Nucleic Acids: The Vectors of Life: Proceedings of the Sixteenth Jerusalem Symposium on Quantum Chemistry and Biochemistry Held in Jerusalem, Israel, 2–5 May 1983

566 Pages·1983·24.61 MB·English

by  Richard E. Dickerson (auth.)

NUCLEIC ACIDS: THE VECTORS OF LIFE
1 tiL J t,k u ~ALLMJ\ M£'G~ 1A uN
(,(rANTIIM ,'HI'M£STR) '\l\in RrOCHEMISTRY
PUblished by the israel Academy of ScienL'es and Humanities,
distributed by Academic Press (N. Y.;,
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VOLUME 10
NlJ(~l-JEIC A(~IDS:
THE VECTORS OF LIFE
PROCEi: DING:: OF rH\', '" 'l.i'l: Hnil j f:.K (ihA Lt, M 5 'tMP'-'i~ljjM 'Ai
QUANTUM CHEMISTRY AND BIOCHEMISTRY HELD IN
JERIJSAi EM, iSRUL,.2 -5 MAY 1983
Edited b},
BlRNARD PULLMAN
Universite Pierre er Marie Curie (Paris VI)
instituc de Biologie Physico·I..:'himique
(f'ondation Edmond de Rothschild) Paris, France
and
JOSHUA JORTNER
Department of Chemistry
fel-Aviv University, Tel-Aviv, [srael
D. REIDEL PUBLISHING COMPANY
A MEMBER OF THE KLUWER ACADEMIC PUBLISHERS GROUP
OORDRECHT I BOSTON I LANCASTER
library of Congress Cataloging in Publication Data
Jerusalem SymposIUm on Quantum Chemistry and Biochemistry
(l6th: 1983)
Nucleic acids.
(The Jerusalem symposia on quantum chemistry and biochemistry;
v.16)
Includes index.
1. Nucleic acids-Congresses. I. Pullman, Bernard, 1919-
II. Jortner, Joshua. III. Title. IV. Series.
QP620.J46 1983 574.87'328 83-16055
ISBN -13 :978-94-009-7227-8 e-ISBN -13 :978-94-009-7225-4
DOl: 10.1007/978-94-009-7225-4
Published by D. Reidel Publishing Company,
P.O. Box 17,3300 AA Dordrecht, Holland.
Sold and distributed in the U.S.A. and Canada
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All Righ ts Reserved
~ 1983 by D. Reidel Publishing Company, Dordrecht, Holland
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TABLE OF CONTENTS
PREFACE ix
R. E. DICKERSON / Base Sequence, HeLix Structure and
Intrinsic Information Readout in DNA 1
S. ARNOTT, R. CHANDRASEKARAN, L. C. PUIGJANER and J. K. WALKER /
New WrinkLes on DNA 17
O. KENNARD / X-Ray AnaLysis of OLigonucLeotides and the C.hanging
Concept of DNA Structure 33
M. LENG, B. HARTMANN, B. MALFOY, J. PILET and M. PTAK /
DynamicStructureof Z-DNA 49
F. QUADRIFOGLIO, G. MANZINI, N. YATHINDRA and R. CREA /
ReLative StabiLity of Band Z Structures in 01igo
deoxynucLeotides with Different ALternating Base
Sequence and Length 61
A. PULLMAN, B. PULLMAN and R. LAVERY /ELectrostatic MoLecuLar
PotentiaL versus FieLd in NucLeic Acids and their
Constituents 75
T. M. JOVIN, L. P. McINTOSH, D. A. ZARLING, D. J. ARNDT-JOVIN,
M. ROBERT-NICOUD and J. H. VAN DE SANDE I Probin~ for
and with Left-handed DNA: PoLy rd(A-br5C).d(G-T)} A
Member of New FamiLy of Z-Forming DNAs 89
~
V. SASISEKHARAN, M. BANSAL and G. GUPTA / Structures of DNA:
A Case Study of Right and Left Handed DupLex in the
B-Form 101
D. R. KEARNS, P. A. MIRAU, N. ASSA-MUNT and R. W. BEHLING /
Two DimensionaL NMR Investigation of the StructuraL
Propert i es of DNAS 113
J. S. COHEN, Chi-wan CHEN and R. H. KNOP / Secondary Structure
of DNA in SoLution by NMR Methods 127
D. B. DAVIES / Dependence of OLigonucLeotide ConformationaL
Properties on Sugar Ring and Base-sequence.
1H and 13C. N.M.R. Studies 141
vi TABLE OF CONTENH
L L, JAMES, P. BENDEL, ,} L JAMES, ,', W" KEEPERS, p, Ac
KOLLMAN, A. LAPIDOT J. MURPHY-BOESCH and J. E,
TAYLOR / Conforl'l1at'ir!nal Fi,?J!ihil,ih Of Nucle;', Acids 1'):1
H. SHINDO, U. MATSUMOTO, H, AkUTSU and 1 FUJIWARA! 31p NMR
Studies or the Structur~ and Dynamics of DNA in
Hydrated Fi bers 16'~
N. C. SEEMAN and N. R. KALLENBACH / Nucleic Acid Junctions:
The Tensors of Life? ]83
P.O.P. TS'O, D. M. CHENG, D. FRECHET and L. S. KAN / NMR
Studies on Short HeLices 20)
W. K. OLSON / Theoretical Probes of NucLeic Acid Conformation 217
N. YATHINDRA and R. MALATHI / A Novel Conformational EquivaLence
between the HeminucLeotide Blocks of the Nucleotide Repeat.
Its ImpLications in Conformation Analysis of NucLeic
Acids 229
A. BANERJEE and H. M. SOBELL ! Presence of Nonlinear
Excitations 1n DNA Structure and Their Relationshin
to DNA Premelting and to Druq Intercalation ' 253
U. HEINEMANN and W. SAENGER / RibonuL:ease T,: Mechanism of
Specific Guanine Recognition and RNA HydroLysis 265
D. M. CROTHERS, S. D. LEVENE and Hen-Ming WU I DNA Bending
and Protein-DNA Interactions 277
D. PORSCHKE / Dynamics and Specificity of Protein-nucleic
Acid Interactions in Model Systems 283
C. CAZENAVE, M. CHABBERT, J-J. TOUU1E and C. HELENE / The recA
Gene Product from E. CoLLa Binding to Single-stranded
and DoubLe-stranded DNA 295
T. MONTENAY-GARESTIER, M. TAKASUGI and T. LE DOAN I FLuorescence
Decay Studies of Peptide-nucLeic Acid CompLexes 30S
] PORTUGAL, J. AYMAtU, r1. FORNELLS, J.A. SUBIRANA, PONS and
~1.
L GIRALT ;' Alteration of the B Form of DNA bv Basic
Peptides . 317
R. OSTERBERG, D. PERSSON and P. ELIAS / The Interaction of Certain
Nutleic Acids with Proteins and Metal Ions in Solution
~3J
G FELSr:NP:I.I!, J D. McGHF:F.:: f\lJCKOL ;:jnd !I. [{AIJ I Cl,r'omatin
Higher Order St!'lJ[ turF "lnd Gene f:xprpssiop 34:
TARLe: OF CONTENT<: vii
F. CRAr~f:I~ and W. FREIST i Prot~i"-nuc!.eir: Acid Inter·action. The
AmirlOacvlatiof'1 of T-RNA and its Evolutionary Aspect 353
H. EISENBERG; Conformatiun of DNA. T~e Nucleosome and
Chromatin. Hydrat iof'1 u{ D~h 365
E. N. TRIFONOV ! NucLeosoma I DNA St ruct ure 373
J. P. EBEL, C. BRANLAN1,. P. CARBON, B. EHRESr·1ANN, L. EHRESMANN,
A. KROL and P. STIEGLER / Sequence and Secondary
Structure Conservatior in Ribosomal RNAs in the
Course of Evolution 387
D. MORAS, A. C. DOCK, P. DUMAS, E. WESTHOF, P. ROMBY and
R. GIEG€ / The Versatile Transfer RNA MoLecuLe:
CrystaLLography of Yeast tRNAAsp 403
R. GIEGE, P. ROMBY, C. FLORENTZ, J. P. EBEL, P. DUMAS,
E. WESTHOF and D. MORAS / SoLution Conformation
of tRNAs: Correlation with Crystal Structures 415
c. W. HILBERS, A. HEERSCHAP, J.A.L.l. Walters and C.A.G.
HAASNOOT / NMR Studies of the Structure of Yeast
tRNAPhe in Solution and of its CompLex with the
Elon~atior Factor Tu from B. Stearothermophilus 427
P. M. KAISER Electronic Interactions in RNA Constituents and
I
thei Effects on Helical Conformations 443
v
G GUPTA and R. H. SARMA / Correlated InternaL Motions in
Left-handed DNA DoubLe Helices: Z-B Transition
Driver by Drug Bindina 457
J. R. RUBIN/ M. SABAT and M. SUNDARALINGAM / The Binding of
the Carcinostatic Drugs Cis- [Pt<NH)3)2Cl2] and
[Ru(NH3)5Cl]Cl2 with Yeast Transfer RNAPhe. Absence
of Binding to Watson-Crick Base Pairs 471
R. REIN and M. SHIBATA I Structures and Mechanisms of Mispairing
in a HeLical Environmef'1t including Sequence Effect 479
S. NEIDLE, R. KURODA, A. AGGARWAL and S. A. ISLAM / Drug Nucleic
Acid Interactions: Proflavine Intercalation into
Double-helici'll, Fr-agments of RNA and DNA 495
F. B. HOWARD and H. TODD MILES! Consequences of Substituting
2NHZA for A in Synthetil DNA'S 511
viii TABLE OF CONTENTS
P. S. MILLER, C. H. AGRIS, K. R. BLAKE, A. MURAKAMI, S. A. SPITZ
P. M. REDDY and P.O.P. TS'O / Nonionic OLigo
nucLeotide AnaLogs as new TooLs for Studies on the
Structure and Function of NucLeic Acids Inside
Living CeLLs 521
H.-D. LUDEMANN, G. KNOPP, F. HANSSKE and M.J. ROBINS / SoLution
ConformationaL Characteristics of ChemicaLLy Modified
Purine (~) Pentosides 537
H. FOLLMANN / DeoxyribonucLeotide Biosynthesis: A CriticaL
Process for Life 545
IUPAC-IUB Joint Commission on BiochemicaL NomencLature (JCBN)
Abbrevations and SymboLs for the Description of Conformations
of PoLynucleotide Chains 559
INDEX OF SUBJECTS 567
PREFACE
The 16th Jerusalem Symposium debated on one of the most im
portant subjects of modern molecular biology: the nucleic acids. It
continued the tradition of gathering the most distinguished experts
in the field.
Placed under the auspices of the of Sciences
Isra~l Acade~y
and Humanities and the Hebrew University of Jerusalem it was sponsored
by the Institut de Biologie Physico-Chimique (Fondation Edmond de
Rothschild) of Paris and the Foundation for Cancer Research
Na~ional
of Bethesda, U.S.A. We wish to express our deep thanks to the Baron
Edmond de Rothschild for his continuous generosity which guarantees
the perenniality of these meetings and to the authorities of the
National Foundation for Cancer Research, in particular Mrs Tamara
Salisbury and Dr. Franklin Salisbury for having joined hands with us
in this venture. We wish also to express our to the adminis
gra~itude
trative staff of the Academy and in particular to Mrs Avigail
Isra~l
Hyam for the efficiency and excellency of the local arrangements.
Bernard Pullman
,Joshua Jortner
B. Pullman and J. Jortner (eds.) , ,Vucleic Acids the Vectors of Life, /-/5.
© 1983 by D. Reidel PuhlisliinK Company.
BASE SEQUENCE. I-!E.LJY ":'TRIJCTIIR!: I\NI' INTRIN<:l( TNFORM.LH]IlN RE.I\DOUT TN DNA
Richard E. Dickerson
8iol')gy Tnst.it.ute
~1olecular
University of California, Los Angeles
Los Angeles. California 90U24, U S.A.
The binding of repressors and similar recognition proteins to specific
DNA sequences involves intrinsic physical and chemic3l properties of
both DNA and protein. most probably a specific pattern of hydrogen
bonds. Sinqle crystal analyses of double-helical DNA oliqomers have
revealed predictable sequence-dependent local variations in helix qeo
metry, of a type that. coul d contY'i bute to the spec ifi city of the
intrinsic readout process.
i~formation
The l'eaduut Of inf '}l'll3+ion f"um hasp sequence in DNA and its
translation into polYpeptide sequence is an extrinsic process, in the
sense that it dors not depend on immedi3te or
~n physi~al shemi~al
similarity between t.he structure of the triolet codons of DNA and the
amino acids of the qrowinq protein chain. A quarter Of a century Of
effort. ha s f il il ed t,.' i'roduC" a 111 a!J::" i b1 e i rlf.ri IE, i '_ conned. i on between
codons a~d polypenti1e, and the translation system works only hy virtue
of a hiqhlv evolved battery Of messenqel s. transfer RNA molecules,
energy sources, and enzymes' In contrast, the readout of base sequence
information by a repressor molecule when it binds selectively to its
operator site is an intrinsic process, relying on a matching Of size,
shape, and (presumably) hydroqen-bonding ~roperties of the DNA and
protein.
What is the structural basis for this information read
intri~si(
out process? One obvious sugqestion is a matching of hydrogen bond
donors and acceptrJrs on the edqes Of ba::,e pair::, i rt rnajor and mincl
grooves Of the DNA, with hydroqen-bonrlinq side chains on the protein
(Seeman et al .• 1976). I\s f iqure I shows. the major groove edge of an
A·T basewrF exhibit.,; the pattern: '3cceptor-donor .. accI"ptor, and t.his
same pattern with minor rositional shifts i; if the basp pair
retai~ed
is tur~ed lround: 1 ~ In contr~~t, the nt3jor qroove edge of ~ G·I
ba se pa iI' ha s t he a symmet.l'i c r1a !:tern: il r:cert!JI--aueDt.r:>r-donot·, "nd. th i ;
pattern is reversed if the hase nair is turned backward. e·G
~nv
recoqnition protein that intoracted ~ith thp ma~')r ar00VP would ;nG ~