Optical reporter compositions

• US 9,005,985 B2
• Filed: 02/07/2013
• Issued: 04/14/2015
• Est. Priority Date: 04/16/2003
• Status: Active Grant

• Current Assignee: APDN (B.V.I.) Inc. (Applied DNA Sciences Incorporated)
• Original Assignee: APDN (B.V.I.) Inc. (Applied DNA Sciences Incorporated)
• Inventors: Kwok, Thomas, Liang, Benjamin MingHwa, So, Stephane Shu Kin
• Primary Examiner(s): Fritchman, Rebecca M
• Application Number:
  US13/761,447
• Publication Number:
  US 20130149706A1
• Time in Patent Office: 796 Days
• Field of Search: 435/6.11, 435/6.12, 977/774, 977/920, 33/53, 335/43
• US Class Current: 436/91
• 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: C08K 5/09 Carboxylic acids; Metal salts thereof; Anhydrides thereof
• CPC Class Codes: C09D 11/03 characterised by features other than the chemical nature of the binder
• CPC Class Codes: C09D 7/63 organic
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2563/185 Nucleic acid dedicated to use as a hidden marker/bar code, e.g. inclusion of nucleic acids to mark art objects or animals
• CPC Class Codes: Y10S 977/774 Exhibiting three-dimensional carrier confinement, e.g. quantum dots
• CPC Class Codes: Y10S 977/92 Detection of biochemical
• CPC Class Codes: Y10T 436/14 Heterocyclic carbon compound [i.e. , O, S, N, Se, Te, as only ring hetero atom]
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

This invention provides compositions that have a light emitting reporter linked to biomolecules, preferably, nucleotide oligomers. The light reporter particles are silylated and functionalized to produce a coated light reporter particle, prior to covalently linking the biomolecules to the light reporter particle. The light reporter particles of the invention can be excited by a light excitation source such as UV or IR light, and when the biomolecule is DNA, the attached DNA molecule(s) are detectable by amplification techniques such as PCR.

Claims

1. A composition of the formula I:

(cOpR)-[L-(NA)]_m 

 

I

wherein;

m is an integer greater than 1;

(cOpR) is a coated optical reporter particle, wherein the cOpR comprises an upconverting phosphor (UCP) material of the formula Na(Y_xYb_yEr_z)F₄, and wherein;

x is from about 0.6 to about 0.95;

y is from about 0.05 to about 0.35; and

z is from about 0.1 to about 0.001;

(NA) is a nucleic acid oligomer of detectable sequence; and

L is a linking group covalently bound to the coated optical reporter particle and to the nucleic acid oligomer;

provided that at least one of the following applies;

x is not from 0.7 to 0.9; and

/or

y is not from 0.08 to 0.29; and

/or

z is not from 0.01 to 0.06.

2. The composition of claim 1, wherein (NA) is a single stranded DNA molecule having a length of between about 40 nucleotides and about 1000 nucleotides or a double stranded DNA molecule having a length of between about 40 base pairs and about 1000 base pairs.

3. The composition of claim 1, wherein L comprises an alkylene moiety having a first end covalently bound to the coated optical reporter particle and a second end covalently bound to the nucleic acid oligomer.

4. The composition of claim 1, wherein L is of the formula:

-A-R¹—

B—

wherein;

R¹ is C_2-8alkylene;

-A- is a group covalently bonded to the surface of the coated optical reporter; and

—

B—

is a group covalently bonded to the 3′

or 5′

end of the nucleic acid oligomer.

5. The composition of claim 4, wherein -A- is —

O—

.

6. The composition of claim 4, wherein —

R¹—

is —

(CH₂)_n— and

wherein n is from 2 to 8.

7. The composition of claim 4, wherein —

B—

is;

—

S—

;

—

O—

;

—

NR^a—

;

—

S—

(CH₂)_p—

;

—

O—

(CH₂)_p—

;

—

NR^a—

(CH₂)_p—

;

—

S—

(CH₂)_q—

C(O)—

NR^a—

(CH₂)_p—

;

—

O—

(CH₂)_q—

C(O)—

NR^a—

(CH₂)_p—

;

—

NR^a—

(CH₂)_q—

C(O)—

NR^a—

(CH₂)_p—

;

—

S—

C(O)—

(CH₂)_r—

C(O)—

NR^a—

(CH₂)_p—

;

—

O—

C(O)—

(CH₂)_r—

C(O)—

NR^a—

(CH₂)_p—

;

or

—

NR^a—

C(O)—

(CH₂)_r—

C(O)—

NR^a—

(CH₂)_p—

;

wherein;

p is from 2 to 8;

q is from 1 to 8;

r is from 2 to 8; and

each R^a is independently hydrogen or C_1-6alkyl.

8. The composition of claim 4, wherein —

B—

is;

—

S—

(CH₂)_q—

C(O)—

NR^a—

(CH₂)_p or

—

NR^a—

C(O)—

(CH₂)_r—

C(O)—

NR^a—

(CH₂)_p;

wherein;

p is from 2 to 8;

q is from 1 to 8;

r is from 2 to 8; and

each R^a is independently hydrogen or C_1-6alkyl.

9. The composition of claim 8, wherein:

p is from 2 to 6;

q is from 1 to 3; and

r is 2 or 3.

10. The composition of claim 4, wherein —

B—

is;

—

S—

CH₂—

C(O)—

NH—

(CH₂)₆—

;

or

—

NH—

C(O)—

(CH₂)₃—

C(O)—

NH—

(CH₂)₆—

.

11. The composition of claim 1, wherein the cOpR is coated with silica.

17. The composition of claim 1, wherein the cOpR comprises a visually detectable light emitting material selected from the group consisting of a fluorescent dye, a ceramic powder, or a quantum dot.

18. The composition of claim 17, where said light emitting materials are excitable by a UV light source or an infrared light source.

19. The composition of claim 1, wherein the cOpR comprises at least one electromagnetic radiation-emitting material.

20. The composition of claim 19, where the electromagnetic radiation-emitting material is detectable by devices which provide sources selected from the group consisting of an infrared radiation source, magnetic field source, a quantum dot or electromagnetic pulse.

12. A composition of the formula II:

(UCP)-[A-R¹—

X—

R²—

C(O)—

NR^a—

R³-(DNA)]_m 

 

II

wherein;

m is an integer greater than 1;

UCP is an upconverting phosphor particle of the formula Na(Y_xYb_yEr_z)F₄, wherein;

x is from about 0.6 to about 0.95;

y is from about 0.05 to about 0.35; and

z is from about 0.1 to about 0.001;

DNA is a single or double stranded deoxyribonucleic acid oligomer;

-A- is a group covalently bound to a surface of the UCP;

R¹ is C_2-8alkylene,

R² is C_1-8alkylene or —

C(O)—

C_1-8alkylene-;

—

X—

is —

O—

, —

S—

or —

NR^a—

;

R³ is C_2-8alkylene; and

R^a is hydrogen or C_1-6alkyl;

provided that at least one of the following applies;

x is not from 0.7 to 0.9; and

/or

y is not from 0.08 to 0.29; and

/or

z is not from 0.01 to 0.06.

13. The composition of claim 12, wherein the composition is of the formula IV:

(UCP)—

[O—

(CH₂)_s—

S—

(CH₂)_t—

C(O)—

NH—

(CH₂)_v-(DNA)]_m 

 

IV

wherein;

s is from 2 to 6;

v is from 2 to 6; and

t is from 1 to 3.

14. The composition of claim 12, wherein the composition is of the formula V:

(UCP)—

[O—

(CH₂)_s—

NH—

C(O)—

(CH₂)_u—

C(O)—

NH—

(CH₂)_v-(DNA)]_m 

 

V

wherein;

s is from 2 to 6;

v is from 2 to 6; and

u is 2 or 3.

15. The composition of claim 12, wherein the composition is of the formula VI:

(UCP)—

[O—

(CH₂)₃—

S—

CH₂—

C(O)—

NH—

(CH₂)₆-(DNA)]_m 

 

VI.

16. The composition of claim 12, wherein the composition is of the formula VII:

(UCP)—

[O—

(CH₂)₃—

NH—

C(O)—

(CH₂)₃—

C(O)—

NH—

(CH₂)₆-(DNA)]_m 

 

VII.

21. A composition of the formula I:

(cOpR)-[L-(NA)]_m 

 

I

wherein;

m is an integer greater than 1;

(cOpR) is a coated optical reporter particle, wherein the cOpR comprises an upconverting phosphor (UCP) material of the formula Na(Y_xYb_yEr_z)F₄, and wherein;

x is from about 0.6 to about 0.95;

y is from about 0.05 to about 0.35; and

z is from about 0.1 to about 0.001;

(NA) is a nucleic acid oligomer; and

L is a linking group covalently bound to the coated optical reporter particle and to the nucleic acid oligomer, wherein the linking group L comprises an alkylene moiety having a first end covalently bound to the coated optical reporter particle and a second end covalently bound to the nucleic acid oligomer.