The seminar on synthetic genomes discussed the role of genomic advances in addressing global challenges such as resource scarcity. It highlighted significant achievements in synthetic biology, including the artificial synthesis of genomes and advancements in DNA sequencing and editing technologies. The ultimate goal is to create novel biological systems for various applications, while also noting potential risks of misuse.

1. GENOME GENETICS
Seminar on
13th Nov 2014
SYNTHETIC GENOMES
Presented by:
Nethravathi R
GN113011

2. • The world is facing increasingly difficult challenges today.
• Population growth resulting in the growing demand for critical
resources such as energy, clean water, food and medicine are
taxing our fragile planet.
• To fulfill these needs we need to exploit technologies.
Can we use the genomic advances to offer
the world viable, sustainable alternatives?

3. SYNTHETIC BIOLOGY
Hot field in life science area that involves the study of
designing and construction of new biological
entities such as enzymes, genetic circuits, and cells or whole
biological systems, and the re-design of existing, natural
biological systems for useful purposes
SYNTHETIC GENOMICS
Study of Invitro chemical synthesis of genetic material i.e.,
DNA in the form of oligonucleotides, genes, or genomes with
Computational techniques for its design.
SYNTHETIC GENOME
Artificially synthesised genome (invitro)

4. PRECONDITIONS OF SYNTHETIC GENOMICS
Recent achievements in
• Whole-genome sequencing
• Development of methods of molecular tools
• DNA-sequencing, DNA-synthesis, and DNA-editing
technologies.
• Bioinformatics
• Deepening of knowledge on mechanisms of functioning of
living systems at a cellular level.

5. Guess who?

6. • John Craig Venter is a leading scientist in genomic research.
• With the invaluable contribution of Celera Genomics that he
funded in 1998, the Human Genome Project was completed three
years ahead of expected date.
• Later, he funded J. Craig Venter Institute (JCVI), with synthetic
genomics as one of the major focuses.
`

7. • After 15 years of investigation and ~$40 million of investment,
JCVI walked out this significant step for synthetic biology.
• The synthetic genome started with design of DNA sequence,
which highly depends on the accurate sequence of
Mycoplasma mycoides genome.
• Venter group spent numerous efforts on comparing different
sequencing results, making necessary corrections, and setting
watermark sequences to differentiate synthetic and natural
genomes.

8. In recent decades....(1)
• The rapid development of molecular biology, genetics and
the related biotechnology and bioengineering kept bringing
surprises to scientists worldwide...
• In 1990, Mandecki et al. assembled a plasmid of 2.1 kbp using
30 chemically synthesized oligonucleotides and the method of
serial cloning
• In 1995, Stemmer et al. synthesized a DNA fragment of 1100
bp containing the TEM-1 gene of ß-lactamase using 56
oligonucleotides and the plasmid of 2700 nucleotidesusing
136 oligonucleotides
• Including the cloning of Dolly (Wilmut et al., 1997) (followed
by cloning of a variety of animals)

9. In recent decades....(2)
• The completion of Human Genome Project (Cheung et al., 2001;
Lander et al., 2001; Venter et al., 2001) (followed by the reports of
complete genome from other species and by the spread of
personalized genome sequencing service)
• In 2002, Cello et al reported about the first synthesis of full-sized
cDNA of the poliovirus genome (about 7500 bp).
• The induction of pluripotent stem cells (Takahashi and
Yamanaka, 2006) (followed by the production of viable iPS mice
(Zhao et al., 2009).
• In 2007, Kodumal et al. obtained the largest synthetic DNA of
32,000 nucleotides containing a cluster of genes encoding the E.
Coli megaenzyme polyketide synthase.

10. In recent decades....(3)
• Recently, another breakthrough was brought by John Craig
Venter and his team, who achieved the first synthetic life—
Mycoplasma that only contains synthetic genome.

11. Published synthetic DNA sequence

12. In 2002 Cello et al.
First synthesis of full-sized cDNA of the
poliovirus genome (about 7500 bp)
steps:...(1)
1. Chemical synthesis and purification of oligonucleotides of
“positive” and “negative” polarity (in accordance with
direction from 5'- to 3'-ends and vice versa)
2. Assembly of DNA segments of 400 – 600 bp due to
overlapping complementary oligonucleotide sites follow by
subsequent ligation or use of PCA assembly of three
genome fragments of 2000 – 3000 bp from these segments
using the cloning methods and subsequent assembly of the
whole genome from these fragments.
Appearance of polymerase cycling assembly (PCA) was the next
step of improvement of gene assembly; PCA was initially used for
synthesis of HIV-2 Rev gene of 303 bp in length. The development
of methodological base resulted in overcoming of a psychological
barrier of 1 kbp.

13. In 2002 Cello et al.
First synthesis of full-sized cDNA of
the poliovirus genome (about 7500 bp)
3. The synthetic cDNA Was transcribed into viral RNA by
means of phage T7 RNA polymerase.
4. In cell free extracts this RNA induced synthesis of viral
particles.
5. The resultant de novo viruses exhibited Infectivity and
biochemical and pathogenic characteristics typical for
poliovirus
steps:..(2)

14. second full-sized genome of X174
phage (5386 bp) synthesized
• For the synthesis of the full-sized genomic DNA, they used only
ligation and PCA.
• The whole synthesis took about 2 weeks.
1. All 259 chemically synthesized oligonucleotides (42 nucleoitide
each) purified by means of gel-electrophoresis
2. Covered sequences of both DNA strands were mixed in
equimolar quantities and ligated.
3. The resultant fragments of various length (ligation did not yield full-sized
DNA due to the presence of some quantities of defect oligonucleotides and lack of 100%
effectiveness of oligomer assembly into DNA duplexes) were added up to the
“genome-sized” by means of PCA and amplified.
Smith et al.
steps:..(1)

15. second full-sized genome of X174
phage (5386 bp) synthesized
Smith et al.
4. The linear full-sized genomic DNA was circularized by means
enzymatic ligation and the use of preexisted restriction sites for
preparation of sticky ends.
5. Transfection of cells with the circular synthetic genome resulted
in appearance of infective phages
steps:..(2)

16. POTENTIAL POSITIVE APPLICATIONS
Scientists foresee many including
•new pharmaceuticals
•biologically produced ("green") fuels
•the possibility of rapidly generating vaccines
against emerging microbial diseases
•biofactory
There is the potential for misuse and accidents!

17. CONCLUSION
The ultimate goal of synthetic biology is to build novel
biological systems that have new functions or to engineer
existing biological systems to have better efficiency.
With the many challenges to the understanding of natural
biological systems, the rapid progress of emerging tools for
synthetic biology has begun to provide genomes for
applications in the areas of energy, health care, biochemicals,
and the environment.

18. REFERENCES
• http://syntheticbiology.org/
• http://www.synberc.org/
• www.syntheticgenomics.com
• www.livescience.com/6486-live-organism-synthetic-genome-created.
html
• www.intecopen.com
• Cheng et al, Syntheticbiology. Reviews in advance
biomed.eng.2012,,14:155-178
• Radko et al, The synthesis of artificial genome as the basis of
synthetic biology , Biochemistry Masco supplement series DOI
10.1134/s1990750807040014
• Konig et al, Synthetic biology and Synthetic genomics
applications between hopes and concerns ,
Currentgenomics,2013,14,11-24
• Daniel et al, Synthesising a minimal genome , Journal Science,
vol286,issue5447,2087-2090 (10 December 1999)
• Monya Baker(2011), The next step for synthetic genome, Journal
Nature | vol 473 | 403-408

19. QUESTIONNAIRE