Table Of ContentTHE
NUCLEIC ACIDS
Edited by
ERWIN CHARGAFF J. N. DAVIDSON
Department of Biochemistry Department of Biochemistry
Columbia University University of Glasgow
New York, N. Y. Glasgow, Scotland
Volume III
i960
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First Printing, 1960
Second Printing, 1964
PRINTED IN THE UNITED STATES OF AMERICA
Contributors to Volume III
A. N. BELOZERSKY, A. N. Bach Institute of Biochemistry, Academy of
Sciences of the USSR; Biological Faculty of the University of Moscow,
Moscow, USSR
JOHN M. BUCHANAN, Division of Biochemistry, Department of Biology,
Massachusetts Institute of Technology, Cambridge, Massachusetts
GEORGE W. CROSBIE, Department of Biochemistry, The University of
Glasgow, Glasgow, Scotland
F. GROS, Institut Pasteur, Paris, France
R. E. HANDSCHUMACHER, Department of Pharmacology, School of Medi-
cine, Yale University, New Haven, Connecticut
MAHLON B. HOAGLAND, John Collins Warren Laboratories of the Hunting-
ton Memorial Hospital of Harvard University at the Massachusetts Gen-
eral Hospital, Boston, Massachusetts
H. GOBIND KHORANA, British Columbia Research Council, University of
British Columbia, Vancouver, Canada*
L. G. LAJTHA, Radiotherapy Department, The Churchill Hospital, Head-
ington, Oxford, England
C. L. SADRON, University of Strasbourg and The Center of Research on
Macromolecules, Strasbourg, France
HEINZ SCHUSTER, Max-Planck-Institut für Virusforschung, Tübingen,
Germany
D. SHUGAR, Institute of Biochemistry and Biophysics, Academy of Sci-
ences; and State Institute of Hygiene, Warsaw, Poland
ROBERT L. SINSHEIMER, Division of Biology, California Institute of Tech-
nology, Pasadena, California
A. S. SPIRIN, A. N. Bach Institute of Biochemistry, Academy of Sciences
of the USSR; Biological Faculty of the University of Moscow, Moscow,
USSR
A. D. WELCH, Department of Pharmacology, School of Medicine, Yale
University, New Haven, Connecticut
* Present address: Institute for Enzyme Research, The University of Wisconsin,
Madison, Wisconsin.
v
Preface
Since 1955, when the first two volumes of this treatise were published,
knowledge relating to the chemistry and the biological importance of the
nucleic acids has continued its vigorous growth; a progress which, however,
has not been uniform in all directions. After much discussion and deliber-
ation we came to the conclusion that, while an entirely new edition was not
yet justified, a way could be found to prevent the premature obsolescence of
a compendium of the kind offered by us. It was decided to provide what
could be called a "diagonal supplement," i.e., a selection of chapters cutting
across, as it were, the systematic arrangement observed in the preceding
volumes. Care was taken to choose topics that had not received sufficient
emphasis before or that had acquired particular importance since the publi-
cation of the earlier volumes. Moreover, a slight shift in perspectives was
also made easier by the decision to limit contributions to the present volume
to authors who had not collaborated in the preceding ones.
Of the twelve articles presented here, the first six, Chapters 29 to 34,
deal with topics related to Volume I of the parent work, whereas Chapters
35 to 40 are thematically near the subject matter treated in Volume II.
As regards the question of nomenclature and abbreviations, we are aware
of the proposals which have been made by the Nomenclature Commission
of the International Union of Pure and Applied Chemistry, Section of Bio-
logical Chemistry; but until these have been universally accepted we have
felt it best to let each author decide and define the manner best suited to
his purpose.
April, 1960 ERWIN CHARGAFF
J. N. DAVIDSON
Vll
Contents of Volume I
1. Introduction BY J. N. DAVIDSON AND ERWIN CHARGAFF
2. Chemistry of Ribose and Deoxyribose BY W. G. OVEREND AND M. STACEY
3. Chemistry of Purines and Pyrimidines BY AARON BENDICH
4. Chemistry of Nucleosides and Nucleotides BY J. BADDILEY
5. Hydrolysis of Nucleic Acids and Procedures for the Direct Estimation of Purine
and Pyrimidine Fractions by Absorption Spectrophotometry BY HUBERT S.
LORING
6. The Separation of Nucleic Acid Derivatives by Chromatography on Ion-Exchange
Columns BY WALDO E. COHN
7. Separation of Nucleic Acid Components by Chromatography on Filter Paper BY
G. R. WYATT
8. The Electrophoretic Separation of Nucleic Acid Components BY J. D. SMITH
9. Color Reactions of Nucleic Acid Components BY ZACHARIAS DISCHE
10. Isolation and Composition of the Deoxypentose Nucleic Acids and of the Corre-
sponding Nucleoproteins BY ERWIN CHARGAFF
11. Isolation and Composition of the Pentose Nucleic Acids and of the Corresponding
Nucleoproteins BY B. MAGASANIK
12. Evidence on the Nature of the Chemical Bonds in Nucleic Acids BYD.M. BROWN
AND A. R. TODD
13r The Physical Properties of Nucleic Acids BY D. O. JORDAN
14. Optical Properties of Nucleic Acids and Their Components BY G. H. BEAVEN,
E. R. HOLIDAY, AND E. A. JOHNSON
15. Nucleases and Enzymes Attacking Nucleic Acid Components BY G. SCHMIDT
Contents of Volume II
16. The Nucleic Acid Content of Tissues and Cells BY I. LESLIE
17. Cytochemical Techniques for Nucleic Acids BY HEWSON H. SWIFT
18. The Isolation and Composition of Cell Nuclei and Nucleoli BY ALEXANDER L.
DOUNCE
19. The Deoxyribonucleic Acid Content of the Nucleus BY R. VENDRELY
20. Nucleic Acids in Chromosomes and Mitotic Division BY B. THORELL
21. The Cytoplasm BY GEORGE H. HOGEBOOM AND WALTER SCHNEIDER
22. Biosynthesis of Pentoses BY GERTRUDE E. GLOCK
23. Biosynthesis of Purines and Pyrimidines BY PETER REICHARD
24. Biosynthesis of Nucleosides and Nucleotides BY F. SCHLENK
25. Biosynthesis of Nucleic Acids BY G. B. BROWN AND P. M. ROLL
26. The Metabolism of the Nucleic Acids BY R. M. S. SMELLIE
27. The Biological Role of the Deoxypentose Nucleic Acids BY R. D. HOTCHKISS
28. The Biological Role of Pentose Nucleic Acids BY J. BRÄCHET
xiii
Errata, The Nucleic Acids, Vol. I
Page 124. Paragraph 3, line 4 should read: Table I.
Page 135. Center label of formula, line 2 should read: carboxamidine.
Page 138. Paragraph 1, line 10 should read: hydrolysis.
Page 138. Paragraph 3, line 1 should read: ribonucleic.
Page 145. Paragraph 1, line 4 should read: simultaneous.
Page 153. Line 1 should read: 6-glycosylaminopurines.
Page 188. Paragraph 5, line 1 should read: synthesis.
Page 197. Paragraph 2, line 2 should read: leads.
Page 208. For Pallade read: Palade. (Footnote 6, Line 1, and Reference
69.)
Page 208. Line 3 should read: Bounce.
Page 221. Paragraph 3, line 5 should read: orthophosphate.
Page 223. Line 2 should read: inosinic.
Page 231. Paragraph 2, line 11 should read: orthophosphate.
Page 247. Last line of text should read: Lactobacillus.
Page 262. Table IV, last column, last entry should read: 0.214.
Page 274. Last line of text should read: most separations.
Page 453. Formula XI:
I I
c c
/- \ /- \
for H read N
I I
HC HC
\ \
Page 463. Figure legend should read: nucleotide.
Page 509. Table II should read:
Thymidine7—(fourth column): for 240.5 read 245.5
Uridine7—(third column): for 8.5 read 7.4; (fourth column):
for 236.5 read 243; (fifth column): for 4.48 read 5.35.
Page 644. For Paladin read: Paladini.
Page 646. For Rush read: Rusch.
Errata, The Nucleic Acids, Vol. II
Page 63. Reference 58 should read: gamotog&i&se.
Page 65. Paragraph 2, line 6 should read: reaction.
Page 132. Heading 5 should read: Enzymes.
Page 156. Line 3 should read: shows.
Page 168. Paragraph 2, line 7 should read: Kosterlitz.
Page 169. Lines 6 and 12, and Reference 63 should read: Di Stefano.
Page 174. Line 6 should read: Ambystoma.
Page 176. First word should read: Her.
Page 190. Paragraph 4, line 6 should read: chromosome.
Pages 211, 218, 228, 239, and 529. For Harmon read: Harman.
Page 238. Paragraph 2, line 12 should read: hemochromogen.
Page 243. Reference 204 should read: Hogeboom.
Page 350. Paragraph 3, line 3 should read: proved to be ineffective.
Page 364. Paragraph 1, line 12, and Paragraph 2, line 9 should read:
Hammarsten.
Page 512. Paragraph 2, line 7, should read: Halvorson.
Page 515. Paragraph 2, line 12 should read: unusually.
Page 518. Paragraph 2, lines 10 and 16 should read: Zamecnik.
CHAPTER 29
Deoxyribonucleic Acids as Macromolecules
C. L. SADRON
University of Strasbourg and The Center of Research
on Macromolecules, Strasbourg, France
I. Introduction 1
II. A Brief Survey of the General Principles of the Determination of Weight,
Shape, and Dimensions of Large Molecules in Solution 2
1. Hydrodynamical Methods 3
2. Optical Methods 6
III. DNA Particles in Dilute Solutions 15
1. The Effect of Inter- and Intramolecular Interactions: Rigidity of DNA
Particles 16
2. Light Scattering in DNA Solutions 19
3. Hydrodynamical Methods 30
IV. Conclusions 33
I. Introduction
One knows that it is possible through proper means to extract from the
cell nucleus a substance called deoxyribonucleic acid (DNA) which plays
a prominent role in the fundamental processes of life. The extraction is
performed by means of physicochemical operations that can vary, accord-
ing to the authors, either in the principles themselves (Hammarsten, Signer,
and Schwander, Sevag, Butler, etc.), or in minor details (Vendrely,
Pouyet).
The result is a dispersion of the substance in an aqueous solvent of a
given pH at a given concentration in an electrolyte such as NaCl. The
problem then is to describe the dispersed particles as individuals. We shall
see that these particles can be considered macromolecules or sometimes as
aggregates of macromolecules which can be separated into their constit-
uents.
In the case of DNA—as it is in general—the complete knowledge of a
given macromolecule implies two types of notions.
First, we need to know the chemical composition of the substance as
well as the relative position of the atomic groups which it contains.
Second, we have to know the weight as well as the shape, configuration,
and dimensions of the macromolecule. For that purpose we have to use
1
2 C. L. SADRON
rather special means pertaining to the field of macromolecular physical
chemistry. Combining the two types of data one can have in principle a
complete and clear description of the macromolecule.
Of course, this distinction of two classes of parameters is somewhat
schematic and, in practice, the cut will not be sharp between them. In
general, the knowledge of data belonging to one group—the first one for
instance—is quite necessary to establish the data of the second one.
The case of DNA will be a very clear example of this fact. According to
the situation that we have described, we shall in this paper, admit that a
certain number of facts concerning the composition and structure of the
DNA macromolecules are well established and we shall devote all our at-
tention to the second group of parameters, that is, weight, shape, and di-
mensions, that we shall call morphological parameters.
Now it is clear that in a solution as it has been prepared by the biochem-
ist, we have no evidence that the macromolecules are all alike. Heteroge-
neity may exist for the two groups of parameters. Since we have chosen
to treat the second only, we shall have to consider that the solution we
have to deal with is in principle polydispersed relatively to the weight,
shape, and dimensions of the particles—or macromolecules—that it con-
tains.
We then have to consider not only one molecular weight, one shape, and
one dimension, but we have to find out the respective laws of distribution
of these three parameters for the assembly of the macromolecules contained
in a given sample of DNA. This problem, which we have set forth in its
more general terms, is one of the most difficult in macromolecular physical
chemistry, and we shall see that we are still far from a complete and satis-
factory answer.
II. A Brief Survey of the General Principles of the Determination
of Weight, Shape, and Dimensions of Large
Molecules in Solution
Before coming to the special case of DNA it may be useful to give, in a
preliminary chapter, a short summary of the general methods which are
used in the determination of the morphological parameters of large mole-
cules in solution.1 We shall as far as possible avoid any detail that does not
apply here, and we shall keep as close as possible to the information strictly
necessary for a through understanding of the results obtained in the case
of DNA.
The methods of investigation can be usefully divided into two groups:
the so called "hydrodynamical" methods and the "optical" methods.
1 For more details see, for example, C. Sadron, Prog, in Biophys. 3, 237 (1953).
29. DEOXYRIBONUCLEIC ACIDS AS MACROMOLECULES 3
1. HYDRODYNAMICAL METHODS
a. Monodispersed Solutions
Let us first assume that we have to deal with a solution containing only
one type of macromolecule. It is possible then by proper operations to ob-
tain, among many other data, the following ones: the Brownian diffusion
constants of the macromolecules (A for translation, B for rotation); their
velocity v of sedimentation in an external field 7 (produced, for instance,
by ultracentrifugation); the intrinsic viscosity [77] of the solution, which is
the limiting value of (77 — ηο)/η& (where ηο = viscosity of the solvent,
η = viscosity of the solution at the concentration c in grams per milliliter)
when c decreases to zero.
These data are related to the macromolecular parameters in the follow-
ing way:
1. The constants of diffusion obey the general laws
A = kT/f (1)
B = kT/C (2)
where k is the Boltzmann constant, T the absolute temperature of the
solution, / and C the unitary coefficients of the viscous friction respectively
exerted by the solvent on the particle when it moves with a constant
velocity of translation or of rotation along a given axis.
The coefficients / and C do not depend on the molecular weight M of the
particle, but they are obviously functions of its shape and dimensions.
2. When the permanent state is attained, the velocity of sedimentation
in the field of inertia 7 is given by the equation
*V7 = M(l - 7 o)/3l/ (3)
spP
where V is the partial specific volume of the particle, po the density of the
ap
solvent, and 31 the Avogadro number. The sedimentation constant S is
given by S = v/y.
3. The relative increase of viscosity (or specific viscosity), TJ = (η —
8P
TJOVTJO ; is proportional at very large dilutions to the number, c3l/M of par-
ticles per unit of volume. It can be shown that ?7 p = (c9l/ilf) F or, accord-
8
ing to the definitions of [77],
M = mF/M (4)
In these equations F is a factor which depends only on the shape and di-
mensions of the macromolecule.
