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GET STARTED IN SYNTHETIC
BIOLOGY
Anggoro Wiseso
UI SynBio Club Class !"#
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Ou$line
% In$ro&u'$ion (&e)ini$ions an& *is$ory+
% ,un&a-en$als o) -ole'ular biology
% Co-.aring Syn$*e$i' Biology /i$* $*eir )rien&s
%A..li'a$ion o) Syn$*e$i' Biology% ,as'ina$ing 0ro1e'$ in SynBio
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Dis'lai-er
% T*is is NOT a 'o-.re*ensi2e loo3 a$ Syn$*e$i'
Biology451us$ an in$ro&u'$ion
% I$ -ay no$ be 6e2ery$*ing6 you nee& $o 3no/7 bu$ I8ll $ry $o
ge$ 'lose% ,or e2ery$*ing else7 $*ere8s Wi3i.e&ia
% ,or -ore &e$aile& $o.i's7 o$*er .eo.le /ill be a -u'* be$$er
sour'e o) in)or-a$ion9% Trans'ri.$ional 'on$rol s$ra$egies7 $*e Regis$ry7 an& 3no/le&ge abou$
/*a$ $y.es o) .ar$s are .ossible9 Sean :earney
% Lab E;ui.-en$9
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W*a$ is syn$*e$i' biology (synbio+>
% Syn$*e$i' Biology is9% T*e &esign an& 'ons$ru'$ion o) ne/ biologi'al .ar$s7 &e2i'es7 an&
sys$e-s7 an&
% T*e re?&esign o) e@is$ing7 na$ural biologi'al sys$e-s )or use)ul
.ur.oses5()ro- Syn$*e$i'Biology5org+
% Basi'ally7 i$8s gene$i' engineering (a3a -ole'ular biology+
)or .ra'$i'al .ur.oses
%
Try $o loo3 a$ gene$i's )ro- engineering .ara&ig-% Genes an& &i))eren$ gene$i' 'o-.onen$s .ar$s% Grou.s o) 'o-.onen$s &e2i'es
% o&el &e2i'es as 'ir'ui$s
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W*a$ is syn$*e$i' biology (synbio+>
% Engineering Goal9
To buil& 'o-.onen$s $*a$ 'an be reliably an& .re&i'$ably
asse-ble& in$o e2er -ore 'o-.li'a$e& sys$e-s
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W*o8s in '*arge>% T*e Biobri'3s ,oun&a$ion (BB,+ is one o) $*e bigges$
ini$ia$i2es /orl&/i&e &ri2ing $*e &e2elo.-en$ o) synbio
% Goals o) $*e BB,9% E&u'a$e $*e .ubli' abou$ synbio an& bio$e'*nology
% a3e bio$e'* si-.le $o &o an& a2ailable $o $*e .ubli'
% De)ine e$*i'al 'on'erns an& .ra'$i'es in synbio
% T*e BB, &e2elo.e& an& -ain$ains $*e 0ar$s Regis$ry
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TAATACGACTCACTATAGGGAGA
DNA Construction = #1 Tech. of 21st Ctry.
,ro- absra'$in)or-a$ion $o
.*ysi'al7
li2ing DNA
&esigns5
!!F9 "!7!!! b.
!"!9 "7!!!7!!! b.
!"9 "!! -illion>
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Ou$line
% In$ro&u'$ion (&e)ini$ions an& *is$ory+
% ,un&a-en$als o) -ole'ular biology
% Co-.aring Syn$*e$i' Biology /i$* $*eir )rien&s
%A..li'a$ion o) Syn$*e$i' Biology% ,as'ina$ing 0ro1e'$ in SynBio
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Synbio 1argon%A .ar$ is a DNA se;uen'e en'o&ing so-e .ar$ o) $*e gene$i'
-a'*inery7 in'lu&ing bu$ no$ li-i$e& $o9% 0ro-o$ers
% Riboso-e bin&ing si$es (RBS+
% 0ro$ein 'o&ing regions
% Ter-ina$ors
%A &e2i'e is a grou. o) .ar$s $*a$ /or3 $oge$*er )or s.e'i)i'
)un'$ions7 su'* as9
% 0ro$ein .ro&u'$ion% Sensing=re.or$ing
% easure-en$
% Signal in2ersion
% Cell signaling
% Cell -o$ili$y
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ore 1argon
%A '*assis is $*e organis- (*os$+ 'on$aining $*e &e2i'es% Usually E. coli or S. cerevisiae(yeas$+
% Also 'an be ba'$erio.*age (2irus+7 .lan$s7 -a--als7 e$'44
any$*ing7 really
% Cloning &oes no$ re)er $o Dolly $*e s*ee.% Re)ers $o -ani.ula$ion o) re'o-binan$ DNA
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Ho/ &o I -a3e -y &e2i'e>
% Lo$s o) /ays $o &o i$7 bu$ $*ere are $/o I /oul& s.e'i)i'ally
re'o--en&9% A Asse-bly (si-ilar $o S$an&ar& Asse-bly+
% Base& on $ra&i$ional 'loning -e$*o&s
% I) a .ar$ is &esigne& $o /or3 /i$* $*ese -e$*o&s7 i$ is sai& $o be a Biobri'3% Gibson Asse-bly
% De2elo.e& re'en$ly
% Ra.i&ly be'o-ing one o) $*e -e$*o&s o) '*oi'e
% T*e ne@$ )e/ sli&es /ill gi2e you an i&ea o) bo$* -e$*o&s7
bu$ )irs$ le$8s $al3 abou$ so-e o) $*e $ools you /ill be using% EnJy-es
% 0las-i&s
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Ou$line
% In$ro&u'$ion (&e)ini$ions an& *is$ory+
% ,un&a-en$als o) -ole'ular biology
% Co-.aring Syn$*e$i' Biology /i$* $*eir )rien&s
%A..li'a$ion o) Syn$*e$i' Biology% ,as'ina$ing 0ro1e'$ in SynBio
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0roble-
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Ele'$ri'al
Engineering
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e'*ani'al Engineering
water = weight water
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Biological Engineering
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Biological Engineering
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PCR
Sequencing
rDNA
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A LIVING HOUSE -Terreform! "a# Tree
Ha#
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% Ho/ is Syn$*e$i' Biology Di))eren$> Syn$*e$i' biology uses
)our .rin'i.les no$ $y.i'ally )oun& in gene$i's7 geno-i's7
or -ole'ular biology9
abs$ra'$ion7
-o&ulari$y7
s$an&ar&iJa$ion7
&esign an& -o&eling5
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Abstraction9
%Abstraction? you 'an use .ar$s=&e2i'es=sys$e-s /i$*ou$*a2ing $o /orry abou$ *o/ $*ey /or35
DNA -a3es .ar$s5
Parts in$o &e2i'es5
Devices 'onne'$e& $o -a3e sys$e-s5
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Modularity9
%parts, devices and systems? 'onne'$e& as sel)?
'on$aine& uni$s an& 'o-bine& in any 'o-bina$ion you
/an$
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Standardization:
%All $*e Tab A8s )i$ in$o all $*e Slo$ B8s5
%An e2ery&ay [email protected] ? all lig*$ bulbs )i$ in$o any so'3e$
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Designing and modeling
% buil& a -o&el
% $es$ $*e &e2i'es 'a.a'i$y% i-.ro2es &esign
% $es$s basi' biologi'al assu-.$ions $*a$ 'oul& be )alse
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Regis$ry o) S$an&ar& biologi'al 0ar$s
% *$$.9==.ar$sregis$ry5org=ainK0age
http://partsregistry.org/Main_Pagehttp://partsregistry.org/Main_Page7/25/2019 Syn Bio Introduction
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DNA is DNA
% E. Coliis our '*assis% Can use .ar$s )ro- any organis-
% Can use .ar$s -a&e by a 'o-.u$er
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Abs$ra'$ion Hierar'*ya h$man in%ention &e!igne& to a!!i!t
'eo'le in engineering com'le( !)!tem!
Se*$ence! of +NAenco&e ,'art!
A!!em#lie! of 'art!ma.e $' &e%ice!
A!!em#lie! of &e%ice!ma.e a !)!tem
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0ar$ se;uen'e o) DNA /i$* *u-an &e)ine& )un'$ion
AAAATG/A///G/TGT/GAT/AAA/G/G/GGTGG/GAATATGGTGGT/AA/G//G///GTTATGG/AATGG/TGGGT/AAAGT/AG/AG/GGAA/GGAG//GAAT/G/G//TGGTT//AGGTGGAAGATGA/GGT//GGGAA
TTG/G//GGAA/AA/GTAAG/A//TGTT//AG//GTTTGT//G/GG/GA/AGTG/G/G/A//ATTAG/GG/A/GGGATTAGGG/TGG/AATTGTG/AG/GTAT/GTGGATAA//ATAA/GGGATG/TGGAG/TTGG/A//AG/GAG/GGGG/GGG/TTT//ATT/G/G//TGG/TG//AGTG//GGTAA/G/GGG/G/AGGG/ATGA/AAAAGAAGGGTAAT/TAGAGG/AT/AAATAA
AA/GAAAGG/T/AGT/GAAAGA/TGGG//TTT/GTTTTAT/TGTTGTTTGT/GGTGAA/G/T/T//TGAGTAGGA/AAAT//G//G//
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0ar$s asse-ble& in$o De2i'es
AAAATG/A///G/TGT/GAT/AAA/G/G/GGTGG/GAATATGGTGGT/AA/G//G///GTTATGG/AATGG/TGGGT/AAAGT/AG/AG/GGAA/GGAG//GAAT/G/G//TGGTT//AGGTGGAAGATGA/GGT//GGGAA
TTG/G//GGAA/AA/GTAAG/A//TGTT//AG//GTTTGT//G/GG/GA/AGTG/G/G/A//ATTAG/GG/A/GGGATTAGGG/TGG/AATTGTG/AG/GTAT/GTGGATAA//ATAA/GGGATG/TGGAG/TTGG/A//AG/GAG/GGGG/GGG/TTT//ATT/G/G//TGG/TG//AGTG//GGTAA/G/GGG/G/AGGG/ATGA/AAAAGAAGGGTAAT/TAGAGG/AT/AAATAA
AA/GAAAGG/T/AGT/GAAAGA/TGGG//TTT/GTTTTAT/TGTTGTTTGT/GGTGAA/G/T/T//TGAGTAGGA/AAAT//G//G//
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0ar$s asse-ble& in$o De2i'es
AAAATG/A///G/TGT/GAT/AAA/G/G/GGTGG/GAATATGGTGGT/AA/G//G///GTTATGG/AATGG/TGGGT/AAAGT/AG/AG/GGAA/GGAG//GAAT/G/G//TGGTT//AGGTGGAAGATGA/GGT//GGGAA
TTG/G//GGAA/AA/GTAAG/A//TGTT//AG//GTTTGT//G/GG/GA/AGTG/G/G/A//ATTAG/GG/A/GGGATTAGGG/TGG/AATTGTG/AG/GTAT/GTGGATAA//ATAA/GGGATG/TGGAG/TTGG/A//AG/GAG/GGGG/GGG/TTT//ATT/G/G//TGG/TG//AGTG//GGTAA/G/GGG/G/AGGG/ATGA/AAAAGAAGGGTAAT/TAGAGG/AT/AAATAA
AA/GAAAGG/T/AGT/GAAAGA/TGGG//TTT/GTTTTAT/TGTTGTTTGT/GGTGAA/G/T/T//TGAGTAGGA/AAAT//G//G//
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DEICE TO SYSTE0las-i&s an& Trans)or-a$ion
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Ou$line
% In$ro&u'$ion (&e)ini$ions an& *is$ory+
% ,un&a-en$als o) -ole'ular biology
% Co-.aring Syn$*e$i' Biology /i$* $*eir )rien&s
%A..li'a$ion o) Syn$*e$i' Biology
% ,as'ina$ing 0ro1e'$ in SynBio
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A..li'a$ion o) Syn$*e$i' Biology
% Naturally Replicating Rubber for Tires
% Delivering Economic, Reneable !ioAcrylic
% Ma"ing #$reen %&emicals' from Agricultural (aste
%
)accine Development% Developing a Suite of !iobased *roducts and
Services
% !iosensor for many sensoring problems
% *roducing !iofuels and Reneable %&emicals as*etroleum Alternatives
% +ncreasing Efficiency in !ioprocessing of
*&armaceuticals
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Ou$line
% In$ro&u'$ion (&e)ini$ions an& *is$ory+
% ,un&a-en$als o) -ole'ular biology
% Co-.aring Syn$*e$i' Biology /i$* $*eir )rien&s
%A..li'a$ion o) Syn$*e$i' Biology
% ,as'ina$ing 0ro1e'$ in SynBio
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mahal0 ti&a. 1at$h &ari langit
/ornell
Slo%enia
Hong 2ong/UH2
3ari!Bettenco$rt
Vi!i#le0 A''licati%e0 Val$a#le0 3ro!'ecti%e
5em#$at #io!en!or
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LL5em#$at #io!en!or.$alita! air &i wila)ahe.!'lora!i min)a.la'i!an 'a!ir6
4ac$n !e'erti ar!eni.&an naftalena &a'atmenero#o! i!ola!imen$1$ ling.$ngan#e#a!6
3emanta$an .$alita!air 'enting &anmemerl$.an !am'el#an)a.6
Bio!en!or baru#er#e&a &ari#io!en!or )ang !$&ah&i.em#ang.an
!e#el$mn)a78$oro!en!i0 'H0
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/O4NELL
Si!tem mem#eri &atatan'a 'erl$
inter'reta!i la#7!e'erti )ang&iha!il.an &ari8$oro!en!i mi!al.an90wirele!!0 .ontin)$
&an real-time6
5engg$na.anShewanella
oneidensis MR-1
!e#agai cha!!i!!6
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arsRar!4
5trB
5trB
5trB
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/UH2% 5em#$at #a.teri
)ang &a'at:melihat6
% Ba.teri
menge.!'re!i.anrho&o'!in )ang'e.a caha)a6
% 5engen&ali.an
gera.an &ane.!'re!i gen6
% +i#an&ing.an#io!en!or lain0 tim
mem#$at
% 5em#$.a 'el$ang a'li.a!ilain !e'erti
% Light-&irecte& #acteria!orter
% 5etal ion! collection
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S4 $t..e#erlang!$nganhi&$' archaea6
S4I &antran!&$!ern)a7HtrI9 $nt$.fotota.!i! 'o!itif
#agi !inar &engan'an1anggelom#ang.$rang &ari >>nm6
S4II &an HtrII$nt$. fotota.!i!negatif #agi !inar&engan 'an1anggelom#ang le#ih&ari >> nm6
/UH25engintegra!i.an !en!or) rho&o'!in .e &alam E6coliE6/oli !ecara alami memili.i T!r &an Tar $nt$. .emota.!i!
tif itif
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negatif 'o!itif
Cahaya Biru
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A&a.$e& )ro-
%