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===Fluorescence===
Fluorescence intensity detection has developed very broadly in the microplate format over the last two decades. The range of applications is much broader than when using absorbance detection, but the instrumentation is usually more expensive. In this type of instrumentation, a first optical system (excitation system) illuminates the sample using a specific wavelength (selected by an optical filter, or a monochromator). As a result of the illumination, the sample emits light (it fluoresces) and a second optical system (emission system) collects the emitted light, separates it from the excitation light (using a filter or monochromator system), and measures the signal using a light detector such as a [[photomultiplier]] tube (PMT). The advantages of fluorescence detection over absorbance detection are sensitivity, as well as application range, given the wide selection of fluorescent labels available today. For example, a technique known as [[calcium imaging]] measures the fluorescence intensity of [[calcium-sensitive dyes]] to assess intracellular calcium levels.{{fact|date=May 2020}}<ref>{{Cite journal|last=Lin|first=Kedan|last2=Sadée|first2=Wolfgang|last3=Mark Quillan|first3=J.|date=February 1999|title=Rapid Measurements of Intracellular Calcium Using a Fluorescence Plate Reader|url=https://www.future-science.com/doi/10.2144/99262rr02|journal=BioTechniques|language=en|volume=26|issue=2|pages=318–326|doi=10.2144/99262rr02|issn=0736-6205|doi-access=free}}</ref>
===Luminescence===
Luminescence is the result of a chemical or biochemical reaction. Luminescence detection is simpler optically than fluorescence detection because luminescence does not require a light source for excitation or optics for selecting discrete excitation wavelengths. A typical luminescence optical system consists of a light-tight reading chamber and a [[Photomultiplier|PMT]] detector. Some plate readers use an Analog PMT detector while others have a [[photon counting]] PMT detector. Photon Counting is widely accepted as the most sensitive means of detecting luminescence. Some plate readers offer filter wheel or tunable wavelength monochromator optical systems for selecting specific luminescent wavelengths. The ability to select multiple wavelengths, or even wavelength ranges, allows for detection of assays that contain multiple luminescent reporter enzymes, the development of new luminescence assays, as well as a means to optimize the signal to noise ratio.{{fact|date=May 2020}}
Common applications include [[luciferase]] -based gene expression assays, as well as cell viability, cytotoxicity, and biorhythm assays based on the luminescent detection of [[Adenosine triphosphate|ATP]].<ref>{{Cite journal|last=Lin|first=Kedan|last2=Sadée|first2=Wolfgang|last3=Mark Quillan|first3=J.|date=1999-02-01|title=Rapid Measurements of Intracellular Calcium Using a Fluorescence Plate Reader|url=https://www.future-science.com/doi/10.2144/99262rr02|journal=BioTechniques|volume=26|issue=2|pages=318–326|doi=10.2144/99262rr02|issn=0736-6205|doi-access=free}}</ref>
===Time-resolved fluorescence (TRF)===
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