Nucleic Acids and Molecular Biology

280 Pages·1989·18.998 MB·English

by  Th. D. Tullius (auth.), Professor Dr. Fritz Eckstein, Dr. David M. J. Lilley (eds.)

Nucleic Acids and
Molecular Biology
Volume 3
Edited by
Fritz Eckstein . David M.J. Lilley
With 70 Figures
Springer-Verlag Berlin Heidelberg New York
London Paris Tokyo Hong Kong
Professor Dr. FRITz ECKSTEIN
Max-Planck-Institut fUr experimentelle Medizin
Abteilung Chemie
Hermann-Rein-StraBe 3
3400 Ol>ttingen, FRO
Dr. DAVID M.J. LILLEY
University of Dundee
Biochemistry Department
Dundee DDI 4HN, UK
Cover illustration by kind permission ofB.W. Mlltthews
ISBN-13:978-3-642-83711-1 e-ISBN-13:978-3-642-83709-8
DOl: 10.1007/978-3-642-83709-8
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@ Springer-Verlag Berlin Heidelberg 1989
Softcover reprint of the hardcover 1st edition 1989
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Preface to the Series
From its inception, molecular biology has always been a discipline of
rapid development. Despite this, we are presently experiencing a
period of unprecedented proliferation of information in nucleic acid
studies and molecular biology. These areas are intimately interwoven,
so that each influences the other to their mutual benefit. This rapid
growth in information leads to ever-increasing specialization, so that
it becomes increasingly difficult for a scientist to keep abreast of
developments in all the various aspects of the field, although an
upto-date knowledge of the field as a whole is highly desirable.
With this background in mind, we have conceived the present
series Nucleic Acids and Molecular Biology. It comprises focused
review articles by active researchers, who report on the newest
developments in their areas of particular interest. The reviews are not
intended to be exhaustive, but rather to place the most recent data into
context. This format will allow our colleagues of familiarize
themselves with new developments in areas outside their own
immediate speciality, thus facilitating a more global view of their own
work. Moreover, we hope sincerely that this will convey some of the
excitement of the interdisciplinary nature of the study of nucleic acids
and molecular biology.
This series is planned to appear annUally. This period will allow
us to return to important topics with sufficient frequency to cover new
developments as they emerge.
FRITZ ECKSTEIN
DAVID MJ. LILLEY
Introduction to Volume 3
The third volume of Nucleic Acids and Molecular Biology contains
articles ranging from nucleic acid structure, through their interactions
with proteins to the control of gene expression. We are particularly
pleased to have a number of authors addressing the subject of RNA in
this volume, including the difficult but important subject of its
chemical synthesis, the complexities of its structures and the
mechanisms of transcript splicing. The probing of DNA structure is
reviewed in papers on the application of hydroxyl radical and 1,10
phenanthroline copper cleavages. A number of important DNA
protein interactions are discussed, including DNA polymerase, the
tryptophan and deoR repressors, and the resolvase enzymes which
cleave Holliday junctions in recombination. Gene transcription is
covered, from the points of view of DNA methylation, mammalian
ribosomal and avian lysozyme genes, and the control of transcription
in the proto-oncogene c-fos. Finally, we have not forgotten the plant
kingdom, with articles on development and transposition in plants.
We are pleased to thank all the authors for the high standard of
their contributions, in keeping with the earlier volumes in this series.
January 1989 FRITZ ECKSTEIN
DAVID MJ. LILLEY
Contents
Structural Studies of DNA Through Cleavage by the
Hydroxyl Radical
TH.D. TULLIUS (With 5 Figures) .......... 1
DNase Activity of 1,10-Phenanthroline-Copper Ion
D.S. SIGMAN and A. SPASSKY (With 9 Figures) 13
Structure of E. coli DNA Polymerase I, Large Fragment, and
Its Functional Implicatiofls
L.S. BEESE and T.A. STEnz (With 9 Figures) ...... 28
Resolution of Model Holliday Junctions in Vitro
S.C. WEST (With 4 Figures) . . . . . . . . . . . 44
Structure and Mechanism of the trp Repressor/Operator
System
R.Q. MARMORSTEIN and P.B. SIGLER (With 7 Figures) 56
The deoR Repressor from E. coli and Its Action in
Regulation-at- a-Distance
K. HAMMER and G. DANDANELL (With 4 Figures) 79
Complexities in Gene Regulation by Promoter Methylation
W. DOERFLER (With 2 Figures) ......... 92
Transcriptional Regulation of Proto-Oncogene c-fos
P.E. SHAW, R.A. HIPSKIND, H. SCHR6TER and
A. NORDHEIM (With 3 Figures) ............. 120
The Structural and Functional Domain Organization of the
Chicken Lysozyme Gene Locus
A.E. SIPPEL, A. STIEF, A. HECHT, A. MOLLER,
M. THEISEN, U. BORGMEYER, R.A.W. Rupp,
TH. GREWAL and TH. GRUSSENMEYER (With 5 Figures) 133
Mammalian Ribosomal Gene Transcription
I. GRUMMT (With 2 Figures) ..... . 148
X Contents
The Chemical Synthesis of Oligo-and Poly-ribonucleotides
C.B. REESE ......................... 164
RNA Structure
M. DELARUE and D. MORAS (With 5 Figures) 182
Pre-mRNA Splicing in Yeast
U. VIIAYRAGHAVAN andJ. ABELSON (With 3 Figures) 197
Trans-Splicing of RNA
J.C. BOOTHROYD (With 5 Figures) 216
Structure and Function of Bacterial RNase P
M. BAER, N. LUMELSKY, C. GUERRIER-TAKADA and
S. ALTMAN (With 4 Figures) . . . . . . . • . . • . . . .. 231
Transposition in' Plants
A. GIERL and H. SAEDLER (With ~ Figures) 251
Transgenic Plants and the Study of Plant Development
R. MASTERSON and J. SCHELL (With 1 Figure) ..... 260
Subject Index .......................... 269
Contributors
You will find the addresses at the beginning of the respective contribution
Abelson, J. 197 Masterson, R. 260
Altman, S. 231 Moras, D. 182
Baer, M. 231 Mii11er, A. 133
Beese, L.S. 28 Nordheim, A. 120
Boothroyd, J.C. 216 Reese, C.B. 164
Borgmeyer, U. 133 Rupp, R.A.W. 133
Dandanell, G. 79 Saed1er, H. 251
Delarue, M. 182 Schell, J. 260
Doerfler, W. 92 SchItSter, H. 120
Gierl, A. 251 Shaw, P.E. 120
Grewal, Th. 133 Sigler, P.B. 56
Grummt, I. 148 Sigman, D.S. 13
Grussenmeyer, Th. 133 Sippel, A.E. 133
Guerrier-Takada, C. 231 Spassky, A. 13
Hammer, K. 79 Steitz, T.A. 28
Hecht, A. 133 Stief, A. 133
Hipskind, R.A. 120 Theisen, M. 133
Lumelsky, N. 231 Tullius, Th.D. 1
Marmorstein, R.Q. 56 Vijayraghavan, U. 197
West, S.C. 44
Structural Studies of DNA Through Cleavage by the
Hydroxyl Radical
TH. D. TULLIUS!
Introduction
Although the overall architecture of DNA has been clear since the work of Watson
and Crick, the-detailed structure of DNA (and its dependence on sequence) is still an
area of active research. The chief experimental difficulty is that DNA as it exists in
biological systems is a very large molecule. The traditional methods for chemical
structure determination (for example, X-ray crystallography and NMR), while able
to provide important insights into the structures of small DNA oligonucleotides, are
at a loss when structural information is needed on much larger natural DNA
molecules.
Fortunately we have other experimental approaches available to us. Chemical
and enzymatic methods for determining details of DNA structure can be applied to
DNA molecules ranging in size from oligonucleotides to chromosomes. In this short
review I discuss the application of one chemical probe, the hydroxyl radical (-OH),
to the problem of DNA structure determination (Tullius 1987). I first introduce the
experimental strategy, and point out the advantages of the hydroxyl radical as a
chemical probe of DNA structure. I next present three examples of the kinds of
problems in DNA structure for which the hydroxyl radical is well-suited: the
measurement of the number of base pairs per helical turn of a DNA molecule (Tullius
and Dombroski 1985); the structural details and sequence dependence of" bent" DNA
(Burkhoff and Tullius 1987, 1988); and the shape of the four-stranded intermediate
in DNA recombination (the Holliday junction) (Churchill et al. 1988; Chen et al.
1988). The use of the hydroxyl radical to make "footprints" of DNA-protein
complexes will not be' covered because of the limited space available. I instead direct
the interested reader to recent papers (Tullius and Dombroski 1986; Tullius et al.
1987; Tullius 1988; Vrana et al. 1988) for more information. Finally, I suggest some
future directions in ~e use of the hydroxyl radical in structural studies of DNA.
Experimental Approach
In our laboratory we like to think of the hydroxyl radical as the chemical analogue
of the X-ray photon (Tullius 1987). Why do we think that this is an apt analogy?
X-ray photons have very short wavelengths, of the same order as chemical bond
lengths (Angstroms), so crystallographic and spectroscopic experiments using
X -rays are capable of providing structural information at the atomic level. Similarly,
1 Department of Chemistry, The Iohns Hopkins University, Baltimore, Maryland 21218, USA
Nucleic Acids and Molecular Biology, Vo1.3
ed. by F. Eckstein and D.M.I. Lilley
© Springer-Verlag Berlin Heidelberg 1989
2 TH. D. WLUUS
the hydroxyl radical is one of the smallest possible molecules, so if it could be used
as a probe it would provide the highest-resolution chemical information on structure.
The problem is how to use the chemistry of the hydroxyl radical to obtain
structural information. This question leads to an important chemical property of the
hydroxyl radical, its high reactivity toward the C-H bonds of organic molecules
(Walling 1975). Its main reaction is the abstraction of a hydrogen atom from an
organic molecule,leaving behind a carbon-based radical. The hydroxyl radical reacts
at· nearly the diffusion-controlled rate with small organic molecules, and exhibits
little selectivity in its reactions. For a more complicated molecule, steric and
electronic factors lead to different rates of reaction with the various C-H bonds. A
"map" of the rates of reaction of the hydroxyl radical with the C-H bonds of a
molecule could therefore provide a "chemical picture" of the structure of the
molecule.
DNA is a good substrate for the hydroxyl radical. It is the reaction of the hydroxyl
radical with the deoxyribose backbone of DNA (Hertzberg and Dervan 1984) that we
use in our chemical method for structure determination. The hydroxyl radical reacts
with the DNA b~ckbone by abstracting a hydrogen atom from a deoxyribose. The
resulting sugar radical breaks down in a secondary series of reactions, leaving behind
a gap in the DNA chain at the position of initial attack. This gap is flanked by the 5'
and 3' phosphates that were originally linked to the the degraded deoxyribose (Tullius
1987). Because the sugar residues along the DNA backbone are chemically identical,
and because the hydroxyl radical is so non-selective in its reactions, the rate of
reaction is nearly identical at each position along the backbone of a "normal" DNA
molecule (Tullius and Dombroski 1985).
The hydroxyl radical can be used as a tool for structure determination because
the cleavage pattern is different and characteristic for DNA molecules of unusual
structure, and for positions on a DNA molecule that are covered by bound protein
(Tullius 1987). The simple cleavage pattern for regular DNA gives a baseline, to
which the more complicated cleavage patterns of unusual DNA molecules are
compared.
The experimental approach for obtaining the hydroxyl radical cleavage pattern
of a DNA molecule relies on the techniques developed for determination of the
sequence of DNA. The gap in the DNA chain introduced by the hydroxyl radical is
similar in structure to the chain break that occurs in the chemical sequencing method
of Maxam and Gilbert. Before reaction with the hydroxyl radical, the DNA molecule
is radioactively labeled at one end of one of its strands. The rate of reaction of the
hydroxyl radical at each nucleotide in a DNA molecule is then easily visualized in
the intensity of the band on a DNA sequencing gel that corresponds to cleavage at
that nucleotide. Accurate quantitation of these intensities (and thus reaction rates)
can be achieved by densitometry of the autoradiograph (as illustrated in the figures
to follow). .
To generate the hydroxyl radical in aqueous solution we use the reaction of the
EDTA complex of iron(II) with hydrogen peroxide:
mr
[Fe(EDTA)]2-+ H202 -+ [Fe(EDTA)]1-+ + .OH
In this reaction (a version of the Fenton reaction) (Walling 1975) iron (II) EDTA