Unimolecular and bimolecular hybridization probes for the detection of nucleic acid target sequences comprise a target complement sequence, an affinity pair holding the probe in a closed conformation in the absence of target sequence, and either a label pair that interacts when the probe is in the closed conformation or, for certain unimolecular probes, a non-interactive label. Hybridization of the target and target complement sequences shifts the probe to an open conformation. The shift is detectable due to reduced interaction of the label pair or by detecting a signal from a non-interactive label. Certain unimolecular probes can discriminate between target and non-target sequences differing by as little as one nucleotide. Also, universal stems and kits useful for constructing said probes. Also, assays utilizing said probes and kits for performing such assays. Also, such probes capable of allelic discrimination.

Detectably labeled dual conformation oligonucleotide probes, assays and kits

A method is provided for monitoring the progress of nucleic acid amplifications that rely on a nucleic acid polymerase having 5'→3' exonuclease activity. An important feature of the method is providing an oligonucleotide probe having a reporter molecule and a quencher molecule at either end such that the quencher molecule substantially quenches any fluorescence from the reporter whenever the oligonucleotide probe is in a single stranded state and such that the reporter is substantially unquenched whenever the oligonucleotide probe is in a double stranded state hybridized to a target polynucleotide.

Method for detecting nucleic acid amplification using self-quenching fluorescence probe

Process gas discharged from a bypass pipe to a gas exhaust system can be prevented from diffusing back to the inside of a process chamber without having to install a dedicated vacuum pump at the downstream side of the bypass pipe. The substrate processing apparatus includes a process chamber accommodating a substrate, a gas supply system supplying process gas from a process gas source to the process chamber for processing the substrate, a gas exhaust system configured to exhaust the process chamber, two or more vacuum pumps installed in series at the gas exhaust system, and a bypass pipe connected between the gas supply system and the gas exhaust system. The most upstream one of the vacuum pumps is a mechanical booster pump, and the bypass pipe is connected between the mechanical booster pump and the rest vacuum pumps located at a downstream side of the mechanical booster pump.

Substrate Processing Apparatus

The present invention provides labeled nucleic acid amplification oligonucleotides, which can be linear or hairpin primers or blocking oligonucleotides. The oligonucleotides of the invention are labeled with donor and/or acceptor moieties of molecular energy transfer pairs. The moieties can be fluorophores, such that fluorescent energy emitted by the donor is absorbed by the acceptor. The acceptor may be a fluorophore that fluoresces at a wavelength different from the donor moiety, or it may be a quencher. The oligonucleotides of the invention are configured so that a donor moiety and an acceptor moiety are incorporated into the amplification product. The invention also provides methods and kits for directly detecting amplification products employing the nucleic acid amplification primers. When labeled linear primers are used, treatment with exonuclease or by using specific temperature eliminates the need for separation of unincorporated primers. This "closed-tube" format greatly reduces the possibility of carryover contamination with amplification products, provides for high throughput of samples, and may be totally automated.

Nucleic acid amplification oligonucleotides with molecular energy transfer labels and methods based thereon

Methods of monitoring hybridization during polymerase chain reaction are disclosed. These methods are achieved with rapid thermal cycling and use of double stranded DNA dyes or specific hybridization probes. A fluorescence resonance energy transfer pair comprises fluorescein and Cy5 or Cy5.5. Methods for quantitating amplified DNA and determining its purity are carried out by analysis of melting and reannealing curves.

Monitoring amplification of DNA during PCR

The present invention is directed to a process of detecting a target nucleic acid using labeled oligonucleotides. This process uses the 5' to 3' nuclease activity of a nucleic acid polymerase to cleave annealed labeled oligonucleotide from hybridized duplexes and release labeled oligonucleotide fragments for detection. This process is easily incorporated into a PCR amplification assay.

Homogeneous assay system using the nuclease activity of a nucleic acid polymerase

The present invention is directed to methods for controlling the light emission of an oligonucleotide labeled with a light-emitting label that are useful in nucleic acid detection assays. A reaction that results in the cleavage of single-stranded oligonucleotide probes labeled with a light-emitting label is carried out in the presence of a DNA binding compound that interacts with the label to modify the light emission of the label. The methods utilize the change in light emission of the labeled probe that results from degradation of the probe. The methods are applicable in general to assays that utilize a reaction that results in cleavage of oligonucleotide probes, and, in particular, to homogeneous amplification/detection assays wherein hybridized probe is cleaved concomitant with primer extension. A homogeneous amplification/detection assay is provided which allows the simultaneous detection of the accumulation of amplified target and the sequence-specific detection of the target sequence.

Methods for in-solution quenching of fluorescently labeled oligonucleotide probes

A process of detecting a target nucleic acid using labeled oligonucleotides which uses the 5' to 3' nuclease activity of a nucleic acid polymerase to cleave annealed labeled oligonucleotide from hybridized duplexes and thus releasing labeled oligonucleotide fragments for detection. This process is easily incorporated into a PCR amplification assay.

Nucleic acid detection by the 5'-3'exonuclease activity of polymerases acting on adjacently hybridized oligonucleotides

A process of detecting a target nucleic acid using labeled oligonucleotides uses the 5' to 3' nuclease activity of a nucleic acid polymerase to cleave annealed labeled oligonucleotide from hybridized duplexes and release labeled oligonucleotide fragments for detection. This process is easily incorporated into a PCR amplification assay.

Reaction mixtures for detection of target nucleic acids

A process of detecting a target nucleic acid using labeled oligonucleotides uses the 5′ to 3′ nuclease activity of a nucleic acid polymerase to cleave annealed labeled oligonucleotide from hybridized duplexes and release labeled oligonucleotide fragments for detection. This process is easily incorporated into a PCR amplification assay.

Process for discrimination of nucleic acid sequence variants

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