Reaction mixtures for detection of target nucleic acids

Claim 2

A reaction mixture for use in a process for the amplification and detection of a target nucleic acid sequence in a sample which reaction mixture, prior to amplification, comprises a pair of oligonucleotide primers and a labeled oligonucleotide, which pair of primers and labeled oligonucleotide are characterized in that: said pair of oligonucleotide primers comprises a first a primer complementary to said target nucleic acid and which primes the synthesis of a first extension product that is complementary to said target nucleic acid, and a second primer complementary to said first extension product and which primes the synthesis of a second extension product; and said labeled oligonucleotide hybridizes to a region of said target nucleic acid or the complement of said target nucleic acid, wherein said region is between one member of said primer pair and the complement of the other member of said primer pair.

Claim 3

The reaction mixture of claim 1 that further comprises a template-dependent nucleic acid polymerase having a 5' to 3' nuclease activity.

Claim 4

The reaction mixture of claim 1 wherein said labeled oligonucleotide is labeled at the 5' terminus.

Claim 5

The reaction mixture of claim 1 wherein said labeled oligonucleotide further comprises a tail of non-nucleic acids or a sequence of nucleotides which is non-complementary to the target nucleic acid sequence.

Claim 6

The reaction mixture of claim 1 wherein said labeled oligonucleotide comprises a first and second label.

Claim 7

The reaction mixture of claim 5 wherein said first and second labels are interactive signal generating labels effectively positioned on said labeled oligonucleotide to quench the generation of detectable signal.

Claim 8

The reaction mixture of claim 1 wherein the 3' terminus of said labeled oligonucleotide is blocked.

Claim 9

The reaction mixture of claim 1 wherein said labeled oligonucleotide is detectable by fluorescence.

Claim 10

The labeled oligonucleotide of claim 5 wherein said first label is a fluorophore and said second label is a quenching agent.

Claim 11

The labeled oligonucleotide of claim 5 wherein said first label is at the 5' terminus and said second label is at the 3' terminus.

Claim 12

The labeled oligonucleotide of claim 1 wherein said labeled oligonucleotide comprises a ligand having a specific binding partner.

Claim 13

The labeled oligonucleotide of claim 11 wherein said ligand is biotin.

Claim 14

A kit for detecting a target nucleic acid sequence in a sample comprising: (a) at least one labeled oligonucleotide containing a sequence complementary to a region of the target nucleic acid, wherein said labeled oligonucleotide anneals within the target nucleic acid sequence bounded by the oligonucleotide primers of part (b) and wherein said labeled oligonucleotide is blocked at the 3' terminus to prohibit incorporation of said labeled oligonucleotide into a primer extension product, wherein said blocking is achieved by adding a chemical moiety to the 3' hydroxyl of the last nucleotide, which moiety does not also serve as a label for subsequent detection or by removing said 3'-hydroxyl; and (b) a set of oligonucleotide primers, wherein a first primer contains a sequence complementary to a region in one strand of the target nucleic acid sequence and primes the synthesis of a first extension product, and a second primer contains a sequence complementary to a region in said first extension product and primes the synthesis of a nucleic acid strand complementary to said first extension product, and wherein each oligonucleotide primer is selected to anneal to its complementary template upstream of any labeled oligonucleotide annealed to the same nucleic acid strand.

Claim 15

A kit for detecting a target nucleic acid sequence in a sample comprising: (a) at least one labeled oligonucleotide containing a sequence complementary to a region of the target nucleic acid, wherein said labeled oligonucleotide anneals within the target nucleic acid sequence bounded by the oligonucleotide primers of part (b) and wherein said labeled oligonucleotide is blocked at the 3' terminus to prohibit incorporation of said labeled oligonucleotide into a primer extension product, wherein said blocking is achieved by adding a chemical moiety to the 3' hydroxyl of the last nucleotide, which moiety does not also serve as a label for subsequent detection or by removing said 3'-hydroxyl; and (b) a set of oligonucleotide primers, wherein a first primer contains a sequence complementary to a region in one strand of the target nucleic acid sequence and primes the synthesis of a first extension product, and a second primer contains a sequence complementary to a region in said first extension product and primes the synthesis of a nucleic acid strand complementary to said first extension product, and wherein each oligonucleotide primer is selected to anneal to its complementary template upstream of any labeled oligonucleotide annealed to the same nucleic acid strand.

Claim 16

The kit of claim 13 wherein said blocking is achieved by adding a chemical moiety to the 3' hydroxyl of the last nucleotide of said labeled oligonucleotide, which chemical moiety is a phosphate group.

Claim 17

The kit of claim 13 wherein said blocking is achieved by removing the 3'-hydroxyl from said labeled oligonucleotide.

Claim 18

The kit of claim 13 further comprising a nucleic acid polymerase having a 5' to 3' nuclease activity.

Claim 19

The kit of claim 16 wherein said nucleic acid polymerase is a thermostable enzyme.

Claim 20

The kit of claim 17 wherein said thermostable nucleic acid polymerase is a DNA polymerase from a Thermus species.

Claim 21

The kit of claim 13, wherein in said labeled oligonucleotide is detectable by fluorescence.

Claim 22

The kit of claim 13 wherein said labeled oligonucleotide is labeled at the 5' terminus.

Claim 23

The kit of claim 13, wherein said labeled oligonucleotide comprises first and second labels wherein said first label is separated from said second label by a nuclease susceptible cleavage site.

Claim 24

The kit of claim 21 wherein said first label is at the 5' terminus and said second label is at the 3' terminus.

Claim 25

The kit of claim 22 wherein the labels in said labeled oligonucleotide comprise a pair of interactive signal-generating labels positioned on said labeled oligonucleotide to quench the generation of detectable signal.

Claim 26

The kit of claim 23, wherein in said labeled oligonucleotide said first label is a flourophore and said second label is a quencher which interacts therewith.