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Handbook of RNA Biochemistry. Vol. 1+2. Edited by Roland K

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Angewandte
Books
Chemie
Biocatalysts and Enzyme
Technology
By Klaus Buchholz,
Volker Kasche and
Uwe T. Bornscheuer.
Wiley-VCH, Weinheim 2005.
448 pp., softcover
E 69.00.—ISBN
3-527-30497-5
Biocatalysts, often also called “catalysts
of life”, are nowadays fascinating
objects of study for scientists from a
wide range of disciplines, and they are
of growing industrial importance. However, the earliest industrial application
of biocatalysts began without a scientific
foundation, and even without any
knowledge about the nature or constitution of enzymes: in 1874, Christian
Hansen founded the first biocatalysts
company, which supplied enzymes for
cheese production. It was not until
over 20 years later that Buchner put forward the theory that enzymes are
actually proteins. That remained a subject of controversy for many years,
until finally, in 1926, Sumner-s crystallization of urease proved that Buchner-s
surmise was indeed correct. Today,
130 years after the founding of the first
enzyme business, the world annual turnover of biocatalysts is estimated to be
worth well over 2 billion US dollars. If
this figure seems rather small, it must
be borne in mind that the value of industrial production using biocatalysts is
many times greater, and its benefits are
increased still further if one takes into
account the positive contribution to susAngew. Chem. Int. Ed. 2005, 44, 5367 – 5368
tainability (economic, ecological, and
social).
How far has our knowledge in the
field of biocatalysts and enzyme technology advanced? Students and scientists who are interested in getting an
answer to that question, whether they
are biologists, chemists, or process technologists, are recommended to read this
book. It will give them insights into the
functions of enzymes, their production,
their areas of application, and the
forms in which they are used, whether
as free or immobilized enzymes, or as
intact cells. Process engineering aspects
are also covered. However, as the
emphasis given to the various topics
tends to reflect the interests and
research fields of the three authors,
one does not always get a treatment
that can be described as balanced. For
example, over 122 pages are devoted to
the subject of immobilization, which is
certainly important, whereas only 43
pages are given to the production,
screening, and optimization of enzymes,
areas in which there have been enormous advances in recent years, and
which should therefore have been covered in more detail. The comprehensive
and up-to-date literature references give
readers easy access to detailed information about the various aspects, and allow
reading in greater depth about topics of
special interest. The detailed list of contents and the index make it easy to find
any particular topic in biocatalysis. At
the beginning of each chapter, there is
a one-page summary of the main learning points, and although these summaries sometimes contain only very general information, they give a quick overview of the contents of the chapter. The
exercises and questions at the end of
each chapter are mostly very relevant
to practical situations, and as they are
quite challenging they provide an effective way of testing what has been
learned and adding depth.
Errors have been kept down to a
reasonably tolerable level. Two examples: on page 13 the enzyme nitrilase is
wrongly stated to be involved in the production of acrylamide, and on page 114
the reaction mechanism shown for leucine dehydrogenase is incorrect.
Although biocatalysts have been
used in industry for many years, and
enzyme technology is a well-established
field, the subject continues to advance
very rapidly, stimulated especially by
the growing emphasis on sustainable
production processes and the introduction of new methods. This book covers
a very wide range of aspects, while also
treating the material in depth, and
therefore it is a good starting point for
readers to approach the fascinating subject of biocatalysis.
Oliver May
Degussa AG
Hanau (Germany)
Handbook of RNA Biochemistry
Vol. 1 + 2. Edited by
Roland K. Hartmann, Albrecht
Bindereif, Astrid
Sch#n and Eric
Westhof. WileyVCH, Weinheim
2005. 931 pp.,
hardcover
E 299.00.—ISBN
3-527-30826-1
This two-volume compendium is a
remarkable and outstanding collection
of state-of-the-art-knowledge of methods that can be applied to study RNAs
and their properties. Each chapter
begins with introduction/background,
describes the specific topic to be covered and the methods used for studying
the topic, ends with data analysis and,
importantly, with a section headed
“troubleshooting”. The contents are divided into five parts, the first two in
Volume 1 and the last three in
Volume 2.
Volume 1. In Part I (RNA synthesis), Section 1 describes the enzymatic
RNA synthesis using bacteriophage T7
RNA polymerase. Section 2 covers the
preparation of RNA with homogeneous
5’-and 3’-ends, RNA with functional
groups at the 5’-end and RNA with 2’fluoro-modified pyrimidine nucleotides.
Sections 3 and 4 deal with RNA ligation
using T4 DNA ligase to generate site-
2 2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
5367
Books
specifically modified long RNA molecules or chimeric RNAs. Sections 5 to 7
describe co- or posttranscriptional modifications of RNA including photoreactive groups, 3’- terminal attachment of
fluorescent dyes and biotin, and chemical synthesis and purification of RNA.
Section 8 shows how and which modified RNAs can serve as tools in RNA
biochemistry.
In Part II (Structure Determination), Section 9 is concerned with RNA
sequencing and modification by radiolabeling and Section 10 with enzymatic
(RNaseT1, T2, and V1) and chemical
methods to probe into the secondary
and tertiary structure of RNA. Section 11 elaborates on RNA-protein
interactions and RNA structure in ribonucleoprotein particles using electophoretic mobility shift assay (EMSA), UV
cross-linking and immunoprecipitation.
Sections 12 to 15 describe footprinting
studies for probing RNA structure and
metal-binding sites using divalent
metal ions and dimethylsulfate. Section 16 describes the measurement of
the stoichiometry of Mg2+ bound to
RNA using 8-hydroxyquinoline-5-sulfonic acid as chelator, and Section 17
describes nucleotide analog interference
mapping and suppressing (NAIM and
NAIS) to study RNA teriary structure
and function, dynamics of RNA helicases, and RNA–protein interactions.
These methods are applied in Section 18
to the RNase P system. Sections 19 and
20 are devoted to metal binding sites
that are identified by thio or thiol
groups to which thiophilic metal ions
have a high affinity, and divalent metal
binding sites are mapped by Fe2+
(Fenton chemistry), and Sections 21
and 22 describe cross-linking between
RNA and protein or between 4-thiouridine and 6-thioguanosine in RNA.
5368
www.angewandte.org
Biophysical methods used to study
RNA structure and function are described in Sections 23 to 29. They cover
small-angle X-ray scattering studies for
RNA and RNA–protein complexes;
temperature-gradient gel electrophoresis of RNA; UV melting and native
gels to obtain information on RNA conformation; sedimentation analysis of
ribonucleoprotein complexes; preparation and handling RNA crystals; fluorophore labeling of RNA for fluorescence
resonance energy transfer (FRET) and
single molecule fluorescence studies;
scanning force microscopy and spectroscopy of RNA.
Volume 2. In Part III, RNA Genomics and Bioinformatics, Section 30 to 34
present a comparative analysis of 6S
RNA secondary structure prediction;
modeling the architecture of structured
RNA within a modular and hierarchical
framework; modeling large RNA
assemblies using a reduced representation; and molecular dynamics simulations of RNA systems based on X-ray
crystal or NMR solution structures. Section 35 describes the searche for RNA
motifs in genomic sequences. Sections 36 to 38 are related as they deal
with approaches to identify novel nonmessenger RNAs in bacteria and to
investigate their biological functions by
RNA mining and functional analysis of
non-mRNAs. Section 39 finally reports
large-scale analysis of mRNA splice variants by microarrays.
In Part IV (Analysis of RNA Function), Sections 40 to 42 describe the isolation of RNA binding proteins using
affinity
matrices
(CNBr-activated
sepharose, streptavidin, antibodies). In
section 43, Northwestern techniques
identify RNA binding proteins from
cDNA expression libraries, Section 44
describes the fluorescence detection of
2 2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
nascent transcripts and RNA-binding
proteins in cell nuclei, three-hybrid
analysis in Section 45 identifies and
characterizes RNA-binding proteins,
and in Section 46 minigenes are used
to analyse alternative splicing. This
part closes with the powerful and frequently applied SELEX (systematic
evolution of ligands by exponential
enrichment) method. Section 47 introduces to SELEX and shows how function is found amongst randomized
sequences. In Section 48, aptamer selection against proteins and carbohydrates
is described, Section 49 deals with in
vivo SELEX strategies, and Section 50
with in vitro selection against small molecules. Section 51 shows how SELEX is
used to identify antisense and protein
target sites in RNA or in nuclear ribonucleoprotein complexes.
Part V (RNAi) deals with small
interference RNA (siRNA). Section 52
describes application of synthesis
siRNSs for gene silencing in mammalian
cells. The book ends with a useful
appendix on UV spectroscopy for the
quantitation of RNA.
The “Handbook of RNA Biochemistry” is a true handbook that should
not be missed in any laboratory engaged
in RNA research. The text is concisely
written, full of good ideas and the “troubleshooting” chapters will help to find
ways out of deadlocks. I congratulate
the authors to this handbook and recommend it to all RNA enthusiasts.
Wolfram Saenger
Institut f5r Chemie und Biochemie/
Kristallographie
Freie Universit9t Berlin
DOI: 10.1002/anie.200585300
Angew. Chem. Int. Ed. 2005, 44, 5367 – 5368
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