Synthetic Society/SB Reality

Construction Technology

Conclusion: It is possible to construct any piece of DNA.

Characteristics as of 1 February 2006:

• Cost. ~$1 per bp
• Length. ~100 bp direct chemical synthesis, ~15,000 bp PCR assembly, ~3,500,000 bp inchworm elongation
• Error Rate. From 1:10 to effectively zero
• Time. 6 hours for 100 bp, 2-6 weeks for 15,000 bp, ~2 months for 50,000 bp, ~7 years for 3,500,000 bp
• Diversity. From one molecule to millions of molecules (heavily dependent on method)
• Terms of Sale. Varied (from no-strings-attached to full-rights-reserved).

Examples & Reference Material:

1. Tumpey TM, Basler CF, Aguilar PV, Zeng H, Solórzano A, Swayne DE, Cox NJ, Katz JM, Taubenberger JK, Palese P, and García-Sastre A. Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science. 2005 Oct 7;310(5745):77-80. DOI:10.1126/science.1119392 |
2. Cello J, Paul AV, and Wimmer E. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science. 2002 Aug 9;297(5583):1016-8. DOI:10.1126/science.1072266 |
3. Smith HO, Hutchison CA 3rd, Pfannkoch C, and Venter JC. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15440-5. DOI:10.1073/pnas.2237126100 |
4. Itaya M, Tsuge K, Koizumi M, and Fujita K. Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15971-6. DOI:10.1073/pnas.0503868102 |
5. Curtis KM, Yount B, and Baric RS. A simple strategy to assemble infectious RNA and DNA clones. Adv Exp Med Biol. 2001;494:475-81. DOI:10.1007/978-1-4615-1325-4_69 |
6. Yount B, Curtis KM, and Baric RS. Strategy for systematic assembly of large RNA and DNA genomes: transmissible gastroenteritis virus model. J Virol. 2000 Nov;74(22):10600-11. DOI:10.1128/jvi.74.22.10600-10611.2000 |
7. Patnaik R, Louie S, Gavrilovic V, Perry K, Stemmer WP, Ryan CM, and del Cardayré S. Genome shuffling of Lactobacillus for improved acid tolerance. Nat Biotechnol. 2002 Jul;20(7):707-12. DOI:10.1038/nbt0702-707 |
8. Pekrun K, Shibata R, Igarashi T, Reed M, Sheppard L, Patten PA, Stemmer WP, Martin MA, and Soong NW. Evolution of a human immunodeficiency virus type 1 variant with enhanced replication in pig-tailed macaque cells by DNA shuffling. J Virol. 2002 Mar;76(6):2924-35. DOI:10.1128/jvi.76.6.2924-2935.2002 |
9. Kodumal SJ, Patel KG, Reid R, Menzella HG, Welch M, and Santi DV. Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15573-8. DOI:10.1073/pnas.0406911101 |

• Craig Venter on "Gene Synthesis Technology: State of the Science" at 1 July 2005 NSABB meeting, Real Audio webcast
  • HINT: Fast-forward to 11 minutes and 30 seconds into the webcast

Ownership, Sharing, & Innovation Technology

MTA examples

Example 1

From: hkeller@MIT.EDU
Subject: Re: Fwd: Re: Strain request
Date: January 31, 2006 2:41:31 PM EST
To: endy@mit.edu

I just spoke with <person> about getting copies of the entire <deleted> series. I explicitly told her I work for you (she asked in what capacity). She did ask why we wanted them and I told her to test them out with some of our constructs to see how useful they are. She is going to send me a sample MTA agreement (via e-mail) by the end of the week. She warned me of the following:

1) They require signature of an MTA before release of the strains (which we knew already).
2) We must provide them with a detailed experimental plan specifying how we plan to use the strains.
3) The strains cannot leave our lab.
4) They request that we share any results that we obtain using the strain(s).
5) No changes can be made to the chromosome of any of the strains.
6) There is a small transfer fee associated with obtaining the strains (she said she would have to speak with <person> to determine what the exact amount is).
I'll forward the MTA on when I receive it. Do you still want to proceed with this, knowing the above?

Example 2
From: "Alex Mallet" <amallet@MIT.EDU>
Date: Mon, 30 Jan 2006 15:12:39<br To:"'Drew Endy'" <endy@mit.edu>
Subject: MTA for Tet system

Hi Drew - Are you ok with me asking the fellow in Germany who developed the [reverse] Tet system that the van Oudenaarden lab is using for an MTA ?
thanks, Alex.

And so on...

BioBrick Examples

Begin forwarded message:
From: <student>
Date: January 23, 2006 7:53:14 PM EST
To: endy@mit.edu
Cc: <advisor>
Subject: Synthetic Biology
Dear Dr. Endy,
My name is <grad student at UCLA>. I am a graduate student in <some lab> at UCLA. I am attempting to construct a gene circuit using the tetR repressor for a metabolic engineering project and I was wondering if it would be possible to obtain your plasmid pSB1A2 containing part BBa_C0040 (a degradable form of the tetR repressor) from the BioBricks project. Thank you for your assistance.
Sincerely, <graduate student at UCLA>

On Jan 23, 2006, at 11:54 PM, Drew Endy wrote:
Randy,
Part request from UCLA below.
Best, Drew

Begin forwarded message:
From: Randy Rettberg <randy@rettberg.com>
Date: January 24, 2006 5:54:41 AM EST
To: Drew Endy <endy@MIT.EDU>
Subject: Re: Synthetic Biology
Sent on to Meagan. I am off to the EU and Cambridge.
Randy

On Jan 31, 2006, at 10:59 AM, Drew Endy wrote:
Hi <student>,
Just a follow-up to your email. Hopefully Meagan has been in touch with you already (below).  But, FYI, request received and should be arriving shortly / arrived.  
Best, Drew

From: <student>@ucla.edu
Subject: Re: BioBrick request
Date: January 31, 2006 2:03:44 PM EST
To: endy@mit.edu
Dr. Endy-
Thank you for your assistance. The part was received late last week.
Sincerely,
<grad student at UCLA>