An Introduction to Single Molecule Biophysics

251 Pages·2017·11.028 MB·English

by  Yuri L. Lyubchenko

AN INTRODUCTION
TO SINGLE MOLECULE
BIOPHYSICS
Foundations of Biochemistry and Biophysics
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AN INTRODUCTION
TO SINGLE MOLECULE
BIOPHYSICS
Edited by
Yuri L. Lyubchenko
College of Pharmacy
University of Nebraska Medical Center
Cover: Image by Salvatore Chiantia, courtesy of Petra Schwille, Max Planck Institute of Biochemistry.
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Library of Congress Cataloging‑in‑Publication Data
Names: Lyubchenko, Yuri L., editor.
Title: Introduction to single molecule biophysics / [edited by] Yuri L.
Lyubchenko.
Other titles: Foundations of biochemistry and biophysics.
Description: Boca Raton : Taylor & Francis, 2017. | Series: Foundations of
biochemistry and biophysics
Identifiers: LCCN 2017033078 | ISBN 9781439806944 (hardback : alk. paper)
Subjects: | MESH: Single Molecule Imaging--methods | Biophysical Phenomena
Classification: LCC QH345 | NLM WN 190 | DDC 572--dc23
LC record available at https://lccn.loc.gov/2017033078
Visit the Taylor & Francis Web site at
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Contents
Series Preface vii
Preface ix
Editor xiii
Contributors xv
1. Single Molecule Fluorescence 1
Ashok Deniz
2. Atomic Force Microscope for Topographic Studies 21
Yuri L. Lyubchenko
3. Atomic Force Microscope Force Spectroscopy 79
Eric A. Josephs, Piotr E. Marszalek, and Zackary N. Scholl
4. Magnetic Tweezers 115
Piero R. Bianco, Yuri L. Lyubchenko, and Zhiqiang Sun
5. Optical Tweezers 141
Marco Capitanio
6. Nanofluidic Transport and Sensing in Biological
and Artificial Nanopores 197
Aleksandr Noy and Meni Wanunu
Index 229
v

Series Preface
Biophysics encompasses the application of the principles, tools, and techniques
of the physical sciences to problems in biology, including determination and
analysis of structures, energetics, dynamics, and interactions of biological mole-
cules. Biochemistry addresses the mechanisms underlying the complex reactions
driving life, from enzyme catalysis and regulation to the structure and function
of molecules. Research in these two areas is having a huge impact in pharmaceu-
tical sciences and medicine.
These two highly interconnected fields are the focus of this book series. It cov-
ers both the use of traditional tools from physical chemistry, such as nuclear mag-
netic resonance (NMR), X-ray crystallography, and neutron diffraction, as well as
novel techniques, including scanning probe microscopy, laser tweezers, ultrafast
laser spectroscopy, and computational approaches. A major goal of this series is
to facilitate interdisciplinary research by training biologists and biochemists in
quantitative aspects of modern biomedical research, and teaching core biological
principles to students in physical sciences and engineering.
Proposals for new volumes in the series may be directed to Lu Han, Executive
editor, at CRC Press/Taylor & Francis Group ([email protected]).
vii

Preface
Single molecule biophysics (SMB) is a relatively new branch of molecular bio-
physics, which utilizes a set of methods that enable imaging or probing of
individual molecules. The attractiveness of SMB is defined by two major features.
The first is biological systems, including cells, which consist of a limited number
of biological molecules or complexes. A study of this kind requires techniques
capable of probing single molecules. Second are the intricate functions of biologi-
cal molecules and systems as they assemble in transient states. Characterization
of these states is critical in understanding the molecular mechanism of the bio-
logical process under study. As they become available, SMB techniques have
been applied to numerous biological problems associated with understanding
the molecular mechanisms of DNA replication, transcription, and translation, as
well as the functions of molecular machines. Many of these examples and others
are discussed in the book in association with a specific method.
The discoveries of major SMB techniques have historically been associated
with Nobel Prizes. For example, the atomic force microscope (AFM) belongs
to the family of scanning probe microscopes, the discovery of which was
awarded the Nobel Prize in Physics in 1986 to G. Binnig and H. Rohrer at IBM,
Zurich, who published their discovery only 4 years prior to the award. Current
single molecule fluorescence methods originate from the 1989 publication
by W. Moerner and L. Kador, with a Nobel Prize awarded to W. Moerner in
2014 for the discovery. Optical traps or tweezers utilize the phenomenon of
manipulating atoms and small particles by focused light beam. By applying
this method in physics to the cooling and trapping of atoms with laser light, the
assembly of a Bose–Einstein condensate was achieved, leading to Nobel Prizes
in Physics in 1997 and 2001.
This introductory book broadly covers the motivations, history, and meth-
odologies of the major single molecule imaging and probing techniques, which
can be applied to numerous important biological systems and questions.
ix