the at least two NTPs or analogs incorporated into the extended oligonucleotide comprises a second reactive group, the method further comprises combining the extended oligonucleotide with a first compound comprising a non-radioactive detectable label covalently linked to a moiety capable of reacting with the second reactive group such that the label is covalently linked to the extended primer, and

(B) if at least one of the at least two NTPs or analogs incorporated into the extended oligonucleotide comprises a first partner of the second binding pair, the method further comprises combining the extended primer with a second compound comprising the non- radioactive detectable label covalently linked to a second binding partner of the second binding pair.

2. The method of claim 1, wherein the non-radioactive detectable labels are fluorophores, phosphorescent moieties, chemiluminescent moieties, chelating moieties, electron dense moieties, magnetic moieties, or energy transfer moieties.

3. The method of claim 1, wherein the non-radioactive detectable labels are fluorophores.

4. The method of claim 1, wherein the two NTPs or analogs incorporated into the extended oligonucleotide are each labeled with a reactive group.

5. The method of claim 4, wherein each reactive group is joined to the NTPs by a linker arm.

6. The method of claim 1, wherein the NTP or NTP analogs are each labeled with a non-radioactive detectable label.

7. The method of claim 3, wherein the NTP or NTP analogs are each labeled with a first binding partner of a second binding pair.

8. The method of claim 7, wherein the first binding partner of the second binding pair is a biotin.

9. The method of claim 7, wherein each first binding partner of the second binding pair is connected to the NTPs by a linker arm.

10. The method of claim 1, wherein the multisignal labeling reagent further comprises a non-inherent charged group that increases the aqueous solubility of the reagent.

11. The method of claim 1, wherein the polymer comprises a first partner of a first binding pair.

12. The method of claim 11, wherein the first binding pair is a ligand/receptor, a hormone/receptor, biotin/avidin, biotin/streptavidin or an antigen/antibody.

13. The method of claim 11, wherein the first partner of the first binding pair is biotin.

14. The method of claim 12, wherein the polymer is a polynucleotide comprising more than one region that is complementary to a portion of the extended oligonucleotide.

15. The method of claim 1, further comprising combining the multisignal labeling reagent with a target molecule such that the multisignal labeling reagent is bound to the target by the first reactive group or the first partner of the first binding pair.