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Preface
No full textGiorgio Vasari, a painter, architect, and art historian during the Italian Renaissance, is
credited with coining the expression “andare a bottega,” (“attending the studio”) referring
to the internship that the apprentice would complete in the master’s studio in order
to learn what could be uniquely transmitted in person and in that particular environment
and that could then lead to making a unique artist of the apprentice.
Nowadays, this same concept holds true in science, and despite the many opportunities
for communication and “virtual presence”, the real physical permanence in a lab is still
the best way for a scientist to learn a technique or a protocol, or a way of thinking. A book
of protocols, such as this, humbly proposes itself as the second-best option. Not quite the
same as being in person in a lab and witnessing the experts’ execution of a protocol, it still
holds many more details and hints than the usually brief methods section found in research
papers. This book of protocols for DNA nanotechnology was composed with this concept
in mind: prolonging the tradition of Methods in Molecular Biology, it tries to simplify
researchers’ lives when they are putting in practice protocols whose results they have
learnt in scientific journals.
DNA is playing a quite important and dual role in nanotechnology. First, its properties
can nowadays be studied with unprecedented detail, thanks to the new instrumental
nano(bio)technologies and new insight is being gathered on the biological behavior and
function of DNA thanks to new instrumentation, smart experimental design, and protocols.
Second, the DNA molecule can be decontextualized and “simply” used as a copolymer
with designed interaction rules. The Watson–Crick pairing code can be harnessed
towards implementing the most complicated and elegant molecular self-assembly reported
to date. After Ned Seeman’s contribution, elegantly complicated branched structures can
be braided and joined towards building nano-objects of practically any desired form.
DNA nanotechnology is somewhat like watching professional tennis players: everything
seems so simple, but then you set foot on the court and realize how difficult it is to
hit a nice shot. When you see the structural perfection of a self-assembling DNA nanoobject,
such as a DNA origami, you marvel at how smart DNA is as a molecule and wonder
how many different constructs you could design and realize. Among the others, this
book tries to show the procedures to follow in order to repeat some of the methods that
lead to such constructs, or to the mastering of the characterization techniques used to
study them. Many details and procedures are the fruit of the blending of artistry, science,
and patience, which are often unseen in a journal paper, but that could be what makes the
difference between a winning shot and hitting the net.
Many research groups share their expertise with the readers in this book. For the sake
of conciseness, we here mention the group leaders, while it is truly from the daily work of
a complete team that the details of a protocol can be worked out. The chapters of this
book can be roughly divided into two parts: some deal with the methods of preparing the
nanostructures, from the rationale of the operations to the techniques for their handling;
some other chapters deal more directly with advanced instrumental techniques that can
manipulate and characterize molecules and nanostructures. As part of the first group,
Roberto Corradini introduces the reader to the methods and choices for taming helix
chirality, Alexander Kotlyar, Wolfgang Fritzsche, Naoki Sugimoto, and James Vesenka share their different methods in growing, characterizing, and modifying nanowires based
on G tetraplexes; Hao Yan and Friedrich Simmel teach all the basics for implementing the
self-assembly of branched DNA nanostructures, and then characterizing the assembly.
Hanadi Sleiman tells about hybrid metal–DNA nanostructures with controlled geometry.
Frank Bier shows the use of rolling circle amplification to make repetitive DNA nanostructures,
while, moving closer to technological use of DNA, Arianna Filoramo instructs on
how to metalize double-stranded DNA and Andrew Houlton reports on the protocol to
grow DNA oligonucleotides on silicon. Also with an eye to the applicative side, Yamuna
Krishnan instructs on how to insert and use DNA nanostructures inside living cells. On
the instrument side, Ciro Cecconi and Mark Williams introduce the readers to methods
for the use of optical tweezers, focusing mainly on the preparation of the ideal molecular
construct and on the instrument and its handling, respectively. John van Noort and
Sanford Leuba give us protocols on how to obtain sound data from single-molecule FRET
and apply it to study the structure of chromatin. Claudio Rivetti teaches the reader how
to extract quantitative data from AFM of DNA and its complexes, while Matteo Castronovo
instructs on the subtleties of using the AFM as a nanolithography tool on self-assembled
monolayers; Jussi Toppari dwelves on the very interesting use of dielectrophoresis as
a method to manipulate and confine DNA, while Matteo Palma and Jennifer Cha explain
methods for confining on surfaces DNA and those very same types of DNA nanostructures
that other chapters tell the reader how to assemble. Aleksei Aksimientev shows the
methods for modeling nanopores for implementing DNA translocation, a technique
bound to find many applications in the near future.
We hope this book will help ignite interest and spur activity in this young research
field, expanding our family of enthusiastic followers and practitioners. There are certainly
still many chapters to be written on this subject, simply because so much is happening in
the labs at this very moment. There will certainly be room for the mainstreaming of protocols
on the use of DNA analogues (starting with the marvelous RNA, of course), for the
design and preparation of fully 3D architectures, for the development of routes towards
functional DNA nanostructures, which will lead to applications. DNA nanostructures can
be “re-inserted” in their original biological context, as microorganisms can be convinced
to replicate nanostructures or even code them. And eventually, applications will require
massive amounts of the nanostructures to be produced and to be manipulated automatically,
possibly with a precision and output rate similar to that of the assembly of microelectronics
circuitry nowadays.
Our personal wish is that the next chapters will be written by some of our readers
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Analysis of power efficiency in high-performance class-B oscillators
No full textThis paper presents an analysis of power efficiency in LC voltage-controlled oscillators (VCOs). Three different class-B topologies are compared under different operating conditions, demonstrating that the CMOS oscillator embedding two tail resonators achieves the best power efficiency and, consequently, best phase-noise-versus-power trade-off. A 65-nm CMOS prototype in post-layout simulations achieves a phase noise of -159 dBc/Hz at 20-MHz offset from the 3.6-GHz carrier, while dissipating 4.5 mW from 1.2-V power supply and covering 21.8% tuning range
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
DNA codes for nanoscience
No full textThe stereochemistry of the interaction and recognition processes of DNA has been traditionally described in the Ångström scale. DNA can also provide recognition processes whose selectivity and stringency can be modulated along different scale lengths, as it takes place in direct and indirect read-out mechanisms between DNA and proteins. Embedded in DNA are informational codes that control its recognition processes also in the nanoscale. These recognition processes can exploit multiple layers of information to drive self-assembly amongst biological and non-biological molecules (1). They are based on the nanoscale superstructural and mechanical properties that are modulated along the DNA chain by its sequence.
Atomic Force Microscopy by imaging single DNA molecules makes it possible:
a) to translate the linear information of the base sequences into these functional elements, and to “sequence” those properties (2-4);
b) to monitor the length-scale and also the time-scale of the equilibration processes in the dynamics of a single DNA chain (5).
Those nanoscale properties of DNA are capable to control gene expression (6) and to lead to recognition processes between a crystal surface and the sequence of the DNA (7). These recognition processes are studied also with the Single Molecule Force Spectroscopy approach (8,9).
(1) B. Samorì & G. Zuccheri, Angew. Chem. Int. Ed. Engl., 44 (8): 1166-81 (2005).
(2) G. Zuccheri, A. Scipioni, G. Gargiulo, V. Cavaliere, G. De Santis, B. Samorì,
Proc. Natl. Acad. Sci. (USA), 98; 3074-3079 (2001).
(3) A. Scipioni, G. Zuccheri, M. Savino, B. Samorì, P. De Santis, Biophys. J., 83 (5): 2408-18 (2002).
(4) G. Zuccheri and B. Samorì, Methods in Cell Biology 68: 357-395 (2002).
(5) A. Scipioni, G. Zuccheri, C. Anselmi, A. Bergia, B. Samorì, P. De Santis, Chem Biol., 9 (12): 1315-21 (2002).
(6) M. Barna, M. Branford, A. Bergia, B. Samori, and P. P. Pandolfi, Developmental Cell, 3: 499-510 (2002).
(7) B. Sampaolese, A. Bergia, A. Scipioni, G. Zuccheri, M. Savino, B. Samorì,. P. De Santis, Proc. Natl. Acad. Sci. (USA) 99: 13566-13570 (2002).
(8) F. Grandi, G. Zuccheri, B. Samorì (to be published)
(9) Y. Bustanji, C. Arciola, M. Conti, E. Mandello, L. Montanaro, B. Saporì, Proc. Natl. Acad. Sci. (USA), 100: 13292-13297 (2003)
Chemical reactivity within a smectic B liquid crystalline phase: A model of enzyme catalysis?
No full textThe rearrangement of allyl p-dimethylaminobenzenesulphonate (ASE) to form a zwitterionic product has already been recognized as an effective probe for the study of reactivity within the smectic B phase [4, 5, 19]. We have used deuterium NMR, linear dichroism and X-ray diffraction techniques to investigate the phase diagram of the ASE-OS35 reaction system. The partitioning of the reactant molecules between coexisting smectic, nematic and/or isotropic phases and the structural organization of the smectic catalytic host at different temperatures and reactant guest concentrations have been characterized. On the basis of these measurements, a model of ASE reactivity in smectic solvents has been developed. The reaction takes place provided that coexisting isotropic or nematic phases are present to act as a reservoir for the ASE reactant molecules prior to their entering the smectic phase; they then react and leave the smectic phase as a zwitterionic product. The analogy between this model of reactivity within smectic phases and the Michaelis-Menten enzyme processes is discussed. This relationship opens up the intriguing possibility of designing new experiments with which to investigate further liquid crystalline models of enzyme catalysis. © Taylor & Francis Group, LLC
Chemical reactivity within a smectic B liquid crystalline phase: A model of enzyme catalysis?
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