confocal course lecture 4

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Lecture 3
Fluorescence and Fluorescence Probes
BMS 524 - “Introduction to Confocal Microscopy and Image Analysis”
1 Credit course offered by Purdue University Department of Basic Medical Sciences,
School of Veterinary Medicine
J.Paul Robinson, Ph.D.
Professor of Immunopharmacology
Director, Purdue University Cytometry Laboratories
These slides are intended for use in a lecture series. Copies of the graphics are distributed and
students encouraged to take their notes on these graphics. The intent is to have the student
NOT try to reproduce the figures, but to LISTEN and UNDERSTAND the material. All
material copyright J.Paul Robinson unless otherwise stated, however, the material may be
freely used for lectures, tutorials and workshops. It may not be used for any commercial
purpose.
The text for this course is Pawley “Introduction to Confocal Microscopy”, Plenum Press, 2nd Ed. A
number of the ideas and figures in these lecture notes are taken from this text.
UPDATED January 2000
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 1 t:/classes/BMS524/524lect3.ppt
Overview
•
•
•
•
Fluorescence
The fluorescent microscope
Types of fluorescent probes
Problems with
fluorochromes
• General applications
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 2 t:/classes/BMS524/524lect3.ppt
Excitation Sources
Excitation Sources
Lamps
Xenon
Xenon/Mercury
Lasers
Argon Ion (Ar)
Krypton (Kr)
Helium Neon (He-Ne)
Helium Cadmium (He-Cd)
Krypton-Argon (Kr-Ar)
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 3 t:/classes/BMS524/524lect3.ppt
Fluorescence
• Chromophores are components of
molecules which absorb light
• They are generally aromatic rings
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 4 t:/classes/BMS524/524lect3.ppt
Fluorescence
•
•
•
•
What is it?
Where does it come from?
Advantages
Disadvantages
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 5 t:/classes/BMS524/524lect3.ppt
Fluorescence
Jablonski Diagram
Singlet States
Triplet States
Vibrational energy levels
Rotational energy levels
Electronic energy levels
S2
ENERGY
T2
S1
IsC
T1
ABS
FL
I.C.
PH
IsC
S0
[Vibrational sublevels]
ABS - Absorbance
S 0.1.2 - Singlet Electronic Energy Levels
FL - Fluorescence
T 1,2 - Corresponding Triplet States
I.C.- Nonradiative Internal Conversion IsC
- Intersystem Crossing
PH - Phosphorescence
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 6 t:/classes/BMS524/524lect3.ppt
Simplified Jablonski Diagram
S’
1
S1
hvex
hvem
S0
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 7 t:/classes/BMS524/524lect3.ppt
Fluorescence
The longer the wavelength the lower the energy
The shorter the wavelength the higher the energy
eg. UV light from sun causes the sunburn
not the red visible light
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 8 t:/classes/BMS524/524lect3.ppt
Fluorescence Excitation Spectra
Intensity
related to the probability of the event
Wavelength
the energy of the light absorbed or emitted
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 9 t:/classes/BMS524/524lect3.ppt
Allophycocyanin (APC)
Protein
300 nm
400 nm
500 nm
© J.Paul Robinson - Purdue University Cytometry Laboratories
632.5 nm (HeNe)
600 nm
700 nm
Excitation
Emisson
Slide 10 t:/classes/BMS524/524lect3.ppt
Arc Lamp Excitation Spectra
Xe Lamp
Irradiance at 0.5 m (mW m-2 nm-1)



Hg Lamp



© J.Paul Robinson - Purdue University Cytometry Laboratories


Slide 11 t:/classes/BMS524/524lect3.ppt
350
300 nm
457 488 514
400 nm
500 nm
Common Laser Lines
610 632
600 nm
700 nm
PE-TR Conj.
Texas Red
PI
Ethidium
PE
FITC
cis-Parinaric acid
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 12 t:/classes/BMS524/524lect3.ppt
Fluorescence
Stokes Shift
Fluorescnece Intensity
– is the energy difference between the lowest
energy peak of absorbence and the highest
energy of emission
Fluorescein
molecule
Stokes Shift is 25 nm
495 nm
520 nm
Wavelength
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 13 t:/classes/BMS524/524lect3.ppt
Light Sources - Lasers
Laser
•
•
•
•
Argon
Krypton-Ar
Helium-Neon
He-Cadmium
Abbrev.
Ar
Kr-Ar
He-Ne
He-Cd
Excitation Lines
353-361, 488, 514 nm
488, 568, 647 nm
543 nm, 633 nm
325 - 441 nm
(He-Cd light difficult to get 325 nm band through some optical systems)
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 14 t:/classes/BMS524/524lect3.ppt
Parameters
• Extinction Coefficient
– 
refers to a single wavelength (usually the absorption
maximum)
• Quantum Yield
– Qf
is a measure of the integrated photon emission over
the fluorophore spectral band
• At sub-saturation excitation rates,
fluorescence intensity is proportional
to the product of  and Qf
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 15 t:/classes/BMS524/524lect3.ppt
Excitation Saturation
• The rate of emission is dependent upon the time the molecule
remains within the excitation state (the excited state lifetime
 f)
• Optical saturation occurs when the rate of excitation exceeds
the reciprocal of f
• In a scanned image of 512 x 768 pixels (400,000 pixels) if
scanned in 1 second requires a dwell time per pixel of 2 x 10-6
sec.
• Molecules that remain in the excitation beam for extended
periods have higher probability of interstate crossings and thus
phosphorescence
• Usually, increasing dye concentration can be the most
effective means of increasing signal when energy is not the
limiting factor (ie laser based confocal systems)
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 16 t:/classes/BMS524/524lect3.ppt
How many Photons?
• Consider 1 mW of power at 488 nm focused to a
Gaussian spot whose radius at 1/e2 intensity is
0.25m via a 1.25 NA objective
• The peak intensity at the center will be 10-3W
[.(0.25 x 10-4 cm)2]= 5.1 x 105 W/cm2 or 1.25 x
1024 photons/(cm2 sec-1)
• At this power, FITC would have 63% of its
molecules in an excited state and 37% in ground
state at any one time
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 17 t:/classes/BMS524/524lect3.ppt
Raman Scatter
• A molecule may undergo a vibrational transition (not
an electronic shift) at exactly the same time as
scattering occurs
• This results in a photon emission of a photon
differing in energy from the energy of the incident
photon by the amount of the above energy - this is
Raman scattering.
• The dominant effect in flow cytometry is the stretch
of the O-H bonds of water. At 488 nm excitation
this would give emission at 575-595 nm
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 18 t:/classes/BMS524/524lect3.ppt
Rayleigh Scatter
• Molecules and very small
particles do not absorb, but scatter
light in the visible region (same
freq as excitation)
• Rayleigh scattering is directly
proportional to the electric dipole
and inversely proportional to the
4th power of the wavelength of
the incident light
the sky looks blue because the gas molecules scatter more
light at shorter (blue) rather than longer wavelengths (red)
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 19 t:/classes/BMS524/524lect3.ppt
Photobleaching
• Defined as the irreversible destruction of an excited
fluorophore (discussed in later lecture)
• Methods for countering photobleaching
–
–
–
–
–
Scan for shorter times
Use high magnification, high NA objective
Use wide emission filters
Reduce excitation intensity
Use “antifade” reagents (not compatible with viable cells)
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 20 t:/classes/BMS524/524lect3.ppt
Photobleaching example
• FITC - at 4.4 x 1023 photons cm-2 sec-1
FITC bleaches with a quantum efficiency
Qb of 3 x 10-5
• Therefore FITC would be bleaching with a
rate constant of 4.2 x 103 sec-1 so 37% of the
molecules would remain after 240 sec of
irradiation.
• In a single plane, 16 scans would cause 650% bleaching
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 21 t:/classes/BMS524/524lect3.ppt
Antifade Agents
• Many quenchers act by reducing oxygen concentration
to prevent formation of singlet oxygen
• Satisfactory for fixed samples but not live cells!
• Antioxidents such as propyl gallate, hydroquinone, pphenylenediamine are used
• Reduce O2 concentration or use singlet oxygen
quenchers such as carotenoids (50 mM crocetin or
etretinate in cell cultures); ascorbate, imidazole,
histidine, cysteamine, reduced glutathione, uric acid,
trolox (vitamin E analogue)
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 22 t:/classes/BMS524/524lect3.ppt
Excitation - Emission Peaks
Fluorophore
FITC
Bodipy
Tetra-M-Rho
L-Rhodamine
Texas Red
CY5
EXpeak
496
503
554
572
592
649
% Max Excitation at
488
568 647 nm
EM peak
518
511
576
590
610
666
87
58
10
5
3
1
0
1
61
92
45
11
0
1
0
0
1
98
Note: You will not be able to see CY5 fluorescence
under the regular fluorescent microscope because
the wavelength is too high.
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 23 t:/classes/BMS524/524lect3.ppt
Fluorescent Microscope
Arc Lamp
EPI-Illumination
Excitation Diaphragm
Excitation Filter
Ocular
Dichroic Filter
Objective
Emission Filter
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 24 t:/classes/BMS524/524lect3.ppt
Fluorescence Microscope with
Color Video (CCD)
© J.Paul Robinson - Purdue University Cytometry Laboratories
35 mm Camera
Slide 25 t:/classes/BMS524/524lect3.ppt
Cameras and emission filters
Cooled
color CCD
camera
Camera
goes here
Color CCD camera does not need optical filters to collect all wavelengths but if
you want to collect each emission wavelength optimally, you need a
monochrome camera with separate emission filters shown on the right (camera
is not in position in this photo).
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 26 t:/classes/BMS524/524lect3.ppt
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 27 t:/classes/BMS524/524lect3.ppt
Probes for Proteins
Probe
FITC
PE
APC
PerCP™
Cascade Blue
Coumerin-phalloidin
Texas Red™
Tetramethylrhodamine-amines
CY3 (indotrimethinecyanines)
CY5 (indopentamethinecyanines)
© J.Paul Robinson - Purdue University Cytometry Laboratories
Excitation
488
488
630
488
360
350
610
550
540
640
Emission
525
575
650
680
450
450
630
575
575
670
Slide 28 t:/classes/BMS524/524lect3.ppt
Probes for Nucleic Acids
•
•
•
•
•
•
•
•
•
•
•
Hoechst 33342 (AT rich) (uv)
DAPI (uv)
POPO-1
YOYO-1
Acridine Orange (RNA)
Acridine Orange (DNA)
Thiazole Orange (vis)
TOTO-1
Ethidium Bromide
PI (uv/vis)
7-Aminoactinomycin D (7AAD)
© J.Paul Robinson - Purdue University Cytometry Laboratories
346
359
434
491
460
502
509
514
526
536
555
460
461
456
509
650
536
525
533
604
620
655
Slide 29 t:/classes/BMS524/524lect3.ppt
DNA Probes
• AO
– Metachromatic dye
• concentration dependent emission
• double stranded NA - Green
• single stranded NA - Red
• AT/GC binding dyes
– AT rich: DAPI, Hoechst, quinacrine
– GC rich: antibiotics bleomycin, chromamycin A3,
mithramycin, olivomycin, rhodamine 800
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 30 t:/classes/BMS524/524lect3.ppt
Probes for Ions
•
•
•
•
INDO-1
QUIN-2
Fluo-3
Fura -2
Ex350
Ex350
Ex488
Ex330/360
© J.Paul Robinson - Purdue University Cytometry Laboratories
Em405/480
Em490
Em525
Em510
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pH Sensitive Indicators
Probe
Excitation
Emission
• SNARF-1
488
575
• BCECF
488
440/488
525/620
525
[2’,7’-bis-(carboxyethyl)-5,6-carboxyfluorescein]
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 32 t:/classes/BMS524/524lect3.ppt
Probes for Oxidation States
Probe
Oxidant
• DCFH-DA
• HE
• DHR 123
(H2O2)
(O2-)
(H2O2)
DCFH-DA
HE
DHR-123
Excitation
Emission
488
488
488
525
590
525
- dichlorofluorescin diacetate
- hydroethidine
- dihydrorhodamine 123
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 33 t:/classes/BMS524/524lect3.ppt
Specific Organelle Probes
Probe
BODIPY
NBD
DPH
TMA-DPH
Rhodamine 123
DiO
diI-Cn-(5)
diO-Cn-(3)
Site
Golgi
Golgi
Lipid
Lipid
Excitation
505
488
350
350
Mitochondria 488
Lipid
488
Lipid
550
Lipid
488
Emission
511
525
420
420
525
500
565
500
BODIPY - borate-dipyrromethene complexes
NBD - nitrobenzoxadiazole
DPH - diphenylhexatriene
TMA - trimethylammonium
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 34 t:/classes/BMS524/524lect3.ppt
Other Probes of Interest
• GFP - Green Fluorescent Protein
– GFP is from the chemiluminescent jellyfish Aequorea
victoria
– excitation maxima at 395 and 470 nm (quantum efficiency
is 0.8) Peak emission at 509 nm
– contains a p-hydroxybenzylidene-imidazolone
chromophore generated by oxidation of the Ser-Tyr-Gly at
positions 65-67 of the primary sequence
– Major application is as a reporter gene for assay of
promoter activity
– requires no added substrates
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 35 t:/classes/BMS524/524lect3.ppt
Multiple Emissions
• Many possibilities for using multiple
probes with a single excitation
• Multiple excitation lines are possible
• Combination of multiple excitation
lines or probes that have same
excitation and quite different
emissions
– e.g. Calcein AM and Ethidium (ex 488)
– emissions 530 nm and 617 nm
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 36 t:/classes/BMS524/524lect3.ppt
Energy Transfer
• Effective between 10-100 Å only
• Emission and excitation spectrum
must significantly overlap
• Donor transfers non-radiatively to the
acceptor
• PE-Texas Red™
• Carboxyfluorescein-Sulforhodamine B
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 37 t:/classes/BMS524/524lect3.ppt
Fluorescence
Resonance Energy Transfer
Molecule 1
Molecule 2
Fluorescence
Fluorescence
ACCEPTOR
DONOR
Absorbance
Absorbance
Wavelength
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 38 t:/classes/BMS524/524lect3.ppt
Conclusions
• Fluorescence is the primary energy source for confocal
microscopes
• Dye molecules must be close to, but below saturation levels for
optimum emission
• Fluorescence emission is longer than the exciting wavelength
• The energy of the light increases with reduction of wavelength
• Fluorescence probes must be appropriate for the excitation source
and the sample of interest
• Correct optical filters must be used for multiple color
fluorescence emission
© J.Paul Robinson - Purdue University Cytometry Laboratories
Slide 39 t:/classes/BMS524/524lect3.ppt
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