Synthetic Biology: A New Paradigm for Biological Discovery

About the Authors
Olivia Scaros graduated from the University of Illinois in 1988 with a Doctor of Pharmacy degree. She has been employed by various pharmaceutical firms, including Sandoz Pharmaceuticals, Bayer Corporation, and Pfizer Inc., both as an employee and a consultant. For the past 13 years, Dr. Scaros’ main focus has been medical writing, including study reports, clinical protocols, articles, and other projects for the pharmaceutical industry.
Richard Fisler is a partner with Beachhead Consulting, a firm specializing in technology evaluation, strategic planning, and market assessment in the life science industry. Prior to his work at Beachhead, he brought a wide variety of high-technology platforms to market through positions in the microarray and live-cell microscopy industries. Additionally, he has spent 11 years in management and engineering in the medical imaging field.
Dr. Gary Sams received his Ph.D. in Cell Biology from the University of Kansas and completed a post-doctoral fellowship in Cancer Molecular Biology at the University of Wisconsin. He worked as a Sales and Marketing executive for 15 years in the life sciences research and drug discovery tools sectors for companies including Promega, EG&G, Digene, and Vysis. Since 1995, Dr. Sams has provided strategic marketing and commercialization services as a Managing Partner of Beachhead Consulting Group. The group’s clients include a wide range of leading life science companies including Applied Biosystems, Invitrogen, Perkin Elmer, and Caliper. Dr. Sams has also worked with many early-stage companies, including Genospectra, 454 Corporation, Cytokinetics, Sequenom, and Nanogen.

Table of Contents

1 Introduction.. 10
1.1 Scope of Report ..11
1.2 Overview of Synthetic Biology .12
1.2.1 Definition of Synthetic Biology ..12
1.2.2 Overview of Current Application Areas.16
1.2.3 Basics of Synthetic Biology .19
1.2.4 Why is Synthetic Biology Important? .19
1.2.5 Synthetic Biology’s Role in Genetics ..20

2 Oligonucleotides/DNA. 21
2.1 Synthetic Oligonucleotide/DNA-based Technologies 22
2.1.1 Expanded Bases22
2.1.2 Nanocircles 25
2.1.3 Recombinant DNA (rDNA) ..26
2.1.4 Aptamers27
2.2 Applications of Synthetic DNA 30
2.2.1 Expanded Bases used in Assays..30
2.2.2 Nanocircles 31
2.2.3 Examples of Recombinant DNA Products.32
2.2.4 Aptamers32
2.2.5 Expert Opinion on Market Potential ..35

3 RNA. 37
3.1 Synthetic RNA-based Technologies .39
3.1.1 RNA Interference (RNAi)39
3.1.2 Antisense Technology40
3.1.3 Riboswitches .41
3.1.4 Riboregulators ..43
3.1.5 Riboswitch/Riboregulator Hybrids .45
3.2 Applications of Synthetic Biology in RNA ..47
3.2.1 RNAi Therapeutics 47
3.2.2 Antisense Technology 48

4 Peptides-based Molecules . 51
4.1 Synthetic Peptide-based Technologies ..51
4.1.1 Synthetic Antibodies.51
4.1.2 Engineered Kinases ..51
4.2 Applications of Synthetic Peptides and Proteins ..53
4.2.1 Synthetic Antibodies.53
4.2.2 Kinases ..64
4.2.3 Novel Delivery Systems 66
4.2.4 Tapet®: Tumor Amplified Protein Expression Therapy ..67
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4.2.5 Hematide (Affymax).68
4.2.6 Genetically Engineered Recombinant Protein Vaccines: Present and
Future Applications .69

5 Metabolites 75
5.1 Synthetic Polyketide Technologies ..75
5.2 Applications of Synthetic Polyketides ..77

6 Organisms 82
6.1 Technologies of Directed Evolution and Microbial Engineering 82
6.2 Applications of Directed Evolution and Microbial Engineering .85
6.2.1 Diversa’s DirectEvolution™..85
6.2.2 Microbial Engineering ..86
6.2.3 Future Application of Microbial Engineering: crHIV-1 88
6.2.4 Bioremediation.90
6.3 Technology of Biosensing Cells 93
6.4 Applications of Biosensing Cells..94
6.4.1 BioFlash™94
6.4.2 Biosensors that Measure Cell Division ..95

7 Environmental Research 97
7.1 Energy Research .97
7.1.1 Berkeley Laboratory .97
7.1.2 The Institute for Biological Energy Alternatives (IBEA)101

8 Synthetic Biology Informatics .. 102

9 Potential Hazards of Synthetic Biology . 103

10 Synthetic Biology Market Overview.. 105
10.1 Synthetic Biology Partnerships .. 105
10.2 Commercial Opportunities and Outlook 107
10.3 Synthetic Biology Market Projections 109
10.3.1 Synthetic Biology Pharmaceutical Market Analysis .109
10.3.2 Life Science Reagents Market ..111
10.4 Open Source 112

11 Selected Synthetic Biology Thought-leader Profiles . 115

12 Expert Interviews 121

13 Synthetic Biology Companies 139

List of Figures
Figure 1-1. Taxonomy of Synthetic Biology Technologies with Current and Future
Applications* 17
Figure 1-2. The process of DNA to RNA to proteins 21
Figure 2-1. Chemical Structure Comparison of DNA and xDNA . 23
Figure 2-2. Synthesis of xA and xT.. 23
Figure 2-3. Examples of Published Knock-down Studies using Aptamers In Vitro or
in Animals. 29
Figure 2-4. DNA-streptavidin Nanocircles 31
Figure 3-1. Initiation and Elongation Steps in the Process of Translation . 38
Figure 3-2. Mechanism of RNAi .. 40
Figure 3-3. The Production of Faulty Proteins and the Inhibition of this Production by
Antisense .. 41
Figure 3-4. Riboswitch-mediated Gene Regulation .. 42
Figure 3-5. Design and Functional Activity of an Antiswitch Regulator 44
Figure 3-6. Engineered RNA Switch System. 46
Figure 3-7. Isis Pharmaceuticals' Proprietary Drug Discovery Process . 48
Figure 4-1. Cell Death Caused by Anthrax Toxin.. 58
Figure 4-2. Mechanism of Action of ABthrax™. 59
Figure 4-3. Components of Bio-Layer’s antibody mimetic abiotic surfaces. 61
Figure 4-4 Key elements of Bio-Layer's novel surface discovery platform.. 62
Figure 4-5. Comparison of the standard amide antibody coupling method of
immobilizing antibodies on beads with the Mix&GoTM protocol. .. 63
Figure 4-6. Example of a commercial immunoassay comparing standard amide
coupling techniques to the Mix&GoTM approach 63
Figure 4-7. Express-si Delivery Technology.. 67
Figure 4-8. Percentage of Patients with Hemagglutination Inhibition (HAI) Treated
with FluBlock at 15, 40, and 160 μg in Comparison with FluZone 15 μg 74
Figure 5-1. Examples of Polyketides 75
Figure 5-2. “Lego-zation” Principle for the Assembly of New Polyketide Synthases 76
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Figure 5-3. The Process of Chemo-biosynthesis Technology used by Kosan
Biosciences 79
Figure 5-4. Heterologous Over-expression for Increased Production of Polyketides. 80
Figure 6-1. An Idealized Biorefinery Concept .. 92
Figure 6-2. E. coli Bacteria Programmed to Form a Bull’s Eye Pattern 94
Figure 10-1. Synthetic Biology Impact on the Human Healthcare Paradigm 108
Figure 10-2. 10-year Antibody Market Projection .. 111
Figure 10-3. 10-year Synthetic Reagents Market Projection 112
Figure 10-4. Registry Parts Index 113
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List of Tables
Table 2-1. Comparison of Aptamer and Antibody Properties. 28
Table 3-1. Companies involved in RNAi Technology .. 47
Table 3-2. Various Companies involved in Antisense Technology . 50
Table 4-1. Biotechnology Companies involved in Synthetic Antibody Production 54
Table 4-2. Product Development Summary of Kinases by Therapeutic Area currently
being Investigated .. 65
Table 6-1. Various Companies involved in Directed Evolution Technologies 84
Table 10-1. Examples of Selected Partnerships of Academic Institutions,
Biotechnology Companies and Pharmaceutical Companies. 106
Table 10-2. Time to Market Analysis of Synthetic Biology Therapeutic Products .. 110
Table 10-3. Ribosome Binding Sites . 113
Table 11-1. Selected Thought-leaders in the Field of Synthetic Biology. 115
Table 13-1. Biotechnology or Pharmaceutical Companies with an Interest in Synthetic
Biology 139