Fluorescence and the World it has Opened

Reading Assignments:

The Molecular Probes Handbook Fluorescence Fundamentals

Fluorescence microscopy - Lichtman & Conchello.pdf (or http://www.nature.com/nmeth/journal/v2/n12/full/nmeth817.html)

Jablonski Diagram

Reading assignment: Jablonski Diagram.pdf
(or http://chemwiki.ucdavis.edu/Wikitexts/UCD_Chem_205%3A_Larsen/ChemWiki_Module_Topics/Jablonski_diagram)

Ground state


Excited state

  • Collisional quenching
  • Fluorescence resonance energy transfer
  • Fluorescence excited-state lifetime

Inter system crossing to triplet state

  • Photobleaching
  • Photo activation


Molar extinction coefficient (e) or EC

Quantum Yield (QY)

Fluorescence intensity per dye molecule is proportional to EC X QY

Stokes Shift

Excitation Spectrum

Emission Spectrum

Fluorescence Excitation Sources

Reading Assignments:

Light Sources.pdf
(or http://zeiss-campus.magnet.fsu.edu/articles/lightsources/lightsourcefundamentals.html)

Semrock – Optical Filters.pdf
(or http://www.semrock.com/1optical-filters-for-laser-based-fluorescence-microscopes.aspx)

Table 1: Lasers for popular fluorophores. “DPSS” = diode-pumped solid-state laser. “OPS” = optically pumped semiconductor laser.
“Doubled” = frequency doubled via a nonlinear optical crystal.

Fluorescence Filters

Reading assignment:

Optical Filters Handbook – Reichman.pdf (or http://www.aic-imagecentral.com/products/pdfs/hdbk4.pdf)

Fluorescence Detectors


Hamamatsu PMT handbook.pdf
(or http://sales.hamamatsu.com/assets/applications/ETD/pmt_handbook/pmt_handbook_complete.pdf)

Hamamatsu Cameras.pdf (or http://www.emez.ethz.ch/education/pastevents/pastev/Cameras_rf.pdf)

Fluorescent Materials in Biology

Reading assignment:
The Fluorescent Toolbox.pdf (“The Fluorescent Toolbox” PMID: 16614209)

Fluorescent dyes

Fluorescent Proteins

Quantum Dots

Fluorescent Antibodies


[Zip Package of all Section 4 Documents]