In the quest to create the first bacterial cell controlled by a synthetic genome, the J. Craig Venter Institute (JCVI), with support from Synthetic
Genomics, Inc. (SGI), developed a variety of powerful new DNA synthesis and assembly methodologies (1–5) to manipulate large, complex DNAs.
These methods include a simple, one-step isothermal in vitro recombination technology capable of joining DNAs ranging from relatively short
oligonucleotides to fragments hundreds of kilobases in length. This approach, commonly referred to as “Gibson Assembly,” is now being used in
laboratories around the world to construct DNA fragments. It has the potential to improve upon traditional cloning methods and opens up a range
of innovative and ultimately very useful real-world applications.
Daniel G. Gibson, Ph.D., Synthetic Genomics, Inc. and
Salvatore Russello, Ph.D., New England Biolabs, Inc.
The use of recombinant DNA technology began
soon after the discovery of DNA ligase and
restriction endonucleases. Soon after, advent of
the polymerase chain reaction (PCR) opened
up new possibilities for amplification of specific
DNA sequences from a complex mixture of
genomic DNA. These technologies have been
a mainstay in the modern scientific laboratory
for several decades and remain useful methods
for cloning potentially valuable or interesting
DNA today. However, as scientists seek to work
with larger DNA fragments, conduct extensive
re-engineering of genetic elements, synthesize
whole genomes and move towards automated approaches, the technologies required to manipulate
DNA also need to evolve.
Investigators at the J. Craig Venter Institute
(JCVI) have developed a number of in vitro
enzymatic strategies to assemble short oligonucleotides into larger double-stranded DNA constructs (1-4). In 2003, JCVI made a significant
advancement in the production of a synthetic
genome by assembling the 5,386 bp genome
of phiX174, a virus that infects bacteria, in just
14 days (5). This approach involved joining
synthetic oligonucleotides by polymerase cycling
assembly, and subsequently amplifying them by
PCR (5-6). The unprecedented speed with which
this was completed laid the foundation for constructing larger and more complex genomes.
In 2004, JCVI began synthesizing the Mycoplasma genitalium genome. It was found that overlapping DNA molecules could be efficiently joined
using three enzyme specificities: (i) exonuclease
activity, that chews back the ends of DNA fragments and exposes ssDNA overhangs that can
anneal to their ssDNA complement; (ii) DNA
polymerase activity, that fills gaps in the annealed
products, and (iii) DNA ligase activity, that covalently seals the resulting nicks in the assembly. A
two-step thermocycle-based in vitro recombination method utilizing these enzymes was used
to join 101 overlapping DNA cassettes into four
parts of the M. genitalium genome, each between
136 kb and 166 kb in size. This milestone
marked the first assembly of a genome derived
from a free-living organism. At 582,970 bp, this
synthetic genome was the largest chemically defined DNA structure synthesized in a laboratory,
and was 18 times larger than any DNA that had
previously been synthesized (4).
Since then, two additional in vitro recombination
methods have been developed by JCVI to join
and clone DNA molecules larger than 300 kb in
a single step (2-4). The simplest of these methods
is Gibson Assembly, a one-step isothermal approach that utilizes the same three enzymatic
activities described previously. This method can
be used to join both ssDNA and dsDNAs.
Gibson Assembly has become the most commonly
used of the in vitro assembly methods discussed
above, as it is easy-to-use, flexible and needs
little or no optimization, even for large, complex
assemblies. All that is required is input DNA with
appropriate overlaps, and an appropriate mix of
the three enzymes – the Gibson Assembly Master
Mix. DNA fragments are added to the master mix
and incubated at 50°C for 1 hour; the resulting assembly product is a fully sealed dsDNA
suitable for a range of downstream applications
(Figure 1). JCVI has used Gibson Assembly to
rapidly synthesize the entire 16,520 bp mouse
mitochondrial genome from 600 overlapping
60-base oligonucleotides (3). It was also used in
combination with yeast assembly to synthesize
the 1.1 Mbp Mycoplasma mycoides genome, which
was then activated in a recipient cell to produce
the first synthetic cell (1).
Applications of Gibson Assembly:
Cloning. Gibson Assembly eliminates the need to
engineer restriction enzyme cut sites within DNA
when assembling fragments together. DNA molecules are designed such that neighboring fragments contain a 20-40 bp overlapping sequence. If
the DNA fragments originate from PCR products,
the overlapping sequence is introduced at the
5′ ends of the primers used in the amplification
reaction (Figure 2). DNA fragments can also be assembled with restriction enzyme digested or PCR
amplified vector to form circular products suitable
for cloning, or for use in downstream applications,
such as rolling circle amplification (RCA). To
produce these vectors by PCR, each primer needs
to include an overlap with one end of the vector, a
restriction site (e.g., Not I) not present within the
insert or inserts to enable it to be released from the
vector, and an overlap with the ends of the DNA
fragment assembly or insert. JCVI has been using
this approach to combine DNA fragments with
vectors, which are then transformed into E.coli.
One or more fragments have been routinely assembled with general cloning vectors, such as pUC19,
and assembled into NEB’s pTYB1 expression vector (NEB #N6701). The latter approach was used
to express several methylase genes, which aided
the genome transplantation efforts at JCVI (8).
Assembly of large DNA constructs. Laboratories
worldwide are beginning to explore the use of
synthetic biology approaches in the production of
pharmaceuticals, industrial compounds, antibiotics, cosmetics and alternative energy sources (7).
This often requires the assembly of a genetic
pathway consisting of multiple enzymes and their
associated regulatory elements. Although template
DNA is still required, Gibson Assembly simplifies construction of these types of molecules from
component fragments. A long stretch of desirable
DNA sequence (e.g., a 40 kb genetic pathway) can
be broken down into several overlapping PCR
products (e.g., eight, 5 kb pieces), which can then
be amplified by conventional PCR and combined
using Gibson Assembly. This approach has been
used to move genetic pathways from one organism
to another and to rapidly swap genes, promoters,
terminators and ribosome binding sites. DNAs
up to ~1 Mbp have been assembled in vitro using
Gibson Assembly (2)
Assembly of chemically-synthesized oligonucleotides into dsDNA fragments. Gibson Assembly
can also be used to directly assemble oligonucleotides into a cloning vector, such as pUC19 (3).
A common problem observed when chemically synthesizing long stretches of oligonucleotides
is the introduction of errors (9). To ensure that
error-free molecules are obtained at a reasonable
efficiency, a strategy employed by SGI and JCVI
involves the assembly of only eight to twelve
60-base oligonucleotides (with 30 bp overlaps)
at one time. The resulting dsDNA molecules are
sequence-verified and assembled into larger DNA
fragments using the same approach. Because
assembly itself does not generally introduce new
errors, the final assembled product can be retrieved
at high efficiencies. Using this approach, many of
the costly and time consuming steps currently used
to synthesize DNA, including PCR and an error
correction, are eliminated.
Site-directed mutagenesis. Gibson Assembly
can also be used to make rapid changes to DNA
fragments, including substitutions, deletions and
insertions. To use Gibson Assembly for mutagenesis, the desired changes are introduced into the
PCR primers, within the overlapping sequences at
assembly points (Figure 3). To modify a DNA sequence in this way, two PCR primers are required:
the first contains the desired nucleotide changes,
and the second contains the reverse complement of
the first primer at the overlapping region. Following amplification and assembly of the fragments,
the designed changes are incorporated into the
final product. The number of changes that can be
made at once depends on the number of fragments
simultaneously assembled. For example, an eightpiece assembly, which contains eight assembly
points, provides eight opportunities to introduce
changes in the DNA sequence. Because the method can be used to assemble large DNA fragments,
mutations can rapidly be made to very large pieces
of DNA. For example, eight modifications can be
introduced into an 80 kb DNA molecule following the assembly of eight 10 kb PCR fragments.
This site-directed mutagenesis strategy was used
during synthesis of the M. mycoides genome. The
cassettes comprising the synthetic genome were
ordered based on an imperfect draft sequence,
which resulted in small differences between the synthetic cassettes and the desired M. mycoides genome sequence. The sequences of 16 cassettes were
successfully edited using this approach (1).
Combinatorial synthesis of DNA Fragments.
In the near future, chromosomes will be designed
and synthesized for processes ranging from biofuel
production to pharmaceutical manufacture. Bacteria
and plants often carry out syntheses that far exceed
what can be readily achieved by the best organic
chemists. The genes that control desirable pathways
can be chemically synthesized, placed in artificial
chromosomes, and “installed” in suitable host cells,
including bacteria, yeast or plant cells. These multigene pathways can be constructed in a combinatorial fashion, such that each member of the library
has a different combination of gene variants. Using
screening and selection methods, cells bearing the
pathway with the desirable trait (highest yield of
a compound, for instance) can be obtained. The
engineered host organism then becomes a biologic
factory used to manufacture the product specified
by the synthetic pathway. Gibson Assembly has
the potential to be used to produce combinatorial
libraries of synthetic or semisynthetic chromosomes
carrying thousands of genes. Figure 4 demonstrates the combinatorial assembly of cassettes
produced from 60-mer oligonucleotides. Here,
1,024 (210) variants of a 1 kb gene, containing 10
single nucleotide changes, are produced from 30
Synthetic & Minimal Cells. For the past 17
years, the genomes of many organisms have been
sequenced and deposited in databases. It has recently been shown that it is possible to reverse this
process and synthesize bacterial cells from digitized
information (1). In order to realize this vision,
researchers at JCVI needed tools and technologies
to sequence, synthesize and transplant genomes.
Although many hurdles needed to be overcome,
synthetic cells can now be produced in the laboratory. As proof of concept, the 1.08 Mbp M. mycoides
JCVI-syn1.0 genome was designed, synthesized and assembled, starting from the digitized genome
sequence, and transplanted into a Mycoplasma
capricolum recipient cell to create new M. mycoides
cells controlled only by the synthetic chromosome. The only DNA present in the cells is the
designed synthetic DNA, including “watermark”
sequences, and other designed gene deletions and
polymorphisms and mutations acquired during the
building process. The new cells have the expected
phenotypic properties and are capable of continuous self-replication (1). The M. mycoides genome
is currently the largest chemically defined DNA
structure that has been synthesized in a laboratory.
It is almost twice as large as the synthetic M. genitalium genome reported in 2008, and more than an
order of magnitude larger than any reported DNA
sequence synthesized outside JCVI. What has been
learned in this “proof of concept” experiment can
now be applied to designing and producing new
organisms with useful properties.
Further, researchers at JCVI have already begun
working on their ultimate objective: to synthesize
a minimal cell with only the machinery necessary
for independent life. Now that a living cell can be
produced from a synthetic genome, components of
a synthetic genome can be removed and transplanted in an iterative fashion until only the essential genes are present and the genome is as small
as possible. This will help to better understand the
function of every gene in a cell and what DNA is
required to sustain life in its simplest form. Gibson
Assembly is one of the core technologies that will
be used to achieve these goals.
Gibson Assembly is a simple and robust method
that enables the simultaneous production of many
different combinations of genes and pathways,
accelerating the progress of synthetic biology.
Furthermore, this powerful technology has the potential to help turn DNA sequence into genes and
pathways useful in the production of biofuels, industrial compounds, pharmaceuticals and vaccines.
The synthesis of genes and pathways, and even
small genomes, has been made easier with Gibson
Assembly, helping to move the field of synthetic biology forward. As the power of DNA sequencing increases and sequencing costs decrease, DNA
databases will continue to fill with novel genes
and pathways waiting to be identified, optimized
and expressed in a heterologous host organism.
It is time to better understand how to turn these
DNA sequences into useful applications.
The ability to quickly construct whole genes and
genomes has the potential to accelerate research
in a variety of other fields. This capability may
also make it possible to quickly respond to
emerging threats, and may allow researchers to
understand how “life” works. The power of large
scale DNA synthesis will dramatically impact
the way research is done and vastly accelerate the pace of science. The Gibson Assembly
Master Mix provides a new and powerful tool for
biotechnology, whose most far-reaching benefits
may not yet even be envisioned.
- Gibson, D.G. et al. (2010) Science, 239, 52–56.
- Gibson, D.G. et al. (2009) Nature Methods, 6, 343–345.
- Gibson, D.G. et al. (2010) Nature Methods, 7, 901–903.
- Gibson, D.G. et al. (2008) Science, 319, 1215–1220.
- Smith et al. (2003) PNAS, 100, 15440–15445.
- Stemmer, W.P. et al. (1995) Gene, 164, 49–53.
- Endy, D. (2005) Nature, 438, 449–453.
- Lartique, C. et al. (2009) Science, 325, 1693–1696.
- Carr et al. (2004) Nucleic Acids Res. 32, e162.