Table Of ContentAdvances in Atom and Single Molecule Machines
Series Editor: Christian Joachim
Fabio Benfenati
Enzo Di Fabrizio
Vincent Torre Editors
Novel
Approaches for
Single Molecule
Activation and
Detection
Advances in Atom and Single Molecule
Machines
Series editor
Christian Joachim
Editorial Board
L. Grill
F. Jelezko
D. Martrou
T. Nakayama
G. Rapenne
F. Remacle
K. Ohmori
For furthervolumes:
http://www.springer.com/series/10425
Fabio Benfenati Enzo Di Fabrizio
•
Vincent Torre
Editors
Novel Approaches
for Single Molecule
Activation and Detection
123
Editors
FabioBenfenati Vincent Torre
Department of Neuroscienceand Neuroscience Area
Neurotechnology ScuolaInternazionale Superiore diStudi
Universityof Genoa, TheItalian Institute Trieste
ofTechnology Italy
Genoa
Italy
Enzo Di Fabrizio
Department of Nanostructures
The ItalianInstitute ofTechnology
Genoa
Italy
ISSN 2193-9691 ISSN 2193-9705 (electronic)
ISBN 978-3-662-43366-9 ISBN 978-3-662-43367-6 (eBook)
DOI 10.1007/978-3-662-43367-6
Springer Heidelberg NewYork Dordrecht London
LibraryofCongressControlNumber:2014943416
(cid:2)Springer-VerlagBerlinHeidelberg2014
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Preface
This book provides a selection of single molecule investigations, presented at the
International meeting held at Palazzo Franchetti in Venice on ‘‘Single Molecule
Activation and Detection in Molecular Devices’’ on October 13–14, 2012. This
meetinggatheredscientistsactiveindevelopingtoolsandmethodologiesforsingle
moleculeanalysisandwasorganizedwithintheFOCUSproject,sponsoredbythe
EU FP7 FET Proactive 7 Programme: ‘‘Molecular Scale Devices and Systems
[ICT-2009.8.7]’’ (grant agreement n, 270483).
The book captures selected contributions from members of the European
‘‘Focus’’consortiumaswellasfromotherdistinguishedscientistsoperatinginthe
fieldofsinglemoleculeanalysis.Thecontributionscollectedhereprovidenotonly
agoodviewoftheactivitiesoftheFOCUSproject,butalsoofferawidespectrum
ofnovelinvestigationsinanemergingandimportantfieldattheinterfacebetween
materialscienceandbiology.AndolfiandLazzarinohavemodifiedthemethodsof
SMFStodevelopSingleCellForceSpectroscopyforanalysingadhesionprocesses
incellsandneurons.Bauer,Kendziora,Ahmed,HungandFrukdescribetheuseof
DNA stretches used to tether the computing molecules in a protoptype of the
molecular device developed within the FOCUS project. Bianco, Bongini, Melli,
Falorsi,Salvi,CojocandLombardihaveintroducedtheforceclampmethodology
in the optical tweezers apparatus so to improve the detection and resolution of
chemicalreactions.DalMaschiodescribesthedevelopmentofholographicbeams
oflight abletoreveal andanalyse molecularproperties atavery finescale andto
characterize also circuit properties. Diaspro, Bianchini, Cella Zanacchi and Vici-
dominidescribehowitispossibletodetectsinglemoleculeusingconventionalfar
field illumination by using stochastic reading methods. Endeman, Feyen, Ghezzi,
Antognazza, Martino, Colombo, Lanzani and Benfenati show how, by using light
sensitive organic semiconductors, it is possible to modulate and control the firing
of neurons and neuronal networks. Izquierdo-Serra and Gorostiza describe the
recentprogressinoptogeneticsinwhichendogenousionchannelscanberendered
light sensitive by the introduction of a light switchable gate. Petrini and Barberis
haveattachedquantumdotstosynapticreceptorsandinthiswaytheycanmonitor
and follow the lateral diffusion of these membrane proteins in their physiological
environment.Limongi,Ferrara,Das,Moretti,Marini,Miele,Accardo,Raimondo,
v
vi Preface
Gentile and Di Fabrizio make use of superhydrophobicity to develop a variety of
novel devices with which they can detect single or very few molecules. Finally,
Naumenko, Cassese, Lazzarino and Bek illustrate how it is possible to detect and
activate single molecules by using the special properties of tips with nanometer
dimensions.
The Venice workshop was very stimulating and inspiring for all the partici-
pants, and we hope that this book will be of interest and inspire its readers.
Acknowledgement
This book would not have been possible without the invaluable help and dedi-
cationofDr.TaniaLimongi,whogaveafundamentalcontributionincoordinating
and assembling the above-listed contributions.
Fabio Benfenati
Enzo Di Fabrizio
Vincent Torre
Contents
Introduction to Single-Molecule Analysis and Computation:
The Focus Project. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Monica Mazzolini and Vincent Torre
Computer-Generated Holographic Beams for the Investigation
of the Molecular and Circuit Function. . . . . . . . . . . . . . . . . . . . . . . . 7
Marco Dal Maschio
Super-Resolution Fluorescence Optical Microscopy:
Targeted and Stochastic Read-Out Approaches . . . . . . . . . . . . . . . . . 27
Alberto Diaspro, Francesca Cella Zanacchi, Paolo Bianchini
and Giuseppe Vicidomini
Superhydrophobic Devices Molecular Detection. . . . . . . . . . . . . . . . . 45
Tania Limongi, Lorenzo Ferrara, Gobind Das, Manola Moretti,
Monica Marini, Ermanno Miele, Angelo Accardo,
Raffaella Raimondo, Francesco Gentile and Enzo Di Fabrizio
Tip-Assisted Optical Nanoscopy for Single-Molecule
Activation and Detection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Denys Naumenko, Damiano Cassese, Marco Lazzarino
and Alpan Bek
DNA as Nanostructuring Element for Design
of Functional Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Dennis M. Bauer, Dania M. Kendziora, Ishtiaq Ahmed,
Yu-Chueh Hung and Ljiljana Fruk
Fast Force Clamp in Optical Tweezers: A Tool to Study
the Kinetics of Molecular Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . 123
Pasquale Bianco, Lorenzo Bongini, Luca Melli, Giulia Falorsi,
Luca Salvi, Dan Cojoc and Vincenzo Lombardi
vii
viii Contents
Investigating Adhesion Proteins by Single Cell
Force Spectroscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Laura Andolfi and Marco Lazzarino
Photoswitchable Ion Channels and Receptors. . . . . . . . . . . . . . . . . . . 169
Antoni Bautista-Barrufet, Mercè Izquierdo-Serra
and Pau Gorostiza
The Use of Light-Sensitive Organic Semiconductors
to Manipulate Neuronal Activity . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
Duco Endeman, Paul Feyen, Diego Ghezzi, Maria Rosa Antognazza,
Nicola Martino, Elisabetta Colombo, Guglielmo Lanzani
and Fabio Benfenati
Probing the Lateral Diffusion of Individual
Neurotransmitter Receptors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Enrica Maria Petrini and Andrea Barberis
Contributors
Angelo Accardo Nanostructures, Istituto Italiano di Tecnologia, Genoa, Italy
Ishtiaq Ahmed Center for Functional Nanostructures, Karlsruhe Institute of
Technology, Karlsruhe, Germany
Laura Andolfi CBM S.c.r.l. Basovizza, Trieste, Italy; CNR-IOM Basovizza,
Trieste, Italy
Maria Rosa Antognazza Center for Nanoscience and Technology @PoliMi,
Istituto Italiano di Tecnologia, Milan, Italy
Andrea Barberis Department of Neuroscience and Brain Technologies, Italian
Institute of Technology (IIT), Genoa, Italy
Dennis M. Bauer Center for Functional Nanostructures, Karlsruhe Institute of
Technology, Karlsruhe, Germany
Antoni Bautista-Barrufet Institut de Bioenginyeria de Catalunya (IBEC),
Barcelona,Spain;InstitutCatalàd’InvestigacióQuímica(ICIQ),Tarragona,Spain
Alpan Bek Middle East Technical University, Cankaya Ankara, Turkey
Fabio Benfenati Department of Neuroscience and Brain Technologies, Istituto
Italiano di Tecnologia, Genoa, Italy; Department of Experimental Medicine,
University of Genova, Genoa, Italy
Paolo Bianchini NanoBioPhotonics—LAMBS, Nanophysics, Istituto Italiano di
Tecnologia, Genoa, Italy
Pasquale Bianco Laboratory of Physiology, Department of Biology, University
of Florence, Florence, Italy
Lorenzo Bongini Laboratory of Physiology, Department of Biology, University
of Florence, Florence, Italy
DamianoCassese IOM-CNR-LaboratorioTASC,AreaSciencePark—Basovizza,
Trieste,Italy
Dan Cojoc IOM—National Research Council, Trieste, Italy
ix
x Contributors
Elisabetta Colombo Department of Neuroscience and Brain Technologies,
Istituto Italiano di Tecnologia, Genoa, Italy
Marco Dal Maschio Department of Neuroscience and Brain Technologies,
Fondazione Istituto Italiano di Tecnologia, Genoa, Italy; Department of Genes,
Circuits and Behavior, Max Planck Institute for Neurobiology, Martinsried,
Germany
Gobind Das Physical Science and Engineering Division, King Abdullah Uni-
versity of Science and Technology, Thuwal, Kingdom of Saudi Arabia
Alberto Diaspro NanoBioPhotonics—LAMBS, Nanophysics, Istituto Italiano di
Tecnologia, Genoa, Italy
Duco Endeman Department of Neuroscience and Brain Technologies, Istituto
Italiano di Tecnologia, Genoa, Italy
Enzo Di Fabrizio Physical Science and Engineering Division, King Abdullah
University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
Giulia Falorsi Laboratory of Physiology, Department of Biology, University of
Florence, Florence, Italy
Lorenzo Ferrara Nanostructures, Istituto Italiano di Tecnologia, Genoa, Italy
PaulFeyen DepartmentofNeuroscienceandBrainTechnologies,IstitutoItaliano
diTecnologia, Genoa, Italy
Ljiljana Fruk Center for Functional Nanostructures, Karlsruhe Institute of
Technology, Karlsruhe, Germany
Francesco Gentile Nanostructures, Istituto Italiano di Tecnologia, Genoa, Italy;
Laboratory BIONEM, Dipartimento di Medicina Sperimentale e Clinica, Uni-
versità degli Studi Magna Graecia di Catanzaro, Catanzaro, Italy
Diego Ghezzi Department of Neuroscience and Brain Technologies, Istituto
Italiano di Tecnologia, Genoa, Italy
PauGorostiza InstitutdeBioenginyeriadeCatalunya(IBEC),Barcelona,Spain;
Centro de Investigación Biomédica en Red en Bioingeniería Biomateriales y
Nanomedicina (CIBER-BBN), Zaragoza, Spain; Institució Catalana de Recerca i
Estudis Avançats (ICREA), Barcelona, Spain
Yu-Chueh Hung Institute of Photonics Technologies, National Tsing Hua Uni-
versity, Hsinchu, Taiwan
MercèIzquierdo-Serra InstitutdeBioenginyeriadeCatalunya(IBEC),Barcelona,
Spain
Dania M. Kendziora Center for Functional Nanostructures, Karlsruhe Institute
of Technology, Karlsruhe, Germany
