Nonisotopic Probing, Blotting, and Sequencing (eBook)

Larry J. Kricka (Herausgeber)

eBook Download: PDF | EPUB

1995 | 2. Auflage
518 Seiten
Elsevier Reference Monographs (Verlag)
978-0-08-053766-5 (ISBN)

Infos

Since the publication of Nonistopic DNA Probe Techniques in 1992, the move away from radioactive materials for research and diagnostics has continued. This is due in part to public awareness of the hazards of radioactive waste and laws making radioactive disposal more difficult and costly and to improvement in both the sensitivity and convenience of nonisotopic techniques. Several new nonisotopic techniques have been developed and substantial improvements made to existing nonisotopic methods since 1992, and these are now included in Nonisotopic Probing, Blotting, and Sequencing. Nonisotopic Probing, Blotting, and Sequencing is an updated, expanded edition of the bestseller, Nonisotopic DNA Probe Techniques. It has been thoroughly revised to include the latest improvements in nonisotopic tagging techniques for macromolecules. Like its predecessor, it enables researchers to select the best nonisotopic method for their needs and maximize success by following its straightforward protocols. - Provides strategies and detailed procedures for labeling, blotting, and probing specific nucleic acid sequences and, with this edition, protein molecules - Gives protocols for nonisotopic DNA sequencing - new in this edition - Gives extensive, practical information - Presents background information for each method - Provides expert accounts from the inventor or developer of each method - Contains seven entirely new chapters - Covers all major types of nonisotopic procedures for labeling and detection

Inhalt

Front Cover 1
Nonisotopic Probing, Blotting, and Sequencing 4
Copyright Page 5
Contents 6
Contributors 12
Preface to the First Edition 16
Preface to the Second Edition 18
PART ONE: Introduction 20
Chapter 1. Labels, Labeling, Analytical Strategies, and Applications 22
I. Introduction 22
II. Nucleic Acid Hybridization and Blotting 25
III. Protein Blotting 42
IV. Patents 42
V. Conclusions 45
References 46
Chapter 2. Methods for Nonradioactive Labeling of Nucleic Acids 60
I. Overview 61
II. Methods for Enzymatic Labeling 66
III. Methods for Chemical Labeling 81
IV. Methods for Chemical Labeling of DNA, RNA, and Oligodeoxynucleotides with Marker Enzymes 95
V. Overview of Factors Influencing Hybridization 98
VI. Overview of Detection Systems 102
References 112
PART TWO: Detection Methods 130
Chapter 3. Detection of Alkaline Phosphatase Labels by Time-Resolved Fluorescence 132
I. Introduction 132
II. Materials 135
III. Procedures 140
References 147
Chapter 4. Detection of Alkaline Phosphatase by Bioluminescence 150
I. Introduction 150
II. Materials 151
III. Procedures 154
IV. Conclusions 160
References 161
Chapter 5. Detection of DNA on Membranes with Alkaline Phosphatase-Labeled Probes and Chemiluminescent CSPD® Substrate 164
I. Introduction 165
II. General Southern Blotting Procedure with Chemiluminescence 165
III. Two-step Hybridization Southern Blotting Procedure—Detection of Single-Copy Genes 173
IV. Troubleshooting and Comments 181
References 182
Chapter 6. Detection of Alkaline Phosphatase by Colorimetry 184
I. Introduction 184
II. Labeling and Detection Strategies 185
III. Hybridization of Biotinylated Probes 188
IV. Detection of Biotinylated Probes 190
V. In Situ Hybridization 192
VI. Conclusions 200
References 201
Chapter 7. Detection of Alkaline Phosphatase by Chemiluminescence Using NADP, Ascorbate, and Indolyl Phosphates 204
I. Introduction 204
II. Materials 208
III. Procedures 208
IV. Discussion 211
References 212
Chapter 8. Detection of Horseradish Peroxidase by Enhanced Chemiluminescence 214
I. Introduction 214
II. Materials 221
III. Procedures 222
References 233
Chapter 9. Detection of Horseradish Peroxidase by Colorimetry 236
I. Introduction 236
II. Materials 242
III. Procedures 243
IV. Conclusions 252
References 252
Chapter 10. Detection of Glucose-6-Phosphate Dehydrogenase by Bioluminescence 256
I. Introduction 256
II. Materials 258
III. Procedures 265
IV. Conclusions 278
References 278
Chapter 11. Detection of Xanthine Oxidase by Enhanced Chemiluminescence 280
I. Introduction 280
II. Materials 282
III. Procedures 283
IV. Conclusions 287
References 288
Chapter 12. Electrochemiluminescent Detection of PCR-Derived Nucleic Acids 290
I. Introduction 290
II. Materials 291
III. Procedures 294
IV. Examples 295
V. Troubleshooting 299
References 301
Chapter 13. Detection of Phosphors by Phosphorescence 304
I. Introduction 304
II. Materials 310
III. Procedures 313
References 323
Chapter 14. Detection of Europium Cryptates by Time-Resolved Fluorescence 326
I. Introduction 326
II. Materials 329
III. Procedures 336
References 346
Chapter 15. Detection of Lanthanide Chelates by Time-Resolved Fluorescence 350
I. Introduction 351
II. Indirect Labeling 351
III. Chemical Europium Labeling of DNA Probes 359
IV. Enzymatic Europium Labeling of DNA Probes 367
V. Europium-Labeled Oligonucleotides 369
VI. Detection of Mutations Using Lanthanide-Labeled Oligonucleotides 382
References 393
Chapter 16. Detection of Lanthanide Chelates and Multiple Labeling Strategies Based on Time-Resolved Fluorescence 396
I. Introduction 396
II. Materials 399
III. Procedures 401
References 408
Chapter 17. Detection of Acridinium Esters by Chemiluminescence 410
I. Introduction 411
II. Materials 422
III. Procedures 425
References 443
Chapter 18. Detection of Energy Transfer and Fluorescence Quenching 448
I. Introduction 449
II. Materials 467
III. Procedures 477
References 489
PART THREE: DNA Sequencing 492
Chapter 19. DNA Sequencing by Nonisotopic Methods 494
I. Introduction 494
II. Automated Fluorescent Detection of DNA Sequences 495
III. Manual Nonisotopic Detection of DNA Sequences 497
IV. Future Developments in Nonisotopic DNA Sequencing 508
V. Conclusions 509
References 509
Chapter 20. Chemiluminescent DNA Sequencing with 1,2-Dioxetanes 512
I. Introduction 513
II. Chemiluminscent DNA Sequencing Procedure Using Biotinylated Primers 515
III. Detection of Biotinylated DNA Sequencing Reactions with Streptavidin and Biotinylated Alkaline Phosphatase 523
IV. Chemiluminescent DNA Sequencing with Hapten-Labeling Primers and Detection with Antibody-Alkaline Phosphatase Conjugates 525
V. Instrumentation 525
VI. Troubleshooting 527
VII. Conclusions 529
References 530
Index 532
Color Plate Section 538

Textauszug

1

Labels, Labeling, Analytical Strategies, and Applications

Larry J. Kricka    Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104

I. Introduction

II. Nucleic Acid Hybridization and Blotting

A. Labels

B. Labeling Procedures

C. Detection of Labels and Nucleic Acid Hybridization Sensitivity

1. Detection Techniques

2. Detection of Nonisotopic Labels

3. Analytical Strategies

III Protein Blotting

IV Patents

V. ConclusionsReference

I INTRODUCTION

Nucleic acid hybridization tests for the detection of specific DNA and RNA sequences and protein blotting assays are now extensively used in research and routine laboratories (Diamandis, 1990; Leary and Ruth, 1989; Matthews and Kricka, 1988; Pollard-Knight, 1991; Rapley and Walker, 1993; Wenham, 1992). These assays have diverse applications in medicine and forensics, and some representative examples of these applications are listed in Table I. Labeled nucleic acid probes are utilized in a variety of assay formats including dot blots, Southern blots (Southern, 1975), Northern blot (Alwine et al., 1977), in situ hybridization, plaque hybridization, and colony hybridization. Western blotting (Burnette, 1981) has become the most prevalent type of protein blotting assay procedure (Table II). An important aspect of these assays is the choice of the substance used to label an assay component and the label detection method. As yet there is no consensus on which substance is the ideal label for detecting either nucleic acids or proteins in the various assay formats. The first assays used a radioactive phosphorus-32 label. However, this label has the major disadvantage of a relatively short half-life (14.2 day) (cf. iodine- 125 used in immunoassay has a half-life of 60 day). Thus nucleic acid hybridization probes have a very short shelf-life. This has placed severe limitations on the routine use and commercialization of probe tests; hence, there are extensive efforts to develop and implement alternatives to the radioactive phosphorus-32 label. Many different substances have been tested as nonisotopic replacements for phosphorus-32, and subsequent chapters of this book provide background and practical details of the application of various nonisotopic labels.

Table I

Applications of Probing and Blotting Assays

Nucleic Acids

Arteriosclerosis

Williams (1985)

Cell line authentication

Thacker et al. (1988)

Forensics

Budowle et al. (1990); Cawood (1989); Thornton (1989)

Blood stains

Gill et al. (1985)

Inherited disorders

Dawson (1990); Ropers (1987)

α1-Antitrypsin deficiency

Andresen et al. (1992); Kalsheker(1993); Storstein et al. (1992)

Becker muscular dystrophy

Prior (1993)

Congenital adrenal hyperplasia

Strachan et al. (1987)

Cystic fibrosis

Kerem et al. (1989); Riordan et al. (1989)

Duchenne muscular dystrophy

Kunkel et al. (1989)

Fragile X syndrome

Fujimura (1992)

Phenylketonuria

DiLella et al. (1986); Woo et al. (1983)

Sickle cell anemia

Saiki et al. (1985)

Thalassemia

Old (1993)

Microbiology

Buck (1989); McGowan (1989); Wolfe (1988)

Chlamydia trachomatis

Carpenter et al. (1993)

Clostridium dificile

Wren et al. (1990)

E. coli

Miller et al. (1988)

Legionella

Wilkinson et al. (1986)

Listeria monocytogenes

Emond et al. (1993)

Mycoplasma pneumoniae

Dular et al. (1988)

Neisseria gonorrhoeae

Sanchez-Pescador et al. (1988)

Oncology

Knudson (1986)

BCR/abl gene rearrangement (chronic myelogenous leukemia)

Crisan (1993)

Pinkel (1993)

Bladder cancer

Sidransky (1993)

B/T cell gene rearrangement (lymphoproliferative disease)

Knowles et al. (1987)

Gastrointestinal cancer

Chen et al. (1993)

Neu oncogene

Slamon et al. (1987)

Papillomavirus (cervical cancer)

Carr(1993)

Parasitology

Plasmodium faliciparum

McLaughlin et al. (1993)

Paternity testing

Odelberg et al. (1988)

Transplantation

HLA typing

Erlich et al. (1986)

Virology

Landry (1990)

Cytomegalovirus

Spector and Spector (1985)

HBV	Akar et al. (1992)

HCV	Urdea (1993)

HIV	Devlin et al. (1993); Findlay (1993); Findlay et al. (1993); Malek et al. (1992); Rapier et al. (1993); Urdea (1993)

Rotavirus

Flores et al. (1983)

Proteins

Inherited disorders

Muscular dystrophy (dystrophin)

Chamberlain (1993)

Oncology

ras proto-oncogene protein p21

Jones et al. (1991)

Parasitology

Giardia intestinalis

Smith and Campbell (1991)

Toxicology

Isometamidium-binding proteins

Smith et al. (1991b)

Virology

HIV-1 (specific antibodies)

Centers for Disease Control (1989)

Table II

Probing and Blotting Assay Procedures

Blotting procedures

Sample

Labeled detection reagent

Colony

bacteria (nucleic acid or protein)

nucleic acid or antibody

Dot

nucleic acid or protein

nucleic acid or antibody

Eastern

protein a

antibody

Northern

RNA

RNA

North-Western

protein

RNA

Southern

DNA

DNA

Western

Protein

antibody

South-Western

protein

DNA

a Separated on an isoelectric focusing gel.

II NUCLEIC ACID HYBRIDIZATION AND BLOTTING

A Labels

The majority of the substances used as labels for nucleic acids have been tested previously in immunoassay. Nonisotopic labels have been the focus of development because of the limitations of radioactive labels such as phosphorus-32...

Produkt-Details

• Erscheint lt. Verlag: 1.6.1995
• Sprache: englisch
• Themenwelt: Naturwissenschaften ► Biologie ► Biochemie
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Zellbiologie
• Themenwelt: Naturwissenschaften ► Physik / Astronomie ► Angewandte Physik
• Themenwelt: Technik ► Umwelttechnik / Biotechnologie
• ISBN-10: 0-08-053766-9 / 0080537669
• ISBN-13: 978-0-08-053766-5 / 9780080537665