Syn Bio Introduction

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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_Page
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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-

    %