Microsystem Technology: A Powerful Tool for Biomolecular Studies

591 Pages·1999·42.92 MB·English

by  J. Michael Koehler

BioMethodsVol. 10
Series Editors
Dr. T. Meier
MyoContract
Biozentrum, Room 388
Universität Basel
Klingelbergstr. 70
CH-4056 Basel
Switzerland
Prof. Dr.H.P.Saluz
Hans-Knöll-Institut
für Naturstofforschung e.V.
Beutenbergstr. 11
D-07745 Jena
Germany
Microsystem Technolog:y
A Powerful Tool for Biomolecular Studies
Edited by
J.M. Köhler
T. Mejevaai
H.P. Saluz
Springer Basel AG
Editors
Dr. J.M. Köhler T. Mejevaia
Institut für Physikal. Rosenstr. 7
Hochtechnologie Jena D-07749 Jena
Hemholtzweg 4 Germany
D-07743 Jena
Germany
Prof. Dr. H.P. Saluz
Hans-Knöll-Institut
für Naturstofforschung e.V.
Beuten bergstr. 11
D-07745 Jena
Germany
Library of Congress Cataloging-in-Publication Data
Microsystem technology: a powerful tool for biomolecular studies /
edited by J.M. Köhler, T. Mejevaia, H.P. Saluz.
p. cm. - (Biomethods)
Includes bibliographical references and index.
ISBN 978-3-0348-9784-6 ISBN 978-3-0348-8817-2 (eBook)
DOI 10.1007/978-3-0348-8817-2
1. Nanotechnology. 2. Biotechnology. 3. Combinatorial chemistry.
4. Molecular biology-Automation. I. Köhler, M. (Michael),
1956-. II. Mejevaia, T. III. Saluz, H. P., 1952-. IV. Series.
TP248.25.N35M53 1999
572- dc21
98-47629
CIP
Die Deutsche Bibliothek - CIP-Einheitsaufnahme
Microsystem technology : a powerful tool for biomolecular studies /
ed by J. M. Köhler ... - Springer Basel AG, 1999
(BioMethods; Vol. 10)
ISBN 978-3-0348-9784-6
The publisher and editor can give no guarantee for the information on drug dosage and administration contained in this
publication. The respective user must check its accuracy by consulting other sources of reference in each individual case.
The use of registered names, trademarks etc. in this publication, even if not identified as such, does not imply that they
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This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifi
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© 1999 Springer Basel AG
Originally published by Birkhäuser Verlag in 1999
Softcover reprint of the hardcover 1st edition 1999
Printed on acid-free paper produced from chlorine-free pulp. TCF oo
Cover design: Markus Etterich, Basel
ISBN 978-3-0348-9784-6
98765432 1
Contents
List of contributors ............................. IX
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . XIII
Colour Plates XV
1 Molecular building principles in nature
J. Michael Koehler and Hans Peter Saluz 1
2 Robotic equipment and microsystem technology
in biological research
Holger Eickhoff, Igor Ivanov, Markus Kietzmann, Elmar Maier,
Markus Kalkum, David Bancroft and Hans Lehrach . . . . . . 17
3 Components and systems for micro liquid handling
Steffen Howitz . . . . . . . . . . . . . . . . . 31
4 Nanotiterplates for screening and synthesis
GUnther Mayer, Klaus Wohlfart, Andreas Schober
and J. Michael Kohler ............. . 75
5 Chip technology for micro-separation
Andrew J. de Mello and Andreas Manz . 129
6 Rapid multisample PCR in miniaturized ultrathin-walled
microwell plates
Alexander N Tretyakov, Rimma A. Pantina, Oleg K. Kaboev
and Hans Peter Saluz ... . . . . . . . . . . . . . . . . . . 179
v
Contents
7 Generation of large libraries
Carola BurgtorJ and Hans Lehrach 189
8 Generation and screening of solution-phase synthetic peptide
combinatorial libraries
Andrew Wallace, Kenneth S. Koblan, Riccardo Cortese,
Jackson B. Gibbs and Antonello Pessi ........ . 225
9 Using oligonucleotide probe arrays to access genetic diversity
R. J Lipshutz, D. Morris, M. Chee, E. Hubbell, M. J Kozal, N Shah,
N Shen, R. Yang and S. P A. Fodor ...... . 241
10 Generation of libraries by print technologies
Eugen Ermantraut, Stefan Waljl and Hans Peter Saluz 255
11 Synthesis and screening of bead-based libraries
Dirk Vt:tter . . . . . . . . . . . . . 265
12 Sensors for biomolecular studies
Jan Rickert, Thomas Wessa and Wolfgang Gapel 279
13 Fluorescence detection of single molecules applicable
to small volume assays
Jarg Enderlein, W. Patrick Ambrose, Peter M. Goodwin
and Richard A. Keller . . . . . . . . . . . . . . . 311
14 Fluorescence correlation spectrometry (FCS):
Measuring biological interactions in microstructures
Gabriele Gradl, Rolf Guenther and Silvia Sterrer ... 331
15 Scanning force microscopy: A micro structured device for imaging,
probing, and manipulation of biomolecules at the nanometer scale
Wolfgang Fritzsche ........................ 353
16 DNA resequencing, mutation detection and gene expression
analysis of oligonucleotide microchips
Andres Metspalu and John M. Shumaker . . . . . . . . . . . . . 371
VI
Contents
17 Miniaturized arrays for DNA analysis
Maryanne J 0 'Donnell and Hubert Koster 399
18 Manipulation of particles, cells and liquid droplets
by high frequency electric fields
Thomas Schnelle, Torsten Muller and Gunter Fuhr 417
19 Optical trapping and manipulation
Karl Otto Greulich . . . . . . . .. 453
20 Computer modeling of protein, nucleic acid, and drug structures
Jurgen Suhnel . . . . . . . . . . . . . . . . . . . 475
21 Optimizing structure and function relationship
of nucleic acid molecules
Michael Famulok, Andres Jiischke and Stefan Wolfl 507
22 Optimisation of molecular function
Christian V. Forst 529
23 Appendix
UdoLuhmann 555
Index ...... . 575
VII
List of contributors
Ambrose, w.P. Eickhoff, H.
CST-I, MS M888, Max-Planck-Institut fUr molekulare Genetik
Los Alamos National Laboratory, Ihnestr.73
Los Alamos, NM 87545, USA D-14195 Berlin-Dahlem, Germany
Bancroft, D. Famulok, M.
GPC Aktiengesellschaft Laboratorium fUr molekulare Biologie -
Genome Pharmaceuticals Corporation Genzentrum Miinchen
Lochhamer Str. 29 Feodor-Lynen-Str.25
D-82I52 Martinsried/Munich, Germany D-81375 Miinchen, Germany
Burgtorf, C. Fodor, S. P. A.
Max-Planck-Institut Affymetrix
fUr molekulare Genetik 3380 Central Expressway
Ihnestr.73 Santa Clara, CA 95951, USA
D-14I95 Berlin-Dahlem, Germany Forst, c.v.
Chee,M. Beckman Institute
Affymetrix University of Illinois
3380 Central Expressway 405 North Mathews Avenue
Santa Clara, CA 95051, USA Urbana, IL 61801, USA
Cortese, R. Fritzsche, W.
Istituto di Ricerche di Biologia Moleculare Microsystems Department
(IRBM) P. Angeletti, Institute of Physical High Technology
Via Pontina KM 30.600, Helmholtzweg 4
J-00040 Pomezia (Roma), Italy D-07743 lena, Germany
Enderlein, J. Fuhr, G.
Institut fUr Analytische Chemie Humboldt-Universitiit zu Berlin,
Chemo-und Biosensorik Institut fiir Biologie,
UniversiUit Regensburg Membranphysiologie,
Postfach 10 1042 Invalidenstr. 43
D-93040 Regensburg, Germany D-10115 Berlin, Germany
Ermantraut, E. Gibbs,J.B.
CLONDIAG CHIP TECHNOLOGIES GmbH Department of Cancer Research,
CCT, Lobstedter Str. 105 Merck Research Laboratories
D-07743 Jena, Germany West Point, PA 19486, USA
IX
List of contributors
Goodwin, P.M. Jaschke, A.
CST-I, MS M888, Institut flir Biochemie, Freie Universitat Berlin
Los Alamos National Laboratory, Thielallee 63
Los Alamos, NM 87545, USA D-14195 Berlin, Germany
Gopel, W. Kaboev, O.
Institute of Physical and Theoretical Chemistry St. Petersburg Nuclear Physics Institute,
and Center of Interface Analysis and Sensors Molecular and Radiation Biophysics Division,
University of Tiibingen 188350, Gatchina, Russia
D-72076 Tiibingen, Germany Kalkum,M.
Max-Planck-Institut flir molekulare Genetik
Gradl,G.
Ihnestr.73
EVOTEC BioSystems GmbH,
D-14195 Berlin-Dahlem, Germany
Humboldt-Universitat zu Berlin
Institut flir Biologie Keller, R. A.
Membranphysiologie CST-I, MS M888,
Invalidenstr. 42 Los Alamos National Laboratory,
D-I0115 Berlin, Germany Los Alamos, NM 87545, USA
Kietzmann, M.
Greulich, K.O.
GPC Aktiengesellschaft
Institut flir Molekulare Biotechnologie e.Y.
Genome Pharmaceuticals Corporation
Postfach 100813
Lochhamer Str. 29
D-07708 Jena, Germany
D-82152 Martinsried/Munich, Germany
Guenther, R.
Koblan, K.S.
EVOTEC BioSystems GmbH,
Department of Cancer Research,
Schnackenburgallee 114
Merck Research Laboratories,
D-22525 Hamburg, Germany
West Point, Pennsylvania 19486, USA
Howitz, S. Kohler, J. M.
GeSiM Gesellschaft flir Silizium Institute of Physical High Technology
Mikrosysteme mbH Helmholtzweg 4
Rossendorfer Technologiezentrum D-07743 Jena, Germany
Bautzner Landstr. 45
Koster, H.
D-01454 GroBerkmannsdorf/Rossendorf,
Sequenom Inc.
Germany
11555 Sorrento Valley Road
Hubbell, E. San Diego, CA 92121, USA
Affymetrix Kozal, M.l
3380 Central Expressway
Affymetrix
Santa Clara, CA 95051, USA
3380 Central Expressway
Santa Clara, CA 95051, USA
Ivanov, I.
GPC Aktiengesellschaft Lehrach, H.
Genome Pharmaceuticals Corporation Max-Planck-Institut flir molekulare Genetik
Lochhamer Str. 29 Ihnestr.73
D-82152 Martinsried/Munich, Germany D-14195 Berlin-Dahlem, Germany
x
List of contributors
Lipshutz, R.J. Morris, D.
Affymetrix Affymetrix
3380 Central Expressway 3380 Central Expressway
Santa Clara, CA 95051, USA Santa Clara, CA 95051, USA
MUller, T.
Luhmann, U.
Humboldt-Universitiit zu Berlin,
Hans Knoll Institut flir Naturstoff-Forschung,
Institut flir Biologie, Membranphysiologie,
Beutenbergstr. 11
Invalidenstr. 43,
D-07746 Jena, Germany
D-I0115 Berlin, Germany
Manz,A. O'Donnell, M.J.
Zeneca/SmithKline Beecham Centre Sequenom Inc.
for Analytical Sciences, 11555 Sorrento Valley Road
Imperial College of Science, Technology San Diego, CA 92121, USA
and Medicine, Pantina, R.
London, SW7 2AY, UK St. Petersburg Nuclear Physics Institute,
Molecular and Radiation Biophysics Division,
Maier,E.
188350, Gatchina, Russia
GPC Aktiengesellschaft
Genome Pharmaceuticals Corporation Pessi, A.
Lochhamer Str. 29 Instituto di Ricerche de Biologia Molecolare
(IRBM) P. Angeletti,
D-82152 Martinsried/Munich, Germany
Via Pontina KM 30.600
Mayer, G. 1-00040 Pomezia (Roma), Italy
Institut flir Physikalische Hoch
Rickert, J.
technologie (IPHT)
Institute of Physical and Theoretical Chemistry
Abt. Mikrosysteme
and Center of Interface Analysis and Sensors
Postfach 100239
University of TUbingen
D-07702 Jena, Germany
D-72076 TUbingen, Germany
de Mello, A.J. Saluz, H.P.
Zeneca/SmithKline Beecham Centre Cell and Molecular Biology,
for Analytical Sciences, Hans Knoll Institut flir Naturstoff-Forschung
Imperial College of Science, Technology Beutenbergstr. 11
and Medicine, D-07746 Jena, Germany
London, SW7 2AY, UK Schnelle, Th.
Humboldt-Universitiit zu Berlin
Metspalu, A.
Institut flir Biologie, Membranphysiologie,
Institute of Molecular and Cell Biology
Invalidenstr. 43,
and Children's Hospital
D-10115, Berlin, Germany
University of Tartu, Estonian Biocentre,
Schober, A.
23 Riia St.
Institut flir Physikalische Hoch
Tartu 51010, Estonia
technologie (IPHT)
Mejevaia, T. Abt. Mikrosysteme
Rosenstr.7 Postfach 100239
D-07749 Jena, Germany D-07702 Jena, Germany
XI