Recombinant DNA Part D

624 Pages·1988·13.281 MB·English

by  Kaplan N.P. (ed.), Colowick N.P. (ed.), Wu R. (ed.)

Preface
Recombinant DNA methods are powerful, revolutionary techniques
for at least two reasons. First, they allow the isolation of single genes in
large amounts from a pool of thousands or millions of genes. Second, the
isolated genes or their regulatory regions can be modified at will and re-
introduced into cells for expression at the RNA or protein levels. These
attributes allow us to solve complex biological problems and to produce
new and better products in the areas of health, agriculture, and industry.
Volumes 153, 154, and 551 supplement Volumes 68, 100, and 101 of
Methods in Enzyrnology. During the past few years, many new or im-
proved recombinant DNA methods have appeared, and a number of them
are included in these three new volumes. Volume 351 covers methods
related to new vectors for cloning DNA and for expression of cloned
genes. Volume 451 includes methods for cloning eDNA, identification of
cloned genes and mapping of genes, chemical synthesis and analysis of
oligodeoxynucleotides, site-specific mutagenesis, and protein engineer-
ing. Volume 551 includes the description of several useful new restriction
enzymes, detail of rapid methods for DNA sequence analysis, and a num-
ber of other useful methods.
YAR Wu
ECNERWAL NAMSSORG
iiix
NAHTAN O. NALPAK
June 25, 1917-April ,51 1986
Nathan O. Kaplan
In the past half century, knowledge in the natural sciences has pro-
gressed at a rate unmatched in previous history. Biochemistry appears
closer than ever to the attainment of its ultimate objective: creation of a
body of knowledge rationalized in a conceptual structure which provides
a solid basis for understanding life processes. In these fabulous times,
there have been fabulous people among whom may be included Nathan
("Nate") Kaplan. His many, varied and massive contributions to cru-
cially important areas of biochemical research added to his creative activ-
ities as an editor, scholar, and academic statesman have left a lasting
impression on the history of these exciting times. We are fortunate in
having an account of his life philosophy and experiences which he himself
provided in "Selected Topics in the History of Biochemistry" (edited by
G. Semenga; Vol. 30, p. 255 et seq. ; Elsevier Science Publishers).
His potential was manifest early in his career at Berkeley where he
collaborated with Barker, Hassid, and Doudoroff in the late 1930s, pro-
viding biochemical expertise crucial for the demonstration that in the
phosphorolysis of sucrose the phosphate ester formed was glucose
1-phosphate. His first scientific publication on sucrose phosphorylase in-
cluded an account of these seminal researches. His full potential was
realized when, under the watchful eye of Fritz Lipmann, his great mentor
and life-long admirer and friend, he made essential contributions in col-
laboration with Lipmann and Dave Novelli to the isolation and character-
ization of coenzyme A, work which later formed part of the basis for the
Nobel Prize to Lipmann.
Nate followed his unerring intuition in continuing his career at the
McCollum-Pratt Institute under the aegis of W. D. McElroy. He built a
body of research on NAD, NAD analogs, and associated dehydrogenases
to earn a leading position as an international authority on the pyridine
nucleotide coenzymes. In the course of these investigations he began a
life-long collaboration with another "biochemist's biochemist"--Sidney
Colowick--which resulted in the creation of the monumental series Meth-
ods in Enzymology, which was to become the definitive source of method-
ology in the biochemical sciences.
Nate, as he so vividly detailed in the account I have referred to above,
stressed the importance of following research wherever it led, even if
assured results might not be immediately evident. As an example, one
notes that his investigations of the pyridine nucleotide cofactors ignited
XV
xvi NAHTAN .O NALPAK
an interest in comparative biochemistry, elaborated in many researches of
major significance for biochemical evolution.
Nate's intuitive insights into things biochemical also extended to an
uncanny ability to assess potential in budding biochemists. His success in
finding and recruiting talent was never better shown than in the creation
of the Graduate Department of Biochemistry at Brandeis in the late 1950s.
Those in the remarkable group he assembled--which included W. Jencks,
L. Grossman, G. Sato, M. E. Jones, L. Levine, H. Van Vunakis, and J.
Lowenstein--owed their start in large part to his unstinting guidance and
encouragement.
He found time to serve on a multitude of policy-making committees
and was always available, however hard pressed, to take over editorial
chores, however onerous. I recall the many hours he spent helping to
organize and edit a Festschrift and symposium celebrating the fact I had
survived to age 65. And then there was the salvage and rebuilding opera-
tion he so unselfishly initiated to revive the ailing Biochemistry Analytical
journal when his old friend, 1A Nason, its Editor-in-Chief, fell seriously
ill.
No project engaged Nate's attention and devotion more than his la-
bors with Colowick to oversee and assure the publication and excellence
of the many volumes which make up the Methods ni Enzymology series,
now numbering more than a hundred, which will stand as a lasting monu-
ment to his memory. Certainly nothing could be more appropriate than
the present dedication.
MARTIN D. KAMEN
Contributors to Volume 153
Article numbers are in parentheses following the names of contributors.
Affiliations listed are current.
GNUEI-INYG AN (17), Institute of Biological (3), DAVlSON JOHN Unit of Molecular Biol-
Chemistry, Washington State University, ogy, International Institute of Cellular
Pullman, Washington 46199 and Molecular Pathology, B-1200 Brus-
(6), PAUL BATES Department of Microbiol- sels, Belgium
ogy, University of California, San Fran- R. DEBLAERE (16), Laboratorium voor
cisco, San Francisco, California 34149 Genetica, RUksuniversiteit Gent, B-9000
HPOTSIRHC F. BECK (28), Institut fiir Bi- Gent, Belgium
ologie III, Albert-Ludwigs-Universitgit, NAMREH A. ED BOER (27), Department of
D-7800 Freiburg i. Br., Federal Republic Biochemistry of the Gorlaeus Laboratory,
of Germany University of Leiden, 2300 RA Leiden,
RAMA M. (25), BELAGAJE Department of The Netherlands
Molecular Biology, Lilly Research Labo- GuY O. (31), DUFFAUD Department of Bio-
ratories, A Division of Eli Lilly and Com- chemistry, State University of New York
pany, Lilly Corporate Center, Indianapo- at Stony Brook, Stony Brook, New York
lis, Indiana 46285 49711
NYVREM J. BmB (9), Department of Ge-
SEMAJ E. DUTCnIK (5), Department of Ge-
netics, John Innes Institute, Norwich
netics, Washington University School of
NR4 7UH, England
Medicine, St. Louis, Missouri 01136
GRANT A. (33), BITTER AMGen, Thousand
KEVIN M. EGAN (33), AMGen, Thousand
Oaks, California 91320
Oaks, California 02319
NEGR3tJ (4), BROSIUS Department of Genet-
NEVETS G. ELLIOTT (33), AMGen, Thou-
ics and Development and Center for Neu-
sand Oaks, California 91320
robiology and Behavior, Columbia Uni-
versity, New York, New York 23001 RETLAW FlEas (26), Laboratory of Molecu-
lar Biology, State University of Ghent,
ESIOqNARF (3), BRUNEL Unit of Molecular
B-9000 Ghent, Belgium
Biology, International Institute of Cellu-
lar and Molecular Pathology, B-1200 R. T. (15), FRALEY Plant Molecular Biology
Brussels, Belgium Group, Biological Sciences Department,
Corporate Research and Development
JUDY NALSSURB (12), Department of Molec-
Staff, Monsanto Company, Chesterfield,
ular Genetics and Cell Biology, The Uni-
Missouri 63198
versity of Chicago, Chicago, Illinois
73606 A. M. (8), FRISCHAUF European Molecular
JuDY CALLIS (21), Horticulture Depart- Biology Laboratory, D-6900 Heidelberg,
ment, University of Wisconsin, Madison, Federal Republic of Germany
Wisconsin 53706 MICHAEL FROMM (21), United States De-
(32), CHANG SHING Microbial Genetics, Ce- partment of Agriculture, Agricultural Re-
tus Corporation, Emeryville, California search Service, Pacific Basin Area Plant
80649 Gene Expression Center, Albany, Califor-
nia 94710
KEITH F. (9), CHATER Department of Ge-
netics, John Innes Institute, Norwich SEMAJ C. GIFFIN (33), AMGen, Thousand
NR4 7UH, England Oaks, California 02319
ix
X CONTRIBUTORS TO VOLUME 153
NASUS S. (12), GOLDEN Department of Biol- MATTHEW O. JONES (33), AMGen, Thou-
ogy, Texas A&M University, College Sta- sand Oaks, California 02319
tion, Texas 34877
SAIBOT KIESER (9), Department of Ge-
TREBOR NROKLESAH (12), Department of netics, John Innes Institute, Norwich
Molecular Genetics and Cell Biology, The NR4 7UH, England
University of Chicago, Chicago, Illinois
H. J. KLEE (15), Plant Molecular Biology
73606
Group, Biological Sciences Department,
CYNTHIA HELMS (5), Collaborative Re- Corporate Research and Development
search, Inc., Lexington, Massachusetts Staff, Monsanto Company, Chesterfield,
37120 Missouri 89136
J.-P. (16), HERNALSTEENS Laboratorium RuuD N. H. KONINGS (2), Laboratory of
Genetische Virologie, Vr~ie Universiteit Molecular Biology, Faculty of Science,
Brussel, B-1640 Sint-Genesius-Rode, University of Nijmegen, Toernooiveld,
Belgium 6525 ED N(jmegen, The Netherlands
MICHEL ETUERPSRETSUEH (3), Unit of Mo- DNOMYAR A. KOSKI (33), AMGen, Thou-
lecular Biology, International Institute sand Oaks, California 91320
of Cellular and Molecular Pathology, C. J. KUHLEMEIER (11), Laboratory of
B-1200 Brussels, Belgium
Plant Molecular Biology, The Rockefeller
H. HOFTE (16), Plant Genetic Systems, University, New York, New York 12001
Inc., B-9000 Ghent, Belgium S. SSOTSHUK (10), Molecular Genetics Re-
PAUL J. J. SAAKYOOH (18), Department of search, Lilly Research Laboratories, A
Plant Molecular Biology, Biochemistry Division of Eli Lilly and Company, Lilly
Laboratory, University of Leiden, 2333 Corporate Center, Indianapolis, Indiana
AL Leiden, The Netherlands 58264
DAVID A. DOOWPOH (9), Department of Ge- CHRISTINE LANG-HINRICHS (22), Institut
netics, John lnnes Institute, Norwich far Mikrobiologie, lnstitut fiir Giirungsge-
NR4 7UH, England werbe und Biotechnologie, Berlin D-IO00
65, Federal Republic of Germany
R. B. HCSROH (15), Plant Molecular Biology
Group, Biological Sciences Department, W. H. R. LANGalDGE (20), Boyce Thomp-
Corporate Research and Development son Institute for Plant Research, Cornell
Staff, Monsanto Company, Chesterfield, University, Ithaca, New York 35841
Missouri 63198 J. (16), LEEMANS Plant Genetic Systems,
HANSEN M. HSIUNG (24), Lilly Research Inc., B-9000 Ghent, Belgium
Laboratories, A Division of Eli Lilly and H. (8), LEHRACH The Imperial Cancer Re-
Company, Lilly Corporate Center, Indi- search Fund, London WC2A 3PX, En-
anapolis, Indiana 46285 gland
ANNA HUI (27), Department of Cell Genet- B. J. LI (20), Department of Biology,
ics, Genentech, Inc., South San Fran- Chungshan University, Kwangchou,
cisco, California 94080 K~angdong, People's Republic of China
IROYASAM (31), INOUYE Department of Bio- SEMAJ R. IClSPUL (4), Department of Pediat-
chemistry, University of Medicine and rics andI nstitute for Molecular Genetics,
Dentistry of New Jersey at Rutgers, Baylor College of Medicine, Texas Medi-
Robert Wood Johnson Medical School, cal Center, Houston, Texas 03077
Piscataway, New Jersey 08854
NERRAW C. MACKELLAR (24), Lilly Re-
HSAKRAP (27), JHURANI Department of Or- search Laboratories, A Division of Eli
ganic Chemistry, Genentech, Inc., South Lilly and Company, Lilly Corporate Cen-
San Francisco, California 08049 ter, Indianapolis, Indiana 46285
CONTRIBUTORS TO VOLUME 153 xi
PAUL E. (31), MARCH Department of Bio- R. AJARAGAN (10), RAO Molecular Genetics
chemistry, University of Medicine and Research, Lilly Research Laboratories, A
Dentistry of New Jersey at Rutgers, Division of Eli Lilly and Company, Lilly
Robert Wood Johnson Medical School, Corporate Center, Indianapolis, Indiana
Piscataway, New Jersey 45880 58264
ANNE MARMENOUT (26), Innogenetics, (26), ERIK REMAUT Laboratory of Molecu-
Zwijnaarde, Belgium lar Biology, State University of Ghent,
(1), MESSING MIHCAOJ Waksman Institute B-9000 Ghent, Belgium
of Microbiology, Rutgers, The State Uni- A. STREANYER (16), Plant Genetic Systems,
versity of New Jersey, Piscataway, New Inc., B-9000 Ghent, Belgium
Jersey 55880 M. A. NOSDRAHCIR (10), Molecular Genet-
YROGERG (30), MILMAN Department of Bio- ics Research, Lilly Research Laborato-
chemistry, The Johns Hopldns University, ries, A Division of Eli Lilly and Company,
School of Hygiene and Public Health, Lilly Corporate Center, Indianapolis, In-
Baltimore, Maryland 50212 diana 46285
N. (8), MURRAY Department of Molecular S. G. SREGOR (15), Plant Molecular Biology
Biology, University of Edinburgh, Edin- Group, Biological Sciences Department,
burgh EH9 3JR, Scotland Corporate Research and Development
KIYOSHI NAGAI (29), Medical Research Staff, Monsanto Company, Chesterfield,
Council Laboratory of Molecular Biol- Missouri 63198
ogy, Cambridge CB2 2QH, England NASUS M. GREBNESOR (7), Institute of Mo-
NARAS A. (23), NARANG Division of Biologi- lecular Biology, University of Oregon,
cal Sciences, National Research Council Eugene, Oregon 30479
of Canada, Ottawa, Ontario, Canada BOR A. TROOREPLIHCS (18), Department of
KIA 6RO Plant Molecular Biology, Biochemistry
DRANYAM V. (5), OLSON Department of Ge- Laboratory, University of Leiden, 2333
netics, Washington University School of AL Leiden, The Netherlands
Medicine, St. Louis, Missouri 01136 (28), KLAUS SCHNEIDER lnstitut fiir Biolo-
(34), ENZO PAOLETTI Laboratory of Immu- gic 11I, Albert-Ludwigs-Universit~it,
nology, Wadsworth Center for Laborato- D-7800 Freiburg i. Br., Federal Republic
ries and Research, New York State De- of Germany
partment of Health, Albany, New York ETTIG1RB E. (25), SCHONER Department of
10221 MoleculaGre netics, Lilly Research Labo-
BEN P. H. SRETEEP (2), Department of Ge- ratories, A Division of Eli Lilly and Com-
netics, University of Groningen, 9751 NN pany, Lilly Corporate Center, Indianapo-
Haren (GR), The Netherlands lis, Indiana 46285
NOIRAM E. SUKREP (34), Laboratory of Im- DLANOR G. RENOHCS (25), Department of
munology, Wadsworth Center for Labo- Molecular Genetics, Lilly Research Labo-
ratories and Research, New York State ratories, A Division of Eli Lilly and Com-
Department of Health, Albany, New York pany, Lilly Corporate Center, Indianapo-
10221 lis, Indiana 46285
AN'rONIA PICClNI (34), Laboratory of Im- DNOMYAR D. (19), SHILLITO Biotechnology
munology, Wadsworth Center for Labo- Research, CIBA-GEIGY Corporation,
ratories and Research, New York State Research Triangle Park, North Carolina
Department of Health, Albany, New York 90772
10221 Guus SNOMIS (26), N.I.Z.O., 6710 Ede, The
OGNI SUKYRTOP (19), Institute for Plant Sci- Netherlands
ences, CH-1892 Zurich, Switzerland ULF (22), STAHL Fachgebiet Mikrobiologie,
xii CONTRIBUTORS TO VOLUME 153
Technische Universitdt Berlin, D-IO00 G. A. NAV (11), ARKEL Department of Mo-
Berlin ,56 Federal Republic of Germany lecular Cell Biology, University of
WING L. SONG (23), Division of Biological Utrecht, 3584 CH Utrecht, The Nether-
Sciences, National Research Council lands
of Canada, Ottawa, Ontario, Canada M. NAV MONTAGU (16), Laboratorium
K1A 6RO Genetische Virologie, Vr~/e Universiteit
Brussel, B-1640 Sint-Genesius-Rode,
DRAHCIR T. YKSORUS (14), Department of
Belgium, and Laboratorium voor
MolecularG enetics and Cell Biology, The
Genetica, Rijksuniversiteit Gent, B-9000
University of Chicago, Chicago, Illinois
Gent, Belgium
73606
ELS J. M. NEVEOHREV (2), Department of
A. A. (20), SZALAY Boyce Thompson Insti-
Biology, Antoni van Leeuwenhoekhuis,
tute for Plant Research, Cornell Univer-
6601 CX Amsterdam, The Netherlands
sity, Ithaca, New York 35841
JEFFREY VIEIRA (1), Waksman Institute of
LOVEmNE P. (21), TAYLOR Carnagie Insti-
Microbiology, Rutgers, The State Univer-
tution of Washington, Stanford, Califor-
sity of New Jersey, Piscataway, New Jer-
nia 50349
sey 55880
(13), THIEL TEgESA Department of Biology, AINIGRIV TOBLAW (21), Department of Bio-
University of Missouri-St. Louis, St.
logical Sciences, Stanford University,
Louis, Missouri 12136 Stanford, California 50349
HANS CHRISTIAN NESREGtgHT (29), Bio- C. (13), WOLK PETER MSU-DOE Plant Re-
struktur Afdeling, Kemisk Institut, /~rhus search Laboratory, Michigan State Uni-
Universitet, 8200 ]lrhus N, Denmark versity, East Lansing, Michigan 48824
BIK-KwooN EYT (14), Section of Biochem- FE1-L. OAY (23), Division of Biological
istry, Molecular and Cell Biology, Divi- Sciences, National Research Council
sion of Biological Sciences, CorneU Uni- of Canada, Ottawa, Ontario, Canada
versity, Ithaca, New York 35841 K1A 6RO
[1] DNA 3
PRODUCTION OF SINGLE-STRANDED PLASMID
[1] Production of Single-Stranded Plasmid DNA
By JEFFREY VIEIRA and JOACHIM MESSING
Introduction
In the study of gene structure and function, the techniques of DNA
analysis that are efficiently carried out on single-strand (ss) DNA tem-
plates, such as DNA sequencing and site-specific ni vitro mutagenesis,
have been of great importance. Because of this, the vectors developed
from the ssDNA bacteriophages M13, fd, or fl, which allow the easy
isolation of strand-specific templates, have been widely used. While these
vectors are very valuable fort he production of ssDNA, they have certain
negative aspects in comparison to plasmid vectors (e.g., increased insta-
bility of some inserts, the minimum size of phage vectors). Work from the
laboratory of N. Zinder showed that a plasmid carrying the intergenic
region (IG) of fl could be packaged as ssDNA into a viral particle by a
helper phage. 1 This led to the construction of vectors that could combine
the advantages of both plasmid and phage vectors. 2 Since that time a
number of plasmids carrying the intergenic region of M13 or fl have been
constructed with a variety of features)
A problem that has been encountered in the use of these plasmid/
phage chimeric vectors (plage) is the significant reduction in the amount
of ssDNA that is produced as compared to phage vectors. Phage vectors
can have titers of plaque-forming units (pfu) of lm/2101 and give yields of a
few micrograms per milliliter of ssDNA. It might then be expected that
cells carryingb oth a plage and helper phage would give titers of 5 × 10H/
ml for each of the two. However, this is not the case due to interference
by the plage with the replication of the phage.4 This results in a reduction
in the phage copy number and, therefore, reduces the phage gene prod-
ucts necessary for production of ssDNA. This interference results in a -01
to 100-fold reduction in the phage titer and a level of ss plasmid DNA
particles of about °101 colony forming units (cfu) per milliliter. 1 Phage
mutants that show interference resistance have been isolated. 5,4 These
mutants can increase the yield of ss plasmid by 10-fold and concurrently
G. P. Dotto, V. Enea, and N. D. Zinder, Virology 114, 463 (1981).
2 N. D. Zinder and J. D. Boeke, Gene 19, 1 (1982).
3 D. Mead and B. Kemper, in "Vectors: A Survey of Molecular Cloning Vectors and Their
Uses." Butterworth, Massachusetts, 1986.
4 V. Enea and N. D. Zinder, Virology 122, 222 (1982).
5 A. Levinson, D. Silver, and B. Seed, J. Mol. Appl. Genet. 2, 507 (1984).
Copyright © 1987 by Academic Press, Inc.
METHODS IN ENZYMOLOGY, VOL. 351 All rights of reproduction in any form reserved.
4 SROTCEV ROF GNINOLC DNA ]1[
increase the level of phage by a similar amount. Whether wild-type (wt)
phage or an interference-resistant mutant is used as helper the yield of
plasmid ssDNA is usually about equal to that of the phage, 3 and as the
plasmid size increases the ratio shifts to favor the phage. 5 In order to
increase both the quantitative and qualitative yield of the plasmid ssDNA,
a helper phage, M13KO7, has been constructed that preferentially pack-
ages plasmid DNA over phage DNA. In this chapter, M13KO7 will be
described and its uses discussed.
M13 Biology
Certain aspects of M13 biology and M13 mutants play an important
role in the functioning of M13KO7, so a short review of its biology is
appropriate. 7,6 M13 is a phage that contains a circular ssDNA molecule of
6407 bases packaged in a filamentous virion which is extruded from the
cell without lysis. It can infect only cells having an F pili, to which it binds
for entering the cell. The phage genome consists of 9 genes encoding 01
proteins and contains an intergenic region of 805 bases. The proteins
expressed by the phage are involved in the following processes: I and IV
are involved in phage morphogenesis, III, VI, VII, VIII, and IX are virion
proteins, V is an ssDNA binding protein, X is probably involved in repli-
cation, and II creates a site-specific (+) strand nick within the IG region of
the double-stranded replicative form (RF) of the phage DNA molecule at
which DNA synthesis is initiated.
Phage replication consists of three phases: (1) ss-ds, )2( ds-ds, and (3)
ds-ss. The ss-ds phase is carried out entirely by host enzymes. For
phases 2 and 3, gene II, which encodes both proteins II and X, is required
for initiating DNA synthesis; all other functions necessary for synthesis
are supplied by the host. The DNA synthesis initiated by the action of the
gene II protein (glIp) leads to both the replication of the ds molecule and
the production of the ssDNA that is to be packaged in the mature virion.
The phage is replicated by a rolling circle mechanism that is terminated by
glIp cleaving the displaced (+) strand at the same site and resealing it to
create a circular ssDNA molecule. Early in the phage life cycle this
ssDNA molecule is converted to the ds RF but later in the phage life cycle
gVp binds to the (+) strand, preventing it from being converted to dsDNA
and resulting in it being packaged into viral particles. The assembly of the
virion occurs in the cell membrane where the gVp is replaced by the
6 D. T. Denhardt, D. Dressier, and D. S. Ray (eds.), "The Single-Stranded DNA Phages."
Cold Spring Harbor Lab., Cold Spring Harbor, New York, 1978.
7 N. D. Zinder and K. Horiuchi, Microbiol. Rev. 49, 101 (1985).