Introduction to Ion Beam Biotechnology

302 Pages·2006·6.253 MB·English

by  Yu Zengliang (auth.)

Introduction to Ion Beam Biotechnology
Yu Zengliang
Introduction to Ion Beam
Biotechnology
Translated by Yu Liangdeng Thiraphat Vilaithong
Ian Brown
With 132 illustrations,including 1 color plate.
Yu Zengliang
Key Laboratory of Ion Beam Bioengineering of Chinese Academy of Sciences
Institute of Plasma Physics
Chinese Academy of Sciences
P.O.Box 1126
Hefei 230031
People’s Republic of China
[email protected]
Cover illustration:Instantaneous expression ofthe GUS gene entering rice embryo cells treated
by 30-keV N ions at a dose of2 × 1015N+/cm2.Rice embryo cell on the left is the control;the
embryo cell on the right is due to GUS,the gene transferred cells show blue color.
Library ofCongress Control Number:2005923442
ISBN-10:0-387-25531-1 e-ISBN 0-387-25586-9
ISBN-13:978-0387-25531-6
Printed on acid-free paper.
© 2006 Springer Science+Business Media,Inc.
All rights reserved.This work may not be translated or copied in whole or in part without the
written permission ofthe publisher (Springer Science+Business Media,Inc.,233 Spring Street,
New York,NY 10013,USA),except for briefexcerpts in connection with reviews or scholarly
analysis. Use in connection with any form of information storage and retrieval, electronic
adaptation,computer software,or by similar or dissimilar methodology now known or hereafter
developed is forbidden.
The use in this publication oftrade names,trademarks,service marks and similar terms,even if
they are not identified as such,is not to be taken as an expression ofopinion as to whether or
not they are subject to proprietary rights.
Printed in the United States ofAmerica. (EB)
9 8 7 6 5 4 3 2 1
springeronline.com
To all the researchers who have
concerned themselves with this
new and fascinating field, and
with thanks to 37 unnamed
graduate students
PREFACE
(to the English edition)
Although low-energy ion beam biotechnology has been the subject of active research
in a few countries, particularly China, for over a decade, and impressive
accomplishments in biology and agriculture have been achieved there, the field is new
and has not yet been well recognized by most of the world. At Chiang Mai University we
have known for quite some time that Prof. Yu Zengliang, Director of The Key Laboratory
of Ion Beam Bioengineering, Institute of Plasma Physics, Chinese Academy of Sciences,
was a founder of this new, highly interdisciplinary branch of science, and that he has
carried out research in this field since the late 1980s. Stimulated by Prof. Yu’s
achievements, Thai scientists, joined by Chinese and American colleagues, organized
research in this area at Chiang Mai University for serving economic development in
Thailand. Only in a few short years, we have made great progress. In the laboratory of
Fast Neutron Research Facility, a specialized bioengineering ion beam line has been
installed. Research on both fundamental interactions between ions and biological
organisms and applications to agricultural and horticultural crop mutation breeding and
gene transfer has been carried out. A number of important results have been achieved and
published. Besides having worked independently, the Thai researchers have had the
pleasure of frequent and close academic exchange with Prof. Yu Zengliang and his
colleagues. As work progressed, the need for a text elaborating the fundamentals of low-
energy ion beam biotechnology grew increasingly clear. We recently learned that Prof.
Yu Zengliang had written and published a book in Chinese on the fundamentals of this
fascinating technology – precisely the kind of monograph needed. The idea of translating
Prof. Yu’s book into English was immediately suggested by Prof. Thiraphat Vilaithong,
President of the Thai Institute of Physics, and warmly supported by Prof. Yu Zengliang
himself. The original Chinese edition of the book consists of twelve chapters and an
appendix. In order to reflect more recent developments in research on the technology,
Prof. Yu has added two chapters (Chapter 13 and Chapter 14 of this English edition) as
well as some parts in Section 2.4. of Chapter 2, Section 6.6. of Chapter 6 and Section
11.3. of Chapter 11. Translating Prof. Yu’s book has been a great challenge, as the job
involves aspects of physics, biology, agriculture, chemistry, and more. We needed
assistance and consultation. We would like to sincerely thank those who have made
important contributions to the creation of this English edition of Prof. Yu’s book. They
are
• Prof. Yu Zengliang, for his full support and suggestions for the translation and
kind cooperation and concern;
viii PREFACE (to the English edition)
• Dr. Gordon L. Hiebert, for his complete reading and commenting of the book
manuscript, two times;
• Dr. Xu An and Dr. Hu Zhiwen, for their enthusiastic assistance in coordinating
the work between the Thai and Chinese sides and effective management of the
work in China;
• Fifty-two graduate students, most of whom are Ph.D. candidates, of The Key
Laboratory of Ion Beam Bioengineering, Institute of Plasma Physics, Chinese
Academy of Sciences, for their invaluable assistance in checking the translations
and re-preparing many figures and references;
• Prof. Pimchai Apavajrut, Prof. Somboon Anuntalabhochai, Prof. Adisorn
Krasaechai, Dr. Somjai Sangyuenyongpipat, and Mr. Boonrak Phanchaisri of
Chiang Mai University, for their reading of and commenting on various chapters
of the book manuscript;
• Dr. Liu Ming, for her help in managing relevant material for translation in the
fields of biology and chemistry;
• Personnel at the Department of Physics, Faculty of Science, Chiang Mai
University, for their support and concern;
• The Thailand Research Fund for its support;
• Mr. Aaron Johnson of Springer Science & Business Media for his efforts in
coordinating the publication;
• Our wives for their long-suffering support and patience.
Yu Liangdeng
Thiraphat Vilaithong
Ian Brown
June 2004
Chiang Mai, Thailand
PREFACE
(from the Chinese edition)
In the mid-1980’s, encouraged by the successful development of ion implantation
modification of material surfaces, the author made attempts to apply ion implantation
techniques to the improvement of agricultural crop varieties. At that time the author was
completely a layman in the area of genetic modification and thus early experiments met
with only partial success. Subsequently, Prof. Wang Xuedong and Prof. Wu Yuejin of the
Anhui Academy of Agriculture were invited to join the research work, and in 1986,
biological effects of ion implantation on rice were discovered. Since then ion
implantation as a new tool for genetic modification has been applied to the breeding of
crops and microbes. In 1988, the author discovered the etching effect of ion beams on
cells and proposed the idea of ion beam processing of cells for gene transfer. Through the
independent research of three Ph.D. students, new varieties of gene-transferred rice were
developed.
Energetic ion implantation of complex biological materials exists in nature. There
are always some energetic ions in the environment. Some of these are implanted into
biological cells, and affect the evolution of life and the health of human beings. In the
past century in particular, mankind's conquest of space has included long journeys to the
moon, and a trip to Mars may not remain just a scientific fantasy. It will become a long-
term research field for scientists to simulate the behavior of energetic charged particles
and to study their effects on human health. The ion implantation technique itself is
relatively simple. We can closely examine radiation damage to organisms due to
implanted ion deposition in cells, as well as the deposited ions themselves. Thus, studies
of the interaction between implanted ions and complex biological systems have attracted
significant interest.
The practice of ion beam genetic modification necessitates study of mechanisms.
This is indeed a difficult subject. Starting from the moment the ions are implanted to the
final biological effects, the timescales involved span from 10-19 to 109 seconds and the
relevant spatial dimensions scale from microbiological damage to macro-property
changes; hence the effects vary tremendously. To understand all the processes in such
broad time and space extremes is not yet possible with our present knowledge and
technological abilities. Even with studies of the primary physical processes, the extreme
complexity of the ion-organism system makes attempts to establish physical models for
the ion-organism interaction very difficult.
In 1989, the author published papers proposing that three factors affected the
interaction between implanted ions and organisms. These are an energy deposition effect,
a mass deposition effect, and a charging effect. This proposal appealed to both physicists
x PREFACE (Chinese edition)
and biologists. In the 2nd National Conference on Ion Implantation Effects on Biology in
1993, three American experts were invited to join Chinese experts. It was at this
conference where the participants and researchers from the Anhui Science and
Technology Press conceived of creating a book that would reflect current research
achievements and future development directions in this new field. The book was finally
completed in three years through an intermittent writing effort. Some of the opinions put
forward in the book have been supported by experiments, but some still remain
speculative. The author’s purpose was to “attract jade by tossing a brick”, aiming at
opening discussions on the subject by physicists and biologists working in the field so
that mistakes in the book could be corrected and an improved theoretical system
established. Thus the title of this book is headed “Introduction”.
Research on low-energy ion interaction with biological materials has been
significantly supported by the National Planning Committee, National Foundation of
Natural Sciences, Chinese Academy of Sciences, and the Anhui Provincial Planning
Committee. This work has become a new growing discipline with an independent
research basis and wide applications to genetic modification in both agriculture and
fermentation industries. During the period of the 7th National Five Year Plan for
Economic Development, the initiation of Director's funds from the Mathematics-Physics
Division of the National Foundation of Natural Sciences as well as critical support from
the National Planning Committee and the Anhui Provincial Committee of Sciences
played a catalytic role in promoting the discipline.
In the development of this field, more than thirty of my graduate students have made
significant contributions. Research of Ph.D. students Shao Chunlin, Huang Weidong,
Han Jianwei, Wu Yuejin, Yang Jianbo, Cui Hairei, Cheng Beijiu, and Deng Jianguo have
provided this book with rich and solid data. The researchers in the Institute of Plasma
Physics, Chinese Academy of Sciences, have offered much assistance in the writing of
the book. Ms. Feng Huiyun and Ms. Liu Junhong worked hard on the language. I would
like to express my sincere appreciation to them all.
Last, but not least, I wish to thank Mrs. Kang Ming. She introduced Prof. Liang
Yude, a famous senior biologist, for later collaborations with biologists. My 10-year
study, from physics into biology, has been supported by Prof. Xu Guanren, Prof. Huo
Yuping and many other biologists and physicists. If it is said that the ten-year work has
achieved something, this success should also be attributed to these people.
Yu Zengliang
CONTENTS
PREFACE (to the English edition) vii
PREFACE (from the Chinese edition) ix
NOTATIONS OFTEN USED xvii
1. GENERAL IDEAS ABOUT IONS ..…………………………...………… 1
1.1. PHYSICAL PROPERTIES OF IONS ………………….………… 1
1.2. FORMATION AND RECOMBINATION OF IONS …….……… 4
1.3. ION POLARIZATION AND GLOMERATION ………….…….. 4
1.4. BIOLOGICAL EFFECTS OF IONS …………………………….. 6
1.5. ION IMPLANTATION AND GENETIC MODIFICATION ……. 8
2. PRODUCTION AND ACCELERATION OF IONS …………………… 11
2.1. EQUIPMENT REQUIREMENTS FOR ION IMPLANTATION
OF BIOLOGICAL SAMPLES …………………………………… 11
2.2. BASIC BEAM LINE STRUCTURE ……………………………... 12
2.2.1. Ion Source …………………………………………….. 13
2.2.2. Analysis System ………………………………………. 16
2.2.3. Accelerating and Focusing System …………………… 17
2.2.4. Target Chamber and Vacuum System ………………… 19
2.3. MEASUREMENT OF BEAM CURRENT ………………………. 20
2.4. SINGLE-ION MICROBEAM FACILITY ……………….………. 23
3. FUNDAMENTALS OF ION IMPLANTATION ……………….………. 31
3.1. INTERACTIONS OF ENERGETIC IONS WITH SOLID
SURFACES ………………………………………………………. 31
3.1.1. Secondary Electron Emission ………………………… 31
3.1.2. Ion Sputtering …………………………………………. 33
3.1.3. X-Ray Emission ………………………………………. 35
3.2. ION IMPLANTATION RANGE …………………………………. 36
3.2.1. Energy Loss and Range ……………………….………. 36
3.2.2. Estimation of The Range ……………………………… 38
3.2.3. Standard Deviation of The Range …………….………. 40
3.2.4. Distribution of Implanted Ion in Non-Crystalline
Targets ………………………………………………… 41
3.2.5. Channeling Effects ……………………………………. 42
xii CONTENTS
3.3. RADIATION DAMAGE …………………………………………. 44
3.3.1. Energy Deposition of Ions in Solids ………………….. 44
3.3.2. Radiation Damage due to Ion Implantation …………... 47
3.4. MONTE-CARLO CALCULATION OF ION IMPLANTATION .. 48
3.4.1. Ion Trajectory …………………………………………. 48
3.4.2. Distribution of Implanted Ions ………………………... 49
3.4.3. Displaced Atoms ……………………………………… 49
3.5. CHEMICAL REACTIONS AND NUCLEAR REACTIONS……. 50
4. INTERACTIONS BETWEEN ENERGETIC IONS AND
BIOLOGICAL ORGANISMS …………………………………… 55
4.1. DESCRIPTION OF TARGET STRUCTURE AND
COMPOSITION ………………………………………………….. 56
4.2. STATE OF THE TARGET DURING ION IMPLANTATION.….. 58
4.2.1. Seeds ………………………………………………….. 58
4.2.2. Cells and Calluses …………………………….………. 60
4.3. CHARGE EXCHANGE EFFECTS ………………………………. 62
4.4. SURFACE ETCHING AND VOLUME DAMAGE ……………... 65
4.5. PRODUCTION OF FREE RADICALS ………………….………. 68
4.6. MASS DEPOSITION REACTIONS ……………………………... 72
4.6.1. Free Radical Reactions ………………………………... 72
4.6.2. Acid-Alkali Balance …………………………………... 73
4.6.3. Mass Deposition Reactions …………………………… 74
4.7. ENERGY LOSS FEATURES …………………………….………. 75
4.8. DOSE AND FLUENCE …………………………………………... 83
4.8.1. Radiation Dose ………………………………………... 83
4.8.2. Linear Energy Transfer ……………………….………. 83
4.8.3. Particle Fluence ……………………………….………. 84
4.8.4. Particle Flux Density ………………………….………. 84
4.8.5. Radiation Energy Flux Density ……………….………. 84
5. REACTION PROCESSES OF ION IMPLANTED BIOLOGICAL
SMALL MOLECULES …………………………………………... 87
5.1. RADIATION DAMAGE TO BIOLOGICAL SMALL
MOLECULES IN SOLUTION ………………………...…………. 87
5.2. DAMAGE TO ION-IMPLANTED BIOLOGICAL SMALL
MOLECULES …………………………………………….………. 89
5.2.1. Structural Damage …………………………….………. 89
5.2.2. Compositional Changes ………………………………. 93
5.2.3. Production of Free Radicals …………………………... 96
5.3. ION DEPOSITION REACTION PROCESSES ………….………. 96
5.4. PHYSICOCHEMICAL REPAIR ………………...……….………. 102
6. DAMAGE AND REPAIR OF ION-IMPLANTED DNA ..……………... 107
6.1. PLASMID DNA NORMALLY USED IN ION IMPLANTATION 108
6.1.1. pBR …………………………………………………. 109
322
6.1.2. M …………………………………………….………. 110
13
6.1.3. pUC …………………………………………………… 112
6.2. BREAKS OF DNA SINGLE STRANDS AND DOUBLE
STRANDS……………………………………………….………… 112