Synthetic Biology Overview Seed Magazine Synthetic Biology Download

Synthetic Biology Overview Seed Magazine – Synthetic Biology Download original (large) image

Synthetic Biology Synthetic biology is a new area of biological research that combines science and engineering. Synthetic biology encompasses a variety of different approaches, methodologies and disciplines, and many different definitions exist. What they all have in common, however, is that they see synthetic biology as the design and construction of new biological functions and systems not found in nature. http: //en. wikipedia. org/wiki/Synthetic_biology

Synthetic Biology Key enabling technologies. DNA sequencing is determining the order of the nucleotide bases in a molecule of DNA. First, large-scale genome sequencing efforts continue to provide a wealth of information on naturally occurring organisms. This information provides a rich substrate from which synthetic biologists can construct parts and devices. Second, synthetic biologists use sequencing to verify that they fabricated their engineered system as intended. Third, fast, cheap and reliable sequencing can also facilitate rapid detection and identification of synthetic systems and organisms. Fabrication A critical limitation in synthetic biology today is the time and effort expended during fabrication of engineered genetic sequences. To speed up the cycle of design, fabrication, testing and redesign, synthetic biology requires more rapid and reliable de novo DNA synthesis and assembly of fragments of DNA, in a process commonly referred to as gene synthesis.

Synthetic Biology History: In 2002 researchers at SUNY Stony Brook succeeded in synthesizing the 7741 base poliovirus genome from its published sequence, producing the first synthetic organism. This took about two years of painstaking work. In 2003 the 5386 bp genome of the bacteriophage Phi X 174 was assembled in about two weeks. In 2006, the same team, at the J. Craig Venter Institute, has constructed and patented a synthetic genome of a novel minimal bacterium, Mycoplasma laboratorium and is working on getting it functioning in a living cell. In 2010, Venter's group announced they had been able to assemble a complete genome of millions of base pairs, insert it into a cell, and cause that cell to start replicating.

Synthetic Biology –Craig Ventner 2008. Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome Daniel G. Gibson, Gwynedd A. Benders, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Holly Baden-Tillson, Jayshree Zaveri, Timothy B. Stockwell, Anushka Brownley, David W. Thomas, Mikkel A. Algire, Chuck Merryman, Lei Young, Vladimir N. Noskov, John I. Glass, J. Craig Venter, Clyde A. Hutchison III and Hamilton O. Smith* Abstract We have synthesized a 582, 970–base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1. 0, contains all the genes of wild-type M. genitalium G 37 except MG 408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted “watermarks” at intergenic sites known to tolerate transposon insertions. Overlapping “cassettes” of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate assemblies of approximately 24 kb, 72 kb (“ 1/8 genome”), and 144 kb (“ 1/4 genome”), which were all cloned as bacterial artificial chromosomes in Escherichia coli. .

Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments

Linear Genom. Bench (Invitrogen) representation of the circular 582, 970 -bp M. genitalium JCVI-1. 0 genome. Features shown include locations of watermarks and the aminoglycoside resistance marker, viable Tn 4001 transposon insertions determined in our 1999 and 2006 studies (3, 4), overlapping synthetic DNA cassettes that comprise the whole genome sequence, 485 M. genitalium protein-coding genes, 43 M. genitalium r. RNA, t. RNA, and structural RNA genes, and B-series assemblies

A plan for the five-stage assembly of the M. genitalium chromosome

Assembly of cassettes by in vitro recombination.

Yeast TAR cloning of the complete synthetic genome.

Synthetic Biology – Craig Ventner 2010 A

Summary: What is synthetic biology? Synthetic biology refers to both: • the design and fabrication of biological components and systems that do not already exist in the natural world • the re-design and fabrication of existing biological systems.

Synthetic Biology There are two types of synthetic biologists. • The first group uses unnatural molecules to mimic natural molecules with the goal of creating artificial life. • The second group uses natural molecules and assembles them into a system that acts unnaturally http: //syntheticbiology. org/FAQ. html

What is the difference between synthetic biology and systems biology? • Systems biology studies complex biological systems as integrated wholes, using tools of modeling, simulation, and comparison to experiment. The focus tends to be on natural systems, often with some (at least long term) medical significance. • Synthetic biology studies how to build artificial biological systems for engineering applications, using many of the same tools and experimental techniques. But the work is fundamentally an engineering application of biological science, rather than an attempt to do more science. http: //syntheticbiology. org/FAQ. html