2013 Biochip Technologies 1 Materials in the Life Sciences

8/10/2019 2013 Biochip Technologies 1 Materials in the Life Sciences

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IMTEK

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Content

Materials

and

surface

modifications

(26.04.13)

Manufacturing

of

Biochips

(14.06.13)

Biochiptechnologies Betweenresearchandroutinediagnostics(stateoftheart, 21.06.13)

Nucleicacidbasedtechniques(28.06.13)

Biochips

for

protein

analytics

(05.06.13)

Otherapplications(12.07.13)

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ummary

. .


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Ourprofile

esearc an eac ng

22 faculties

highly interdisciplinary world of

microsystem technology

IMTEK and industry

MSTBw

Core competences of CPI

Preparation of surfaces with tailor-made

Topological and chemical microstructuring of surfaces

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AFM Biochip-technologies


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Biochiptechnologieshttp://portal.uni-freiburg.de/cpi/biochip-group-dr-brandstetter

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Biochips what are they?(1)

devicesthat can contain anywhere from tens to tens of millions of individual

sensor elements or biosensors

The sensors are acked to ether into a acka e t icall the size of a

microscope slide. Because so many sensors can be put into such a small

area, a huge number of distinct tests can be done very rapidly.

Biochips are often made using the same microfabrication technology used

. , ,

electronic (although they can be).

The key premise behind biochips is, that they can do chemistry on a small

scale. Each biosensor can be thought of as a "microreactor, which does

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chemistry designed tosense a specific analyte.


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Biosensors can be made tosense a wide variety of analytes, including DNA,

rotein antibodies and small biolo ical molecules.

Fluorescence is often used to indicate a sensin event. Automated

microscopy systems can be used to "read" the chip, i.e. determine which

sensors are fluorescing

Most biochips are 2D arrays of sensors placed carefully in a grid

. .

,

microdeposition techniquesare used. The sensors are essentially placed one

at a time, or serially, on the chip.

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HPV_3D_Katrin_N_30s_Cy5

substrat

dot

3

13 microarray

http://en.wikipedia.org/wiki/Biochip#History

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Manufacturingof biochips ingeneral(1)

1. Untreated slide

mixed analyte solution

2. Microarray printing

. mmo sa on

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Manufacturingof biochips ingeneral(2)

step1:print polymer mixed with DNA

step 3:

hybridisation

and

photocrosslinking

via UV-irradiation

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Materials and surface modifications

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Biochip materials (1)

Microscope slide of glass Commercial microscope glass slides

Silica (SiO2) + vitreous silica

- -

Limestone (CaCO3) + borosilicate glass-pyrex

Magnesium Carbonate (MgCO3) + aluminosilicate glass

+ borosilicate glass

Detailled information

Frontiers in biochip technology

by Wan-Li Xing, Jing Cheng

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Published by Birkhuser, 2006ISBN 0387255680, 9780387255682

357 pages


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Biochip materials (2)

Microscope slide of plastic Commercial plastic slides

PMMA (polymethymethacrylate) + PMMA

COC (cyclic olefin copolymer) + TOPAS

Polycarbonate + Polycarbonate

Polypropyrene + Polypropyrene

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Lab Chip, 2007, 7, 856 - 862, DOI: 10.1039/b700322f


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Biochip coatings

directly chemically modified surfaces

n s u syn es s on g ass + ac va e g ass y po y-car o m e,

aminosilane, aldehyde

an za e pro es on unmo e g ass + gra coa ng po ymers on s con g ass

Photocrosslinking on unmodified plastic + plastic-based DNA microarrays using

car o m e c em s ry

+ amine-modified PMMA substrates

+ activated polystyrene, polypropyrene,

polycarbonate (PC) S.A. Fodor, R. Rava, X.C. Huang, A.C. Pease, C.P. Holmes and C.L. Adams. Science 251 (1991) 767773. M.J. Moorcroft, W.R. Meuleman, S.G. Latham, T.J. Nicholls, R.D. Egeland and E.M. Southern. NAR, 2005, Vol. 33, e75.

N. Kimura, R. Oda, Y. Inaki and O. Suzuki. Nucleic Acids Research, 2004, Vol. 32, e68.

H.-Y. Wang,R.L. Malek,A.E. Kwitek,A.S. Greene,T.V. Luu,B. Behbahani,B. Frank,J. Quackenbush, N.H. Lee, Genome Biol. 4 (2003), R5.

M. Dufva, S. Petronis, L.B. Jensen, C. Krag and C.B. Christensen. Biotechniques 37 (2004) 286292, 294, 296.

A. Kumar O. Larsson D. Parodi Z. Lian Nucleic Acids Research 2000 Vol. 28 e98.

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M. Schena, D. Shalon, R.W. Davis, P.O. Brown, Science 270 (1995), 467470.

De Paul S. M., Falconnet D., Pasche S., Textor M., Abel A. P., Kauffmann E., Liedtke R. and Ehrat M.. Anal. Chem. 2005, 77, 5831-5838.

Johnson P. A., Gaspar M. A. and Levicky R. J. Am. Chem. Soc.,2004, 126, 9910-9911.

N. Kimura, T. Nagasaka, J. Murakami, H. Sasamoto, M. Murakami, N. Tanaka and N. Matsubara. Nucleic Acids Research, 2005, Vol. 33, e46.


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2DchipsusingSAMs(selfassembledmonolayers)

typical DNA-chip design:

sequence of the probe

polyT(thymine) tailer

adapted from: E. Southern, K. Mir, M. Shchepinov, Nature Gen., 27 (1999) 5

+ reproducibility (why is acceptance of microarrays below expectations in non-research areas?

Weakness:

+ sensitivity

+ surface properties

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Askyscraperapproach

attachment ofo gonuc eot e pro es

3D

polymer brushes

polymer layer approach allows to

improve the sensitivity

adjust properties of the surface

(hydrophilicity, reactivity)

3D

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polymer networks


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Functional polymermonolayers

chemisor tion of ol mers growth of polymerson surfaces

blockco ol mers

grafting of polymers on

plasma modified

surfaces

via macroinitators

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photochemical attachmentof polymers surface-attachedpolymer networks grafting in between


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Photochemistry of benzophenone

triplet formation upon n,* excitation

biradical reacts with C,H bonds

C O C O C

CCH

350 nmO

H265 nm

hydrogen

abstraction

= 100 s

CC

OHrecombination

Toomey R., Freidank D. and

Rhe J.. Swelling Behavior of

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n, ur ace- ac e

Polymer Networks.Macromolecules, Vol. 37, 2004,

882-887.


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Polymernetworks attached to polymeric substrates

photocrosslinkableovercoat

Me

O OONMesimultaneous crosslinking

Me

polymeric substrate

(e.g. polyurethane)

via pendant benzophenone

units

swelling in

ca. 20 m

~ 1 mm

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Microstructuringinbiochiptechnologies,twoprocedures

I. Contact printing

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http://www.anopoli.com/http://www.anopoli.com/


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Microstructuringinbiochiptechnologies,contactprinting

Omnigrid from GeneMachine

Contact printing procedure

65% humidity, RT

Steel or tungsten needle with reservoir

droplet volume 400 600 pl

droplet diameter 140 200 m

Process variance > 10%

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Pin heads make the difference.

Split pinSpot diameters : 75m to 215 m

Uptake volumes : 0.25l to 0.64 l

li.c

om/

http://www.a

nopo

Solid pin

Spot diameters : 75m to 450 m

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Printing with different, not aqueous, solutions is possible.

PDMAA(Polydimethylmetacrylate) PS (Polystyrene)

200 m

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printing medium: ethanol printing medium: toluene


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Spot diameter is not really controllable.

Split pin

Solid pin

Printing of 0.25 m Cy5-labelled oligo-DNA in 400

mM Napi and 1mg/ml PDMAA-co-5%MABP-co-

2,5%VPA

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sca e n ng

PDMAA layer

PMMA 5 m /ml linin

Printing medium toluene

exposure after

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1. copolymers 2. buffer 3. PT-6000 tungsten

PDMAA-co-5%MABP-co-2 5%VPA a 400 mM Na i

plastic/PMMA glass/Epoxy

(b) 200 mM Napi/3xSSC/0.75 M betaine

2D

. . ..

2D_16_04_07_P2Dsp.2a 2D_16_04_07_N2Dsp.4b

a. a. b.

2D_04_04_07_N2Ds.4a2D_04_04_07_P2Ds.1a

b.

3D3D

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3D_12_04_07_P3Dsp.11a 3D_12_04_07_N3Dsp.2a 3D_03_04_07_N3Ds.4a3D_03_04_07_P3Ds.11


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1. copolymers 2. buffer 3. PT-6000 tungsten

PDMAA-co-5%MABP-co-2,5%VPA (a) 400 mM Napi

plastic/PMMA glass/Epoxy

(b) 200 mM Napi/3xSSC/0,75 M betaine

2D

. . ..

2D_16_04_07_P2Dsp.2a

a. a. b.

2D_xx_04_07_N2Ds.x2D_xx_04_07_P2Ds.x

b.

2D_16_04_07_N2Dsp.4b

3D3D

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3D_12_04_07_P3Dsp.11a 3D_12_04_07_N3Dsp.2a 3D_xx_04_07_N3Ds.x3D_xx_04_07_P3Ds.x


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Microstructuringinbiochiptechnologies,contactlessprinting

II. Contactless printing/Piezo Electric Dispenser

http://www.scienion.de

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II. Piezo Electric dispenser

Piezo Electric dispenser(Scienion AG)

Contactless printing procedure

um y,

droplet volume 410 pl,

droplet volume and diameter is

adjustable

Process variance < 10%

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Microstr ct ring in biochip technologies contactless printing


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Photos after print

2D 3D

3D2D = printing with PBS without polymer

3D = printing with PBS 1 mg/ml PDMAA-co-

5%MABP-co-2,5%VPA

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i i i bi hi h l i l i i


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rop e s ac ng

1mg/ml polymer in distilled water

=

PMMA = Polymethylmetacrylate

Small droplet with 10x

Large droplets with 20x

Photo after print

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PSS PMMA

Mi t t i i bi hi t h l i t tl i ti


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onu -s ruc ur ng

1mg/ml PDMAA-co-

5%MABP-co-2,5%VPA inPBS

Exposure after wash with

PBS and 0.1% (v/v) Tween)

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Dot morphology how to analyze?


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Dotmorphology,howtoanalyze?

Dot morphology, depending on

surface properties

print solution contact angle

analyte concentration

,

AFM

Raster electron microscope

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Microstructuring in biochip technologies contactless printing


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r n ng w a ves, avo ng

donut-morphology

1mg/ml PDMAA-co-5%MABP-co-2,5%VPA in PBS

Additive Glycerol

0 2.5 5 10 25%(v/v)

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Microstructuring in biochip technologies contactless printing


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r n ng w w ou re a ose

1mg/ml PDMAA-co-5%MABP

-co-2,5%VPA in PBS

-T+T

125 mg/ml Trehalose (T) in PBS

Donut-structure without

Homogeneity in the dot

morphology, using Trehalose

-T

- - - -

http://en.wikipedia.org/wiki/Trehalose

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glucopyranoside(,

Trehalose) Exposure with a fluorescence microscope


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MicrostructuringMicrostructuring ininbiochipbiochip technologiestechnologies


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MicronasMicronas BiochipBiochip technlogytechnlogy


Contactless printing procedure

80% humidity, RT

droplet volume 390 pl,

photodiode diameter 180 m

pr n ng on s ruc ure sur aces


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Microstructuringinbiochiptechnologies


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MicronasBiochiptechnlogy


printing directly on a photodiode

180 m

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Microstructuringinbiochiptechnologies


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MicronasBiochiptechnlogy


printing directly on a photodiode

pattern matching using a software

ed

notprin

d

printe

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MicrostructuringMicrostructuring inbiochiptechnologies,summaryinbiochiptechnologies,summary


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gg p g , yp g , y

Piezo Electric dispenser (Scienion AG)

Droplet volume control

Droplet diameter tunable (>100m)

r nt ng on y w t aqueous so ut ons

1mg/ml polymer


Omnigrid from GeneMachine

Contact rintin rocedure

Steel or tungsten needle with reservoir

droplet volume 400 600 pl

.

Printing of different solutions

> 1mg/ml polymer possible

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Process variance > 10%


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Thank you for your attention!

http://www.bilder-welten.net/de/produkt_detail.php?id=23019&catid=1623

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Literature


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E. Southern, K. Mir, M. Shchepinov, Nature Gen., 27 (1999) 5

Frontiers in biochip technology, by Wan-Li Xing, Jing Cheng, Edition: illustrated, published by

Birkhuser,2006, ISBN 0387255680, 9780387255682, 357 pages

Lab Chip,2007, 7, 856 - 862, DOI: 10.1039/b700322f

S.A. Fodor, R. Rava, X.C. Huang, A.C. Pease, C.P. Holmes and C.L. Adams. Science 251

(1991) 767773.

. . , . . , . . , . . , . . . . .

NAR,2005, Vol. 33, e75.

N. Kimura, R. Oda, Y. Inaki and O. Suzuki. Nucleic Acids Research,2004, Vol. 32, e68.

H.-Y. Wan R.L. Malek A.E. Kwitek A.S. Greene T.V. Luu B. Behbahani B. Frank J.

Quackenbush, N.H. Lee, Genome Biol. 4 (2003), R5.

M. Dufva, S. Petronis, L.B. Jensen, C. Krag and C.B. Christensen. Biotechniques 37 (2004)

286292, 294, 296.

A. Kumar, O. Larsson, D. Parodi, Z. Liang, Nucleic Acids Research,2000, Vol. 28, e98.

M. Schena, D. Shalon, R.W. Davis, P.O. Brown, Science 270 (1995), 467470.

De Paul S. M., Falconnet D., Pasche S., Textor M., Abel A. P., Kauffmann E., Liedtke R. and

.. . . , , - .

Johnson P. A., Gaspar M. A. and Levicky R. J. Am. Chem. Soc.,2004, 126, 9910-9911.

N. Kimura, T. Nagasaka, J. Murakami, H. Sasamoto, M. Murakami, N. Tanaka and N.

Matsubara. Nucleic Acids Research 2005 Vol. 33 e46.

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Toomey R., Freidank D. and Rhe J.. Swelling Behavior of Thin, Surface-Attached PolymerNetworks. Macromolecules, Vol. 37,2004, 882-887.

2013 Biochip Technologies 1 Materials in the Life Sciences

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