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"elp#Sy!thetic Biology

Registry Help Pages: 

TOC

 

At-a-Glance

 

FAQ

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Synthetic Biology  O!r Philosophy 

Parts  Plas"i# Bac$%ones  BioBric$ Pre&i' an# S!&&i'  Stan#ar#s  Asse"%ly

Stan#ar#s  Asse"%ly (etho#s  Shipping

$hat is Sy!thetic Biology

"A Scientist discovers that which exists; an Engineer creates that which never was."  

% &heodore vo! 'arme!

For a few illio! years( evolutio! has e!sured that the !atural world is filled with a diverse array of

orga!isms a!d systems that wor)* &he goal of iology is to study these orga!isms a!d systems a!d

explai! how they operate i! a road a!d specific se!se*

Sy!thetic iology uses much of the same tech!iques a!d equipme!t of the iological scie!ces( ut

i!stead of research a!d !ew discoveries( a sy!thetic iologist loo)s to co%opt a!d improve upo! the

ge!etic luepri!ts of existi!g orga!isms( to desig! a!d create !ovel iological devices a!d systems*

 A sy!thetic iologist may loo) to ma!ipulate orga!isms i!to io%factories for the productio! of iofuels(

the upta)e of ha+ardous material i! the e!viro!me!t( or creati!g iological circuits* ,icroorga!isms( i!

particular( are small( easily powered( are co!ducive to co!trol( a!d much of their framewor) a!d

machi!ery is )!ow!* As the cost of seque!ci!g a!d -NA sy!thesis co!ti!ues to drop( amitious ideas

for sy!thetic iology are ecomi!g more affordale a!d achievale( a!d u!til the! the Registry also

provides physical parts through the Repository*

$hy Sy!thetic Biology ased o! sta!dard parts

&o desig! these !ew systems( sy!thetic iologists will loo) to !atural iological systems to fi!d

fu!ctio!al u!its of -NA or sy!thesi+e !ew o!es that do !ot !aturally exist* &hese fu!ctio!al u!its are

tested a!d characteri+ed a!d may ecome compo!e!ts i! a iological device or system* $e refer to

them as parts# a seque!ce of -NA that e!codes for a specific iological fu!ctio!*

&he stan#ar# i! .sta!dard parts. mea!s that these parts meet estalished criteria* AssemlySta!dards( li)e the BioBric$ Stan#ar#( e!sure compatiility etwee! parts a!d defi!e how part

samples will e assemled together y the e!gi!eer* Part samples that elo!g to the same Assemly

Sta!dard ca! e assemled together creati!g !ew( lo!ger( a!d more complex parts( while still

mai!tai!i!g the format of the Assemly Sta!dard* &his idempotent  assemly mea!s that a!y !ewly

composed part will adhere to its Assemly Sta!dard without !eed for ma!ipulatio!( a!d ca! e used

i! future assemlies without issue*

&he goal of most e!gi!eers is to simplify a!d sta!dardi+e the process of creatio!* By simplifyi!g a!d

sta!dardi+i!g iology( the e!gi!eer ca! go o! to use parts to create their iological systems withoutspe!di!g time researchi!g each i!dividual compo!e!t or worryi!g aout how to assemle them

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together* &he goal o& the Registry is to aid i! this process y creati!g a lirary of sta!dard parts that

have ee! tested( characteri+ed( a!d orga!i+ed so that users ca! fi!d what they !eed whe!

developi!g !ew iological systems*

$hat is the Registry

/et 0 /ive 10 Share2* &he philosophy ehi!d the Registry a!d what ma)es it a great resource for

sy!thetic iology*

&he Registry is a co!ti!uously growi!g commu!ity collectio! of iological parts that ca! e mixed a!d

matched to uild sy!thetic iology devices a!d systems* Fou!ded i! 3445 at ,I&( the Registry is part

of the sy!thetic iology commu!ity6s efforts to ma)e iology easier to e!gi!eer* It provides a resource

of availale iological parts that have ee! user%tested a!d characteri+ed for users developi!g

sy!thetic iology pro7ects*

&he Registry provides these resources for the co!ti!ued growth of sy!thetic iology i! educatio!(

academic research( a!d !ew i!dustry* &he Registry is part of the i/8, Fou!datio!*

/et 0 /ive 10 Share2

&he Registry is a! ope! commu!ity that ru!s a!d grows o! the ./et 0 /ive 10 Share2. philosophy*

9sers get parts( samples( data( a!d tools from the Registry to wor) o! their sy!thetic iology pro7ects*

&hey6ll give ac) to the Registry the !ew parts they6ve made( as well as data a!d experie!ce o! !ew

a!d existi!g parts* Fi!ally( users will share experie!ce a!d collaorate i! the Registry6s ope!

commu!ity through their wi)is( the forums( a!d other social tools*

$hy use the Registry

 The Catalog of Parts and Devices

:ou ca! rowse the Registry6s ;atalog of Parts 0 -evices where parts a!d devices are orga!i+ed y

various criteria( i!cludi!g fu!ctio!( chassis( a!d sta!dards* :ou ca! also use the Registry search

tools to fi!d parts y descriptors( or specific part !ames* Parts ra!ge from fou!datio!al such as

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promoters( termi!ators to u!ique a!d i!teresti!g li)e gas vesicle parts( pigme!t parts( wi!tergree!

smelli!g parts( etc*

 Documentation & Characterization

&here is already a wealth of i!formatio! aout each part a!d device( telli!g you how they wor) a!d

how to use them* ,a!y of the Registry parts a!d devices have ee! user%tested a!d characteri+ed(

so that you ca! focus o! uildi!g your system i!stead of researchi!g each !ecessary compo!e!t*

 The Registry Repository 

Floati!g acteria( Bacto%Blood( ;amridge pigme!t parts# i/8, teams a!d las co!ti!ue to add

i!teresti!g a!d !ovel parts( devices a!d systems to the Registry* Physical samples are also se!t to

the Registry( added to the Registry Repository a!d tested for their quality 1seque!ce( gel results( etc2*

If you6ve fou!d a! i!teresti!g part( a!d a sample of it is availale( you ca!  request it from the Registry*

:ou do!6t have to ma)e it from scratch<

 The BioBrick Standard 

&he sta!dard i! .sta!dard parts. e!sures compatiility etwee! parts( allowi!g them to

e assemled together creati!g !ew lo!ger a!d more complex parts( while still mai!tai!i!g the

structural eleme!ts of the sta!dard* &his idempotent  characteristic mea!s that a!y !ewly composed

part will adhere to its sta!dard without !eed for ma!ipulatio!( a!d ca! e used i! future assemlies

without issue* ,ost of the parts o! the Registry adhere to the BioBric) Sta!dard( so their samples ca!easily e assemled( this allows the e!gi!eer to focus o! desig! i!stead of assemly*

 Open Community 

&he Registry is a! ope! commu!ity where i!formatio! a!d experie!ce is shared* Si!ce the Registry

uses the wi)i format( users ca! easily ma)e or add cha!ges( i!cludi!g more i!formatio! o! a part6s

characteristics( writi!g aout their experie!ce with a device( etc* &he Registry also has a forum a!d

comme!ts system( which is used as a place for discussio!*

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$hat are iological parts

 A iological part 1or simply( part2 is a seque!ce of -NA that e!codes for a iological fu!ctio!( for

example apromoters or  protei! codi!g seque!ces*

 At its simplest( a asic part is a si!gle fu!ctio!al u!it that ca!!ot e divided further i!to smaller

fu!ctio!al u!its* Basic parts ca! e assemled together  to ma)e lo!ger( more complex composite

parts( which i! tur! ca! e assemled together to ma)e devices that will operate i! livi!g cells*

Basic a!d ;omposite Parts

 A %asic part is a fu!ctio!al u!it of -NA that ca!!ot e sudivided i!to smaller compo!e!t

parts* BBa)R**+, is an e'a"ple o& a %asic part a pro"oter reg!late# %y la"%#a cl. 

 A co"posite part is a fu!ctio!al u!it of -NA co!sisti!g of two or more asic parts assemled

together* BBa)/,0+*1is an e'a"ple o& a co"posite part consisting o& a r%s protein co#ing

region &or a re# &l!orescent protein an# ter"inator. 

 A #evice is a type of composite part that co!ducts a! operatio! i! the cell* BBa)/120**1 is an

e'a"ple o& a #evice 3hich !ses BBa)R**+, an# BBa)/,0+*1 to reg!late pro#!ction o& re#

&l!orescent protein in cells 3ith la"%#a cl. 

Parts in relation to...

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"ere we have a part sa"ple 1lue2 for BBa=R44>? mai!tai!ed i! a plas"i# %ac$%one 1gree!2* :ou ca! see that the

part sample is fla!)ed y the plasmid ac)o!e6s pre&i' 1P2 a!d s!&&i' 1S2( which dictates the part sample6sasse"%ly

stan#ar#*

Sa"ples % &he Registry has samples of specified parts i! its dataase availale for requestor through our  -NA -istriutio! 'its* A sample is a physical copy of a part* $e receive a sample

of a part from users 1mai!tai!ed i! our plasmid ac)o!e2( add them to the Registry6s Repository(

a!d ru! quality co!trol tests to ma)e sure that the sample matches the part* It is importa!t to

u!dersta!d that there is a differe!ce etwee! a part o! the Registry6s dataase( a!d the part

sample that you6ll e usi!g i! the la*

Asse"%ly Stan#ar#s % A part is compatile with a! assemly sta!dard( as lo!g as its

seque!ce meets the requireme!ts of said assemly sta!dard@ this mea!s that the part does !ot

have a!y i!ter!al restrictio! sites that would i!terfere with assemly( referred to as illegal

restrictio! sites* :ou ca! chec) to see if a part meets a! assemly sta!dards requireme!ts y

loo)i!g at the seque!ce a!d features ox* It is important to remember that a part does not include

the prefix and suffix as defined by an assembly standard.

Asse"%ly (etho#s is the physical process of comi!i!g two 1or more2 asic or composite

part samples together i! series to form a larger composite part* &here are ma!y differe!t

assemly methods( each with their ow! adva!tages*

Plas"i# Bac$%ones % A plasmid ac)o!e propagates a sample of a part( located i!

etwee! the prefix a!d suffix of the plasmid ac)o!e* As such the plasmid ac)o!e ca! dictate

the assemly sta!dard a!d assemly method of that part sample*

4'a"ple

:ou6ll !otice that BBa=R444 is a part that is compatile with all Registry

supported asse"%ly stan#ar#s*

If you were to fi!d a physical locatio! for this part 1usi!g the /et &his Part page2 you6ll see

that there are several availale sa"ples i! differe!t plas"i# %ac$%ones 1pSB?;5 a!d pSB?A3*

&he pSB?;5 plas"i# %ac$%one has a prefix a!d suffix as defi!ed y the BioBric)

RF;?4C stan#ar#* &he availale sa"ples of BBa=R444 are fla!)ed y this prefix a!d suffix*

I! order to asse"%le a! availale sample of BBa=R444 to a differe!t part usi!g the 5A

 Assemly method( you will !eed to ma)e sure that a sample of the other part  is o! a plas"i#

%ac$%one that also elo!gs to the BioBric) RF;?4C stan#ar#*

$hy use Registry partsD

 The Catalog of Parts and Devices

:ou ca! rowse the Registry6s ;atalog of Parts 0 -evices where parts a!d devices are orga!i+ed yvarious criteria( i!cludi!g fu!ctio!( chassis( a!d sta!dards* :ou ca! also use the Registry search

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tools to fi!d parts y descriptors( or specific part !ames* Parts ra!ge from fou!datio!al such as

promoters( termi!ators to u!ique a!d i!teresti!g li)e gas vesicle parts( pigme!t parts( wi!tergree!

smelli!g parts( etc*

 Documentation & Characterization

&here is already a wealth of i!formatio! aout each part a!d device( telli!g you how they wor) a!d

how to use them* ,a!y of the Registry parts a!d devices have ee! user%tested a!d characteri+ed(

so that you ca! focus o! uildi!g your system i!stead of researchi!g each !ecessary compo!e!t*

 The Registry Repository 

Floati!g acteria( Bacto%Blood( ;amridge pigme!t parts# i/8, teams a!d las co!ti!ue to add

i!teresti!g a!d !ovel parts( devices a!d systems to the Registry* Physical samples are also se!t to

the Registry( added to the Registry Repository a!d tested for their quality 1seque!ce( gel results( etc2*

If you6ve fou!d a! i!teresti!g part( a!d a sample of it is availale( you ca!  request it from the Registry*

:ou do!6t have to ma)e it from scratch<

 The BioBrick Standard 

&he sta!dard i! .sta!dard parts. e!sures compatiility etwee! parts( allowi!g them to

e assemled together creati!g !ew lo!ger a!d more complex parts( while still mai!tai!i!g the

structural eleme!ts of the sta!dard* &his idempotent  characteristic mea!s that a!y !ewly composed

part will adhere to its sta!dard without !eed for ma!ipulatio!( a!d ca! e used i! future assemlieswithout issue* ,ost of the parts o! the Registry adhere to the BioBric) Sta!dard( so their samples ca!

easily e assemled( this allows the e!gi!eer to focus o! desig! i!stead of assemly*

 Open Community 

&he Registry is a! ope! commu!ity where i!formatio! a!d experie!ce is shared* Si!ce the Registry

uses the wi)i format( users ca! easily ma)e or add cha!ges( i!cludi!g more i!formatio! o! a part6s

characteristics( writi!g aout their experie!ce with a device( etc* &he Registry also has a forum a!d

comme!ts system( which is used as a place for discussio!*

$hat types of parts are there

If you visit the ;atalog of Parts a!d -evices( you ca! rowse through parts y typeEfu!ctio!( alo!g

with other criteria* :ou ca! read the help pages for the differe!t Registry part types elow*

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 Pro"oters# A promoter is a

-NA seque!ce that te!ds to

recruit tra!scriptio!al

machi!ery a!d lead to

tra!scriptio! of the

dow!stream -NA seque!ce*

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 Ri%oso"e Bin#ing Sites# A

riosome i!di!g site 1RBS2 is

a! RNA seque!ce fou!d i!

mRNA to which riosomes ca!

i!d a!d i!itiate tra!slatio!*

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 Protein #o"ains# Protei!

domai!s are portio!s of

protei!s clo!ed i! frame with

other protei!s domai!s to

ma)e up a protei! codi!g

seque!ce* Some protei!

domai!s might cha!ge the

protei!6s locatio!( alter its

degradatio! rate( target the

protei! for cleavage( or e!ale

it to e readily purified*

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 Protein co#ing se5!ences#

Protei! codi!g seque!ces

e!code the ami!o acid

seque!ce of a particular

protei!* Note that some

protei! codi!g seque!ces o!ly

e!code a protei! domai! or

half a protei!* thers e!code

a full%le!gth protei! from start

codo! to stop codo!* ;odi!g

seque!ces for ge!e

expressio! reporters such as

GacH a!d /FP are also

i!cluded here*

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 Translational !nits#

&ra!slatio!al u!its are

composed of a riosome

i!di!g site a!d a protei!

codi!g seque!ce* &hey egi!

at the site of tra!slatio!al

i!itiatio!( the RBS( a!d e!d at

the site of tra!slatio!al

termi!atio!( the stop codo!*

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 Ter"inators# A termi!ator is

a! RNA seque!ce that usually

occurs at the e!d of a ge!e or

opero! mRNA a!d causes

tra!scriptio! to stop*

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 6NA# -NA parts provide

fu!ctio!ality to the -NA itself*

-NA parts i!clude clo!i!g

sites( scars( primer i!di!g

sites( spacers( recomi!atio!

sites( co!7ugative tra!fer

eleme!ts( tra!sposo!s(

origami( a!d aptamers*

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 Pri"ers# A primer is a short

si!gle%stra!ded -NA

seque!ces used as a starti!g

poi!t for P;R amplificatio! or

seque!ci!g* Although primers

are !ot actually availale via

the Registry distriutio!( we

i!clude commo!ly used primer 

seque!ces here*

Co"posite parts# ;omposite

parts are comi!atio!s of of

two or more BioBric) parts*