Gene Transfer: Delivery and Expression of DNA and RNA, A Laboratory Manual

Subject Area(s): Developmental Biology; Gene Therapy; Cell Biology; Molecular Biology; Laboratory Techniques

Edited by Theodore Friedmann, University of California, San Diego; John Rossi, Beckman Research Institute of the City of Hope, Duarte, California

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Visit the following URL to view a sample protocol http://www.cshprotocols.org/cgi/content/full/2006/1/pdb.prot4447

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Understanding gene function and regulation requires rigorous testing in live cells and organisms. Recent advances have provided a variety of new strategies for delivering DNA and RNA into cells and probing their expression, as well as new clinical applications that rely upon the introduction of genetic material. The vast number of available techniques for clinical and laboratory research often makes selecting the optimal method a difficult process. Gene Transfer: Delivery and Expression of DNA and RNA provides the first comprehensive guide to technical approaches for delivering nucleic acids into cells and organisms and of ensuring (even manipulating) appropriate expression. The detailed, step-by-step protocols cover a variety of methods, both well established and newly evolving. These include viral and nonviral methods of gene delivery, transgenic approaches, strategies for the regulation of transgene expression, and modification of the host response. The introductory matter to each chapter includes concise technical and theoretical discussions with considerations for selection of the appropriate system and strategies for delivery.

1. Introduction: T. Friedmann and J. Rossi
VIRAL VECTORS
2. Retroviral Vectors: K. Cornetta, K.E. Pollok, and A.D. Miller
3. Development of Lentiviral Vectors Expressing siRNA: G. Tiscornia, O. Singer, and I.M. Verma
4. HIV–2 Vectors in Human Gene Therapy: Design, Construction, and Therapeutic Potential: K.V. Morris and F. Wong–Staal
5. SIV Vectors as Vehicles for DNA Delivery: E. Verhoeyen, F.–L. Cosset, and D. Nègre
6. Production and Use of Feline Immunodeficiency Virus–based Lentiviral Vectors: D.T. Saenz, R. Barraza, N. Loewen, W. Teo, and E.M. Poeschla
7. Lentivirus Transduction of Hematopoietic Cells: M.–J. Li and J.J. Rossi
8. Spleen Necrosis Virus–based Vectors: Z. Parveen, M. Mukhtar, and R.J. Pomerantz
9. Foamy Virus Vector Production and Transduction of Hematopoietic Cells: N.C. Josephson and D.W. Russell
10. Simian Foamy Virus Type–1 Vectors: J. Park and A. Mergia
11. Generation of VSV–G–pseudotyped Retroviral Vectors: J.–K. Yee
12. Targeted Gene Transfer with Surface–engineered Lentiviral Vectors: E. Verhoeyen and F.–L. Cosset
13. Preparation of Pseudotyped Lentiviral Vectors Resistant to Inactivation by Serum Complement: G.H. Guibinga and T. Friedmann
14. Generation of 2A Peptide–linked Multicistronic Vectors: A.L. Szymczak–Workman, K.M. Vignali, and D.A.A. Vignali
15. Construction of First–generation Adenoviral Vectors: P. J. Ross and R.J. Parks
16. Production and Characterization of Helper–dependent Adenoviral Vectors: D.J. Palmer and P. Ng
17. Cell and Tissue Targeting: Y. Kawakami and D.T. Curiel
18. Stable Producer Cell Lines for AAV Assembly: G. Chadeuf and A. Salvetti
19. Strategies for the Design of Hybrid Adeno–associated Virus Vectors: A. Asokan and R.J. Samulski
20. Recombinant Herpes Simplex Virus Vectors: W.F. Goins, D. M. Krisky, J.B. Wechuck, D. Wolfe, S. Huang, and J.C. Glorioso
21. Herpes Simplex Virus Type–1–derived Amplicon Vectors: W.J. Bowers and H.J. Federoff
22. γ–2 Herpesvirus Saimiri–based Vectors: A. Whitehouse
23. Gene Delivery Using HSV/AAV Hybrid Amplicon Vectors: O. Saydam, D.L. Glauser, and C. Fraefel
24. Polyomaviruses: SV40: D.S. Strayer, C. Mitchell, D.A. Maier, and C.N. Nichols
25. SV40 In Vitro Packaging: A Pseudovirion Gene Delivery System: C. Kimchi–Sarfaty and M.M. Gottesman
26. Baculovirus–based Display and Gene Delivery Systems: A.R. Mäkelä, W. Ernst, R. Grabherr, and C. Oker–Blom
27. Safe, Simple, and High–capacity Gene Delivery into Insect and Vertebrate Cells by Recombinant Baculoviruses: K.J. Airenne, O.H. Laitinen, A. J. Mähönen, and S. Ylä–Herttuala
28. Alphaviruses: Semliki Forest Virus and Sindbis Virus as Gene Delivery Vectors: K. Lundstrom
29. Gene Transfer into Mammalian Cells Using Targeted Filamentous Bacteriophage: A. Baird
30. Selection, Isolation, and Identification of Targeting Peptides for Ligand–directed Gene Delivery: M. Trepel, W. Arap, and R. Pasqualini
31. Rescue and Propagation of Tropism–modified Measles Viruses: T. Nakamura and S.J. Russell
32. Picornavirus–based Expression Vectors: S. Mueller and E. Wimmer
33. Reverse Genetics of Influenza Viruses: G.A. Marsh and P. Palese
NONVIRAL TECHNIQUES AND VECTORS
34. An Overview of Condensing and Noncondensing Polymeric Systems for Gene Delivery: D.B. Shenoy and M.M. Amiji
35. Transfection of Hippocampal Neurons with Plasmid DNA Using Calcium Phosphate Coprecipitation: B. Goetze and M. Kiebler
36. Gene Delivery to Skin Using Biolistics: W.C. Heiser
37. Optimizing Electrotransfection of Mammalian Cells In Vitro: S. Li
38. Micro In Utero Electroporation for Efficient Gene Targeting in Mouse Embryos: T. Shimogori
39. Lipoplex and LPD Nanoparticles for In Vivo Gene Delivery: S.–D. Li, S. Li, and L. Huang
40. Bioresponsive Targeted Charge Neutral Lipid Vesicles for Systemic Gene Delivery: W. Li and F.C. Szoka, Jr.
41. HVJ Liposomes and HVJ Envelope Vectors: Y. Kaneda
42. Polylysine Copolymers for Gene Delivery: S.W. Kim
43. PEI Nanoparticles for Targeted Gene Delivery: F. Alexis, J. Zeng, and S. Wang
44. Cyclodextrin–containing Polycations for Nucleic Acid Delivery: J.D. Heidel
45. Bionanocapsules Using the Hepatitis B Virus Envelope L Protein: T. Yamada, J. Jung, M. Seno, A. Kondo, M. Ueda, K. Tanizawa, and S. Kuroda
46. Formulations of Solid Lipid Nanoparticles for Transfection of Mammalian Cells In Vitro: C. Rudolph and J. Rosenecker
47. PEGylated Poly–l–lysine DNA Nanoparticles: P.B. Davis and T.H. Kowalczyk
48. Water–soluble Lipopolymers and Lipopeptides for Nucleic Acid Delivery: R.I. Mahato, Z. Ye, and S.W. Kim
49. Cationic Polysaccharides for DNA Delivery: I. Yudovin–Farber, H. Eliyahu, and A.J. Domb
50. Sustained Release of Plasmid DNAs Encoding Platelet–derived Growth Factor and Hyaluronan Synthase 2 from Cross–linked Hyaluronan Matrices and Films: W. Chen
51. Linear Polyethylenimine: Synthesis and Transfection Procedures for In Vitro and In Vivo: M. Ogris and E. Wagner
52. Protein Nanospheres for Gene Delivery: Preparation and In Vitro Transfection Studies with Gelatin Nanoparticles: S. Kommareddy and M.M. Amiji
53. Vesicular Stomatitis Virus–G Conjugate: A. Miyanohara
54. High–throughput Methods for Screening Polymeric Transfection Reagents: G.T. Zugates, D.G. Anderson, and R. Langer
55. Poly(Lactic Acid) and Poly(Ethylene Oxide) Nanoparticles as Carriers for Gene Delivery: N. S. Csaba, A. Sánchez, and M. J. Alonso
56. Biodegradable Nanoparticles: J.K. Vasir and V. Labhasetwar
57. Transposon–mediated Delivery of Small Interfering RNA: Sleeping Beauty Transposon: B.S. Fletcher
58. Efficient DNA Delivery into Mammalian Cells by Displaying the TAT Transduction Domain on Bacteriophage λ
59. Cell–penetrating Peptide–mediated Delivery of Peptide Nucleic Acid Oligomers: P. Lundberg, K. Kilk, and Ü. Langel
REGULATION OF TRANSGENE EXPRESSION
60. Conditional Mutagenesis of the Genome Using Site–specific DNA Recombination: K. Ohtsubo and J.D. Marth
61. Expression and Validation of Ribozyme and Short Hairpin RNA in Mammalian Cells: M. Amarzguioui
62. Mifepristone–inducible Gene Regulatory System: K. Schillinger, X. Ye, S. Tsai, and B.W. O'Malley
63. Dimerizer–mediated Regulation of Gene Expression: V.M. Rivera, L. Berk, and T. Clackson
64. RheoSwitch System: A Highly Sensitive Ecdysone Receptor–based Gene Regulation System Induced by Synthetic Small–molecule Ligands: P. Kumar and A. Katakam
65. Site–specific Integration with Phage φC31 Integrase: R.T. Hillman and M.P. Calos
66. Creating Zinc Finger Nucleases to Manipulate the Genome in a Site–specific Manner Using a Modular–assembly Approach: M. Porteus
SPECIALIZED TECHNIQUES OF GENE AND VECTOR DELIVERY
67. Assembly of De Novo Bacterial Artificial Chromosome–based Human Artificial Chromosomes: J. Basu and H.F. Willard
68. Delivery of Naked DNA Using Hydrodynamic Injection Techniques: D.L. Lewis, M. Noble, J. Hegge, and J. Wolff
69. Nonviral Gene Transfer across the Blood–brain Barrier with Trojan Horse Liposomes: W. M. Pardridge
70. Sonoporation: An Efficient Technique for the Introduction of Genes into Chick Embryos: S. Ohta, O. Yukiko, K. Suzuki, M. Kamimura, K. Tachibana, and G. Yamada
71. Genetic Manipulation of Mammalian Cells by Microinjection: D.W. Rose
72. Magnetofection: C. Plank and J. Rosenecker
73. Photochemical Internalization for Light–directed Gene Delivery: A. Bonsted, A. Høgset, E. Wagner, and K. Berg
TRANSGENIC APPROACHES
74. Pronuclear Microinjection in Mice: W. Tsark
75. Knockdown Transgenic Mice Generated by Silencing Lentiviral Vectors: O. Singer, G. Tiscornia, and I.M. Verma
APPENDIX
Cautions
Subject Index

Reviews

“This volume is a very comprehensive and practical guide describing all the virally, chemically and physically mediated gene transfer techniques I have come across and a few more!...It is a very useful resource.”
—Society for General Microbiology Quarterly

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