Topics in Fluorescence Spectroscopy

by Lakowicz, Joseph R.

• ISBN13: 9780306473876
• ISBN10: 0306473879
• Format: Hardcover
• Copyright: 2003-04-01
• Publisher: Plenum Pub Corp

Summary

During the past 15 years, there has been remarkable progress in the analysis and manipulation of DNA and its use in nanotechnology. DNA analysis is ubiquitous in molecular biology, medical diagnostics, and forensics. Much of the readout technology is based on fluorescence detection. This volume contains contributions from many experts in the field who present an overview of many aspects of DNA technology. These chapters provide an understanding of the underlying principles and technology, rather than an exhaustive review of the literature. Written in a clear straightforward style, this book is an excellent introduction for any scientist to the use of fluorescence in DNA analysis. DNA Technology is an essential reading for all academics, bench scientists, and industry professionals wishing to take advantage of the latest and greatest in this continuously emerging field. Key Features: *Comprehensive overview of the complexities of DNA analysis, *Covers topics of universal interest to a broad field of scientists, *Accessible utility in presenting state-of-the-art DNA technology, *Chapters authored by key figures in the field.

Author Biography

Dr. J.R. Lakowicz is Professor of Biochemistry at the University of Maryland School of Medicine and Director of the Center for Fluorescence Spectroscopy. Dr. Lakowicz has published over 400 scientific articles, has edited numerous books, holds 16 issued patents, and is the sole author of the widely used text, Principles of Fluorescence Spectroscopy, also published by Kluwer Academic/Plenum Publishers, now in its Second Edition.

Table of Contents

1. DNA Sequencing Using Fluorescence Detection
Steven A. Soper, Clyde Owens, Suzanne Lassiter, Yichuan Xu, and Emanuel Waddell
1.1. General Considerations	1	(20)
1.1.1. What Is DNA?	1	(1)
1.1.1.1. Organization of Genome	1	(1)
1.1.1.2. Functions of Genes	2	(1)
1.1.2. What Is DNA Sequencing?	2	(3)
1.1.2.1. DNA Sequencing Factories	2	(3)
1.1.3. Structure of DNA	5	(1)
1.1.3.1. Nucleotide Bases	5	(1)
1.1.3.2. Watson-Crick Base Pairing	5	(1)
1.1.4. Methods for Determining the Primary Structure of DNA	6	(4)
1.1.4.1. Maxam-Gilbert Sequencing	7	(3)
1.1.4.2. Sanger Chain Termination Method	10	(1)
1.1.5. Modes of Electrophoresis	10	(6)
1.1.5.1. Slab Gel Electrophoresis	14	(1)
1.1.5.2. Capillary Gel Electrophoresis	15	(1)
1.1.6. Detection Methods for DNA Sequencing	16	(5)
1.1.6.1. Autoradiographic Detection	16	(1)
1.1.6.2. Fluorescence Detection	16	(60)
1.2. Fluorescent Dyes for DNA Labeling and Sequencing	21	(13)
1.2.1. Visible Fluorescence Dyes for DNA Labeling	24	(6)
1.2.2. ET Dyes for DNA Sequencing	30	(2)
1.2.3. Near-Infrared Dyes for DNA Sequencing	32	(2)
1.3. Instrumental Formats for Fluorescence Detection in DNA Sequencing	34	(6)
1.3.1. Fluorescence Scanning Instruments	36	(1)
1.3.2. Fluorescence Imaging Systems for DNA Sequencing	37	(3)
1.4. Dye Primer/Terminator Chemistry and Fluorescence Detection Formats	40	(19)
1.4.1. Single Color/Four Lane	43	(2)
1.4.2. Single Color/Single Lane	45	(2)
1.4.3. Single Color/Two Lane	47	(3)
1.4.4. Four Color/Single Lane	50	(1)
1.4.5. So Which Sequencing Format It Better?	51	(3)
1.4.6. Single Color/Four Lifetime Sequencing	54	(15)
1.5. Single Molecule DNA Sequencing Using Fluorescence Detection	59	(6)
References	65	(4)
2. Fluorescence in Nucleic Acid Hybridization Assays
Larry E. Morrison
2.1. Introduction	69	(3)
2.1.1. Heterogeneous Versus Homogeneous Hybridization Assays	70	(1)
2.1.2. Amplified Hybridization Assays	71	(1)
2.2. Heterogeneous Hybridization Assays	72	(10)
2.2.1. Non-Amplified Heterogeneous Hybridization Assays	72	(4)
2.2.2. Amplified Heterogeneous Hybridization Assays	76	(6)
2.2.2.1. Signal Amplification in Heterogeneous Hybridization Assays	77	(1)
2.2.2.2. Target Amplification in Heterogeneous Hybridization Assays	78	(4)
2.3. Homogeneous Hybridization Assays	82	(14)
2.3.1. Non-Amplified Homogeneous Hybridization Assays	82	(9)
2.3.1.1. Dual Label Formats	82	(6)
2.3.1.2. Single Label Formats	88	(3)
2.3.2. Amplified Homogeneous Hybridization Assays	91	(61)
2.3.2.1. Dual Interacting Label Formats	91	(4)
2.3.2.2. Single Label Formats	95	(1)
2.3.2.3. Nucleic Acid Binding Dyes	95	(57)
2.4. Conclusions	96	(1)
References	97	(9)
3. Energy Transfer Fluorescent Labels for DNA Sequencing and Analysis	105	(24)
Jin Xie, Su-Chun Hung, Alexander N. Glazer, and Richard A. Mathies
3.1. Introduction
3.2. Theory of Fluorescence Resonance Energy Transfer	106	(1)
3.3. Sanger Dideoxy Chain-Termination Sequencing	107	(1)
3.4. Energy-Transfer Fluorescent Primers	107	(9)
3.5. ET Cassette for Construction of Energy-Transfer Fluorescent Primers	116	(3)
3.6. Energy-Transfer Fluorescent Terminators	119	(1)
3.7. Short Tandem Repeat Analysis with Capillary Array Electrophoresis and ET Labels	120	(2)
3.8. Biotinylated Energy Transfer Cassettes	122	(1)
3.9. Template-Directed Dye-Terminator Incorporation	123	(2)
3.10. Conclusions	125	(4)
Acknowledgments	125	(1)
References	125	(4)
4. On-the-Fly Fluorescence Lifetime Detection in Capillary Electrophoresis for DNA Analysis
Linda B. McGown
4.1. Introduction	129	(1)
Measuring Fluorescence Lifetime On-the-Fly in CE	131	(2)
4.2. Analysis of On-the-Fly Lifetime Data	133	(1)
4.3. Lifetime Detection of Labeled DNA Primers	133	(5)
4.4. DNA Sequencing	138	(1)
Restriction Fragment Length Polymorphism Analysis	142	(4)
4.5. Conclusions	146	(1)
References	148	(3)
5. Fluorescent Nucleoside Analogues as DNA Probes
Mary E. Hawkins
5.1. Introduction	151	(1)
5.2. Pteridine Nucleoside Analogues	152	(9)
5.2.1. Background	152	(9)
5.2.1.1. Effect of pH on Fluorescence Emission	152	(3)
5.2.1.2. Fluorescence of Pteridine Analogue-Combining Oligonucleotides	155	(1)
5.2.1.3. Melting Temperatures	156	(96)
5.3. Applications Using Pteridine	161	(9)
5.3.1. Integrase Assay	161	(3)
5.3.2. Bulge Hybridization Probes	164	(1)
5.3.3. Anisotropy	165	(3)
5.3.4. Intracellular Transport of Oligonucleotides	168	(1)
5.3.5. DNA Conformation	169	(1)
5.4. 2-Amino Purine	170	(2)
5.4.1. Background	170	(1)
5.4.2. Applications	170	(8)
5.5. 1,N6-Ethenoadenosine	172	(1)
5.6. Summary and Outlook	172	(5)
Acknowledgments	173	(1)
References	174	(3)
6. Lanthanide-Labeled DNA
Paul R. Selvin
6.1. Overview	177	(1)
6.2. Lanthanide as Luminescent Labels	178	(11)
6.2.1. Representative Chelats	178	(4)
6.2.2. Sensitivity	182	(1)
6.2.3. Multiple Labeling and Selected Applications	183	(6)
6.3. Imaging	189	(3)
6.3.1. Alternative Time-Resolved Probes	192	(5)
6.4. Lanthanides as Donors in Resonance Energy Transfer	192	(1)
6.5. Advantages of LRET	193	(4)
6.6. LRET Applied to Protein-DNA Interactions	197	(5)
6.6.1. Protein-Induced DNA Bends	197	(17)
6.7. New DNA Dyes Based on LRET with Tuneable Emission Color and Excited-State Lifetime	202	(5)
6.8. Conclusion	207	(1)
References	208	(5)
7. DNA Arrays for Genetic Analyses and Medical Diagnosis
Sabato D'Auria, Mose Rossi, Joanna Malicka, Zygmunt Gryczynski, and Ignacy Gryczynski
7.1. Introduction	213	(1)
7.2. Sample Preparation	214	(6)
7.2.1. Spotting Method	214	(2)
7.2.2. In Situ Syntheses Method	216	(9)
7.3. Fluorescence Probes	220	(3)
7.4. Arrayers	223	(2)
7.5. Image Analysis	225	(4)
7.5.1. Array Target Segmentation	226	(1)
7.5.2. Background Intensity Extraction	227	(1)
7.5.3. Target Detection	227	(1)
7.5.4. Target Intensity Extraction	228	(1)
7.5.5. Ratio Analysis	228	(1)
7.5.6. Multiple Image Analysis	229	(15)
7.6. Applications	229	(4)
7.7. Pespectives	233	(6)
Acknowledgment	234	(1)
References	234	(5)
8. Flow Cytometric Sizing of DNA Fragments
W. Patrick Ambrose, Hong Cai, Peter M. Goodwin, James H. Jett,
Robert C. Habbersett, Erica J. Larson, W. Kevin Grace,
James H. Werner, and Richard A. Keller
8.1. Introduction	239	(1)
8.2. Single Molecule Detection	239	(5)
8.3. DNA Fragment Sizing	244	(21)
8.3.1. Apparatus	247	(1)
8.3.2. Data Analysis	248	(1)
8.3.3. Sample Preparation	249	(1)
8.3.4. Sizing of X DNA, R Digests, and X Concatamers	249	(3)
8.3.5. Applications	252	(39)
8.3.5.1. PAC Clones	252	(3)
8.3.5.2. PCR Fragments	255	(5)
8.3.5.3. Bacteria Species and Strain Discrimination .	260	(5)
8.4. Summary	265	(6)
Acknowledgments	268	(1)
References	268	(3)
9. Fluorimetric DNA Biosensors
Paul A. E. Piunno and Ulrich J. Krull
9.1. Introduction	271	(2)
9.2. Fluorimetric Fiber Optic Biosensors	273	(1)
9.3. Evanescent Wave Biosensors	274	(5)
9.4. Nonevanescent Intrinsic Mode Biosensors	279	(2)
9.5. Selectivity and Calibrations Issues	281	(3)
9.6. A Reagentless Biosensor	284	(2)
9.7. Future	286	(5)
References	287	(4)
10. Technicolor Genome Analysis
Michael J. Difilippantonio and Thomas Ried
10.1. Introduction	291	(3)
10.1.1. Historical Perspective	291	(3)
10.2. Principles behind FISH	294	(9)
10.2.1. Preparation of Cytological Specimens	296	(3)
10.2.2. Preparation of DNA Probes	299	(1)
10.2.3. Labeling of DNA Probes	300	(1)
10.2.4. Hybridization of Probe to Speciment	301	(1)
10.2.5. Detection and Visualization	302	(1)
10.2.6. High Sensitivity Detection Procedures	302	(1)
10.3. Applications of FISH	303	(4)
10.3.1. Gene Mapping	303	(1)
10.3.2. Somatic Hybrid Analysis	304	(1)
10.3.3. Clinical and Cancer Cytogenetics	305	(1)
10.3.4. Chromosome Evolution	305	(2)
10.4. Karyotype Analysis	307	(4)
10.4.1. Comparative Genome Hybridization	308	(2)
10.4.2. Spectral Karyotyping	310	(1)
References	311	(6)
Index	317