C-shaped probe

• US 20060040275A1
• Filed: 10/15/2004
• Published: 02/23/2006
• Est. Priority Date: 10/16/2003
• Status: Abandoned Application

• Current Assignee: New York University
• Original Assignee: New York University
• Inventors: Tyagi, Sanjay, Rosmarin, David, Blaser, Martin Jack, Pei, Zhiheng
• Application Number:
  US10/966,321
• Publication Number:
  US 20060040275A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2525/307 Circular oligonucleotides
• CPC Class Codes: C12Q 2565/1015 labels being on the same oligonucleotide
• CPC Class Codes: F16H 57/04 Features relating to lubrication or cooling or heatingin hydrokinetic gearing F16H41/30; control of lubrication or cooling in hydrostatic gearing F16H61/4165

Abstract

A nucleic acid probe for identifying a target nucleic acid sequence including a linker structure including a 5′ end and a 3′ end; 5′ marker mechanism for producing an identifying signal to the target nucleic acid sequence, wherein the 5′ marker mechanism is conjugated to the 5′ end of the linker structure; and 3′ marker mechanism for producing an identifying signal to a target nucleic acid sequence, wherein the 3′ marker mechanism is conjugated to the 3′ end of the linker structure and wherein identification of the target nucleic acid sequence occurs when the 5′ marker mechanism and 3′ marker mechanism are in close physical proximity to each other. A nucleic acid probe for identifying a target nucleic acid including a marker pair mechanism for producing an identification signal to identify a target nucleic acid sequence; and linker mechanism for linking the marker pair mechanism together. A biosensor including a fluorophore quencher pair; and a linker sequence for linking the fluorophore quencher pair. A probe for use in a polymerase chain reaction (PCR).

Claims

1. A nucleic acid probe for identifying a target nucleic acid sequence comprising:

a linker structure including a 5′

end and a 3′

end;

5′

marker means for producing an identifying signal to a target nucleic acid sequence, wherein said 5′

marker means is conjugated to said 5′

end of said linker structure; and

3′

marker means for producing an identifying signal to the target nucleic acid sequence, wherein said 3′

marker means is conjugated to said 3′

end of said linker structure and wherein identification of the target nucleic acid sequence occurs when said 5′

marker means and 3′

marker means are in close physical proximity to each other.

2. The nucleic acid probe according to claim 1, wherein said linker structure is made of material selected from the group consisting of deoxyribonucleotides (DNA), ribonucleotides (RNA), modified nucleotides, a carbon backbone, modified internucleotide linkages, and combinations thereof.

3. The nucleic acid probe according to claim 1, wherein said 5′

marker means includes a first nucleic acid sequence for linking said 5′

marker means to said 5′

end of said linker structure and for hybridizing with a target nucleic acid sequence.

4. The nucleic acid probe according to claim 1, wherein said 3′

marker means includes a second nucleic acid sequence for linking said 3′

marker means to said 3′

end of said linker structure and for hybridizing with a target nucleic acid sequence.

5. The nucleic acid probe according to claim 1, wherein said identifying signal is selected from the group consisting of acceptor-donor signals, protein-ligand signals, enzyme-cofactor signals, antibody-antigen signals, protein-protein unit signals, protein-protein subunit signals, nucleic acid binding proteins-binding site signals, luminescent-quenching signals, fluorophore-quencher label signals (fluorescence resonance energy transfer (FRET)), fluorescent signals, radioluminescent signals, chemiluminescent signals, bioluminescent signals, electrochemiluminescent signals, and combinations thereof.

16. A method of detecting a polymerase chain reaction (PCR) product in a sample by applying the probe according to claim 1 to a polymerase chain reaction (PCR) solution.

17. A kit for detecting a target nucleic acid sequence comprising the nucleic acid probe of claim 1.

6. A nucleic acid probe for identifying a target nucleic acid sequence comprising marker pair means for producing an identification signal to identify a target nucleic acid sequence;

and linker means for linking said marker pair means together.

7. The nucleic acid probe according to claim 6, wherein said linker means is made of compounds selected from the group consisting of deoxyribonucleotides (DNA), ribonucleotides (RNA), modified nucleotides, a carbon backbone, modified internucleotide linkages, and combinations thereof.

8. The nucleic acid probe according to claim 6, wherein said marker pair means includes a first and a second nucleic acid sequence for linking said marker pair means to said linker means, wherein said first and said second nucleic acid sequences hybridize with a target nucleic acid sequence.

9. The nucleic acid probe according to claim 6, wherein said marker pair means is selected from the group consisting of acceptor-donor protein pairs, protein-ligand pairs, enzyme-cofactor pairs, antibody-antigen pairs, protein-protein unit pairs, protein-protein subunit pairs, nucleic acid binding proteins-binding site pairs, luminescent-quenching label pairs, fluorophore-quencher label pairs (fluorescence resonance energy transfer (FRET)), and combinations thereof.

10. The nucleic acid probe according to claim 6, wherein said identification signal is the generation of a signal selected from the group consisting of a fluorescent signal, radioluminescent signal, chemiluminescent signal, bioluminescent signal, and electrochemiluminescent signal.

11. The nucleic acid probe according to claim 6, wherein said identification signal is the reduction of a signal selected from the group consisting of a fluorescent signal, radioluminescent signal, chemiluminescent signal, bioluminescent signal, and electrochemiluminescent signal.

12. A biosensor comprising a fluorophore quencher pair;

and a linker sequence for linking said fluorophore quencher pair.

13. The biosensor according to claim 12, wherein said linker sequence is made of material selected from the group consisting of deoxyribonucleotides (DNA), ribonucleotides (RNA), modified nucleotides, a carbon backbone, modified internucleotide linkages, and combinations thereof.

14. The biosensor according to claim 12, wherein said fluorophore quencher pair includes a first and a second nucleic acid sequence for linking said fluorophore quencher pair to said linker sequence, wherein said first and said second nucleic acid sequences hybridize with a target nucleic acid sequence.

15. A nucleic acid sequence probe for identifying a nucleic acid target sequence, wherein said nucleic acid sequence probe has the formula:

5′

end X_n-A_n-Z_n-B_n—

Y_{n 3}′

end

wherein,

X=5′

marker means for producing an identification signal;

Y=3′

marker means for producing an identification signal, wherein said identification signal is produced when said 3′

marker means is in close physical proximity to said 5′

marker means;

A=first nucleic acid sequence including at least one nucleic acid selected from the group consisting of adenine, guanine, cytosine, thymine, and uracil;

B=second nucleic acid sequence including at least one nucleic acid selected from the group consisting of adenine, guanine, cytosine, thymine, and uracil;

Z=linking segment made of compounds selected from the group consisting of deoxyribonucleotides (DNA), ribonucleotides (RNA), modified nucleotides, a carbon backbone, modified internucleotide linkages, and combinations thereof;

n=an integer≧

1 and indicates the number of compounds; and

dotted lines represent bonds.