detection systems. 1introduction 2theoretical background biochemistry/molecular biology 3theoretical...
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Detection systems
1 Introduction
2 Theoretical background Biochemistry/molecular biology
3 Theoretical background computer science
4 History of the field
5 Splicing systems
6 P systems
7 Hairpins
8 Detection techniques
9 Micro technology introduction
10 Microchips and fluidics
11 Self assembly
12 Regulatory networks
13 Molecular motors
14 DNA nanowires
15 Protein computers
16 DNA computing - summery
17 Presentation of essay and discussion
Course outline
Scale
Scale: 100 μm
Optical microscopy
Watch out!A cover slide!
Life under a microscope
History of microscopy
History of microscopy
History of microscopy
1673
1720
18801665
History of microscopy
Today’s microscopy
Bright-field microscopy
Also called resolving power
Ability of a lens to separate or
distinguish small objects that are close
together
Light microscope has a resolution of 0.2
micrometer
wavelength of light used is major factor
in resolution shorter wavelength greater resolution
Microscope resolution
produces a dark image against a brighter
background
Cannot resolve structures smaller than
about 0.2 micrometer
Inexpensive and easy to use
Used to observe specimens and microbes
but does not resolve very small
specimens, such as viruses
Bright-field microscopy
has several objective lenses (3 to 4) Scanning objective lens 4X Low power objective lens 10X High power objective lens 40X Oil immersion objective lens 100X
total magnification product of the magnifications of the
ocular lens and the objective lens Most oculars magnify specimen by a
factor of 10
Bright-field microscopy
Microscope objectives
Microscope objectives
Working distance
Oil immersion objectives
Bright-field image of Amoeba proteus
Uses a special condenser with an opaque
disc that blocks light from entering
the objective lens
Light reflected by specimen enters the
objective lens
produces a bright image of the object
against a dark background
used to observe living, unstained
preparations
Darki-field microscopy
Dark-field image of Amoeba proteus
Microscope image
Fluorescence microscopy
Lamps Xenon Xenon/Mercury
Lasers Argon Ion (Ar) 353-361, 488, 514
nm Violet 405 405 nm Helium Neon (He-Ne) 543 nm, 633 nm Helium Cadmium (He-Cd) 325 - 441 nm Krypton-Argon (Kr-Ar) 488, 568, 647 nm
Excitation sources
Irradiance at 0.5 m (mW m-2 nm-1)
Xe Lamp
Hg Lamp
Arc lamp excitation spectra
Dichroic Filter
Objective
Arc Lamp
Emission Filter
Excitation Diaphragm
Ocular
Excitation Filter
EPI-Illumination
Fluorescent microscope
transmitted lightwhite light source
630 nm band pass filter
620 -640 nm light
Standard band pass filters
transmitted lightwhite light source
520 nm long pass filter
>520 nm light
Standard long pass filters
transmitted lightwhite light source
575 nm short pass filter
<575 nm light
Standard short pass filters
Chromophores are components of molecules
which absorb light
E.g. from protein most fluorescence results
from the indole ring of tryptophan residue
They are generally aromatic rings
Fluorescence
S0
S1
T0
transition involving emission/absorption of photon
radiationless transition
abso
rptio
n
+hν
fluor
esce
nce
-hν
inte
rnal
co
nver
sion
inte
rsys
tem
cr
ossi
ngin
tern
al
conv
ersi
on
Jablonski diagram
S0
S’1Energy
S1
hvex hvem
Simplified Jablonski diagram
Fluorescence
The longer the wavelength the lower the
energy
The shorter the wavelength the higher the
energy e.g. UV light from sun causes the
sunburn not the red visible light
Ethidium
PE
cis-Parinaric acid
Texas Red
PE-TR Conj.
PI
FITC
600 nm300 nm 500 nm 700 nm400 nm
457350 514 610 632488 Common Laser Lines
Some fluorophores
495 nm 520 nm
Stokes Shift is 25 nmFluoresceinmolecule
Fluorescence Intensity
Wavelength
Stokes shift
Change in the energy between the lowest energy peak of absorbance and the highest energy of emission
The rate of emission is dependent upon the time the
molecule remains within the excitation state (the excited
state lifetime τf)
Optical saturation occurs when the rate of excitation
exceeds the reciprocal of τf
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 (i.e. laser based confocal systems)
Material Source: Pawley: Handbook of Confocal Microscopy
Excitation saturation
Defined as the irreversible destruction of
an excited fluorophore
Methods for countering photo-bleaching 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)
Photo-bleaching
Not a chemical process
Dynamic quenching
Collisional process usually controlled by mutual
diffusion
Typical quenchers
oxygen
Aliphatic and aromatic amines (IK, NO2, CHCl3)
Static Quenching
Formation of ground state complex between the
fluorophores and quencher with a non-fluorescent
complex (temperature dependent – if you have
higher quencher ground state complex is less
likely and therefore less quenching
Quenching
Fluorophore EXpeak EMpeak
% Max Excitation at488 568 647 nm
Excitation and emission peaks
Material Source: Pawley: Handbook of Confocal Microscopy
FITC 496 518 87 0 0
Bodipy 503 511 58 1 1
Tetra-M-Rho 554 576 10 61 0
L-Rhodamine 572 590 5 92 0
Texas Red 592 610 3 45 1
CY5 649 666 1 11 98
FITC 488 525
PE 488 575
APC 630 650
PerCP™ 488 680
Cascade Blue 360 450
Coumerin-phalloidin 350 450
Texas Red™ 610 630
Tetramethylrhodamine-amines 550 575
CY3 (indotrimethinecyanines) 540 575
CY5 (indopentamethinecyanines) 640 670
Probe Excitation Emission
Probes for proteins
Hoechst 33342 (AT rich) (uv) 346 460
DAPI (uv) 359 461
POPO-1 434 456
YOYO-1 491 509
Acridine Orange (RNA) 460 650
Acridine Orange (DNA) 502 536
Thiazole Orange (vis) 509 525
TOTO-1 514 533
Ethidium Bromide 526 604
PI (uv/vis) 536 620
7-Aminoactinomycin D (7AAD) 555 655
Probes for nucleotides
GFP
GFP - Green Fluorescent 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
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 nm) emissions 530 nm and 617 nm
Multiple emissions
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
Non radiative energy transfer – a quantum
mechanical process of resonance between
transition dipoles
Energy transfer
FRETIntensity
Wavelength
Absorbance
DONOR
Absorbance
Fluorescence Fluorescence
ACCEPTOR
Molecule 1 Molecule 2
Fluorescence resonance energy tranfer
Confocal microscopy
confocal scanning laser microscope
laser beam used to illuminate spots on
specimen
computer compiles images created from
each point to generate a 3-dimensional
image
Confocal microscopy
Reduced blurring of the image from light scattering
Increased effective resolution
Improved signal to noise ratio
Clear examination of thick specimens
Z-axis scanning
Depth perception in Z-sectioned images
Magnification can be adjusted electronically
Benefits of confocal microscopy
Fluorescent Microscope
Objective
Arc Lamp
Emission Filter
Excitation Diaphragm
Ocular
Excitation Filter
Objective
Laser
Emission Pinhole
Excitation Pinhole
PMT
EmissionFilter
Excitation Filter
Confocal Microscope
The different microscopes
767, 1023, 1279
511, 1023
00Start
Specimen
Frames/Sec # Lines1 5122 2564 1288 6416 32
Scan path of the laser beam
Resolution
comparison
PK2 cells
stained for microtubules
stained for microtubules (green) and nuclei (blue)
Copapod appendage
Eye of Drosophila
http://www.confocal-microscopy.com/WebSite/SC_LLT.nsf?opendatabase&path=/Website/ImageGallery.nsf/(ALLIDs)/63BCB66085E1015BC1256A7E003B6DD3
Fibroblast
http://www.confocal-microscopy.com/WebSite/SC_LLT.nsf?opendatabase&path=/Website/ImageGallery.nsf/(ALLIDs)/63BCB66085E1015BC1256A7E003B6DD3
http://www.confocal-microscopy.com/WebSite/SC_LLT.nsf?opendatabase&path=/Website/ImageGallery.nsf/(ALLIDs)/63BCB66085E1015BC1256A7E003B6DD3
Spirogyra crassa
SEM and TEM
electrons scatter when they pass
through thin sections of a specimen
transmitted electrons (those that do
not scatter) are used to produce
image
denser regions in specimen, scatter
more electrons and appear darker
Electron microscope
Transmission electron microscope
Transmission electron microscope
Provides a view of the internal structure of a
cell
Only very thin section of a specimen (about
100nm) can be studied
Magnification is 10000-100000X
Has a resolution 1000X better than light
microscope
Resolution is about 0.5 nm
transmitted electrons (those that do not
scatter) are used to produce image
denser regions in specimen, scatter more
electrons and appear darker
Transmission electron microscope
Transmission electron microscope
Transmission electron microscope
TEM of a plant cell
TEM of outer shell of tumour spheroid
No sectioning is required
Magnification is 100-10000X
Resolving power is about 20nm
produces a 3-dimensional image of
specimen’s surface features
Uses electrons as the source of
illumination, instead of light
Scanning electron microscope
Scanning electron microscope
Scanning electron microscope
Scanning electron microscope
Contrast
Incident Electron Beam
Contrast formation
Ribosome
Ribosome with SEM
SEM of tumour spheroid
Scanning electron microscope
Fly head