1.  Field of the Invention
This invention generally relates to systems and methods for performing measurements of DNA amplification such as PCR.  In particular, this invention relates to “real time” measurements of PCR with multiplexing capability.  Certain embodiments relate to a system which uses particles, such as paramagnetic microspheres, and an imaging chamber of a measurement device which is also capable of controllable thermal cycling for assisting the PCR process. 
2.  Description of Related Art
Polymerase chain reaction (PCR) is a molecular biology technique for enzymatically replicating DNA without using a living organism.  PCR is commonly used in medical and biological research labs for a variety of tasks, such as the detection of hereditary diseases, the identification of genetic fingerprints, the diagnosis of infectious diseases, the cloning of genes, paternity testing, and DNA computing.  PCR has been accepted by molecular biologists as the method of choice for nucleic acid detection because of its unparalleled amplification and precision capability.  DNA detection is typically performed at the end-point, or plateau phase of the PCR reaction, making it difficult to quantify the starting template.  Real-time PCR or kinetic PCR advances the capability of end-point PCR analysis by recording the amplicon concentration as the reaction progresses.  Amplicon concentration is most often recorded via a fluorescent signal change associated with the amplified target.  Real-time PCR is also advantageous over end-point detection in that contamination is limited because it can be performed in a closed system.  Other advantages include greater sensitivity, dynamic range, speed, and fewer processes required. 
Several assay chemistries have been used in real-time PCR detection methods.  These assay chemistries include using double-stranded DNA binding dyes, dual-labeled oligonucleotides, such as hairpin primers, and hairpin probes.  Other chemistries include exonuclease based probes such as hydrolysis probes.  Various PCR and real-time PCR methods are disclosed in U.S. Pat.  Nos.  5,656,493; 5,994,056; 6,174,670; 5,716,784; 6,030,787; and 6,174,670, which are incorporated herein by reference. 
A drawback of current real-time PCR is its limited multiplexing capability.  Current real-time PCR technologies use reporter fluorochromes that are free in solution.  This design necessitates the use of spectrally distinct fluorochromes for each assay within a multiplex reaction.  For example, a multiplex reaction designed to detect 4 target sequences would require an instrument capable of distinguishing 4 different free floating fluorochromes by spectral differentiation, not including controls.  These requirements not only limit the practical multiplexing capability, but also increase costs since such instruments typically require multiple lasers and filters.  Current real-time PCR technologies have multiplexing capabilities from about 1-6 plex.