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Thomas H. LaBean, Erik Winfree and John H. Reif- Experimental Progress in Computation by Self-Assembly of DNA Tilings

Thomas H. LaBean, Erik Winfree and John H. Reif- Experimental Progress in Computation by Self-Assembly of DNA Tilings

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07/06/2012

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DIMACSSeriesinDiscreteMathematics andTheoreticalComputerScienc
ExperimentalProgressinComputationby Self-AssemblyofDNATilings 
ThomasH.LaBean,ErikWinfree,andJohnH.Rei
Abstract. 
ApproachestoDNA-basedcomputingbyself-assemblyrequirethe useofDNAnanostructures,calledtiles,thathaveecientchemistries,ex- pressivecomputationalpower,andconvenientinputandoutputIOmech- anisms.WehavedesignedtwonewclassesofDNAtiles,TAOandTAE,botofwhichcontainthreedouble-heliceslinkedbystrandexchange.Structural analysisofaTAOmoleculehasshownthatthemoleculeassemblesecientlfromitsfourcomponentstrands.Herewedemonstrateanovelmethodfor IOwherebymultipletilesassemblearoundasingle-strandedinputscaolstrand.Computationbytilingtheoreticallyresultsintheformationofstruc- turesthatcontainsingle-strandedoutputreportedstrands,whichcanthen beisolatedforsubsequentstepsofcomputationifnecessary.Weillustratethe advantagesofTAOandTAEdesignsbydetailingtwoexamplesofmassivelparallelarithmetic:constructionofcompleteXORandadditiontablesbylin- earassembliesofDNAtiles.Thethreehelixstructuresprovideexibilityfor topologicalroutingofstrandsinthecomputation,allowingtheimplementation ofstringtilemodels
1.Introduction 
Inhisseminalpaperonmolecularcomputation 
Adl94 
,Adlemandemon- stratedagenerate-and-separatealgorithmforsolvingDirectedHamiltonianPatProblemsDHPP.Intherstphaseofhisalgorithm,acombinatoriallibraryof DNAmoleculesrepresentingpotentialsolutionstotheproblemisgeneratedby randomhybridizationandligationofasmallnumberofoligonucleotidespecies.Ithesecondphase,asequenceofanityseparationandotherlaboratoryprocedureisolatestheDNAmoleculesrepresentingtheactualsolution;thesequenceofthimolecule,andthustheanswertothemathematicalproblem,canthenbedetermined.However,thegenerate-and-separatestrategyhastwodiculties.First,for moderatelylargeproblems,ana  ivegenerationstrategymustgenerateanastro- nomicalnumberofDNAstrandstorepresentallpotentialsolutions.Second,the numberoflaboratoryprocedures,eachtimeconsuminganderror-prone,growswitthesizeoftheproblemTherstdicultycanbeavoidedbyinterspersingthegenerateprocedureandtheseparationprocedures 
FB97,FB9
.SimpleexamplesofthisapproacincludeDNAimplementationsofdynamicprogramming 
BB9
andbreadth-rs
 
0000copyrightholder 
12
 
122THOMASH.LABEAN,ERIKWINFREE,ANDJOHNH.REI
search 
MAS99,YS9
.However,thisapproachusuallycomesatthecostof makingtheseconddicultymoresevere,bymultiplyingthenumberofprocedurerequired. Ourworkhasfocusedonanotherapproach:computationbyself-assemblySelf-assemblyisthespontaneousself-orderingofsubstructuresintosuperstruc- turesdrivenbyannealingof,inthiscase,Watson-Crickbase-pairingDNAsequences.Computationbyself-assemblyentailsthebuildingupofsuperstructurefromstartingunitssuchthattheassemblyprocessitselfperformstheactualcomputation.Adlemanmadeuseofasimpleformofcomputationbyself-assemblyihisoriginalexperiment 
Adl94 
:hisalgorithmdoesnotblindlygenerateallpos- siblesequencesofvertices;instead,theoligonucleotidesequencesandthelogicof Watson-Crickcomplementarityguidetheself-assemblyprocessessothatonlyvalipathsaregenerated.Wehavegeneralizedthisapproachtotwo-dimensional2D self-assemblyprocesses,whereitcanbeseenthatcomputationbyself-assemblyiTuring-universal 
Win9
.Thebuildingblocksintheseconstructionsarebranched DNAcomplexes,whichwecal
DNAtile
,consistingofseveralindividualDNoligonucleotidesthatassociatewithwell-denedsecondarystructure.DNAtiles aredesignedtocontainseveralshortsectionsofunpaired,single-strandDNAssDNAextendingfromtheendsofselectedhelicesthatfunctionasbindingdomainswhichwecal
pads 
.Individualtilesinteractbyannealingwithotherspecictiles viatheirssDNApadstoself-assembleintodesiredsuperstructures.Theuseofpadwithcomplementarybasesequencesallowstheneighborrelationsoftilesinthe- nalassemblytobeintimatelycontrolled;thustheonlylarge-scalesuperstructureformedduringassemblyarethosethatencodevalidmappingsofinputtooutput.Consequently,theseconddicultymentionedpreviouslyhasbeenaddressed: ratherthanimplementingaDNAcomputingalgorithmusingasequenceofmultipllaboratoryprocedures,ourapproachessentiallyusesonlyfour:mixingtheinput oligonucleotidestoformtheDNAtiles,allowingthetilestoself-assembleintosu- perstructures,ligatingstrandsthathavebeenco-localized,andthenperformingsingleseparationtoidentifythecorrectoutputWenowgiveabriefdescriptionofthemathematicaltilingandDNAconstruc- tiontechniquesunderlyingourwork. 1.0.1
ComputationbyTiling. 
AclassofdominotilingproblemsweredenebyWang 
Wan6
.Oneisgivenanitesetofunitsizesquaretiles,eachof whosesidesarelabeledwithsymbolsoveranitealphabetthepads.Additionalrestrictionsmayincludetheinitialplacementofasubsetofthesetilesandthedimensionsoftheregionwheretilesmustbeplaced.Theproblemitoplacethetiles,chosenwithreplacementandwithoutrotation,tocompletelllthegivenregionsothateachpairofabuttingtileshaveidenticalsymbolson theircontactingsides.Proofsoftheundecidabilityoftheinnitetilingproblem relyonconstructionswhereintilingpatternssimulatesingle-tapeTuringMachines  
Buc62,Wan63,Ber66,Rob71,Wan7
.Otherresultsincludereductionsof NP-completeproblemstonite-sizetilingproblems 
LP8
;tilingsandpatternsigeneralaresurveyedin 
GS8
1.0.2
DNAasaConstructionMaterial
Nano-fabricationofstructuresinDNwaspioneeredbySeemanstartinginthe1980se.g.,see 
See82 
.Seemanand hisstudentshavebuiltamultitudeofingeniousconstructionsincluding:DNbranchedjunctions 
SCK89,WMKS91,DZS9
,knots 
SC
9
,Borromean rings 
MSS9
,acube 
CS9
,andatruncatedoctahedron 
ZS94 
reviewedine.g. 
 
COMPUTATIONBYSELF-ASSEMBLYOFDNATILINGS12
 
See98 
.Recently,theyhavereportedtheconstructionfromDNAofananomechanicaldevicecapableofcontrolledmovement 
MSSS9
Themostrelevantconstructsforourcurrentpurposesarethedouble-crossoveDXcomplexes,whichconsistoftwodouble-helicesinterlockedbyexchangeof oligonucleotidestrandsattwoseparatecrossoverpoints 
FS9
.InDXcomplexesaparticularoligonucleotidestrandbase-pairswithitscomplementinonehelixthen crossesovertocontinuebase-pairingwithitscomplementarysectiononasecond, adjacenthelix;themultiplecrossoverpointsconstrainthehelixaxestobeco-planar. BecauseDXcomplexescanbeusedasDNAtilesinself-assemblyreactions,wewiloftenrefertothemassuch. DXcomplexescomeinvevarietiesthatdierfromoneanotherinthegeometrofstrandexchangeandthetopologyofthestrandpathsthroughthetile.Antiparallelcrossoverscauseareversalindirectionofstrandpropagationthroughthe tilefollowingexchangeofstrandtoanewhelix.Wewillprimarilyconcernourselves withtilescontaininganti-parallelcrossoversDAOandDAEratherthanthoswithparallelcrossoversDPE,DPOW,DPON,becauselaboratorycharacteriza- tionsofparalleltilesshowedthemtobelessstablestructurallythananti-parallel tiles 
FS93 
.DXtilesprovideuptofourssDNApadsforencodingassociationswitneighboringtiles.DXcomplexeshavebeenshowntobesucientlyrigidtoavoiformationofcircularstructuresasseenwiththemoreexibledsDNA 
LYQS9
Recently,2DlatticesconsistingofhundredsofthousandsofDXunitshavebeeconstructedandobservedbyatomicforcemicroscopy 
WLWS9
,andDXcomplexesandlatticeshavebeenusedsuccessfullyassubstrateforenzymaticreactionincludingcleavageandligation 
LSS99 
1.0.3
Parallelism,SpeedandTilingDepth. 
Themassiveparallelisminherent inDNA-basedcomputershas,sinceitsinception,driventhinkingintheeld.Icomputationbyself-assembly,parallelismrevealsitselfinmanyways.Eachsu- perstructuremaycontaininformationrepresentingadierentcalculation 
global parallelism 
.Growthoneachindividualsuperstructuremayoccuratmanyloca- tionssimultaneously 
localparallelism 
.Self-assemblymayberestrictedsuchthat certainassemblyreactionscanproceedonlyafterothershavebeencompleted 
serialself-assembl
.Alternatively,self-assemblyreactionsmaybelimitedbyno suchrestrictions 
 freeself-assembl
.Asexamples,BCAtilesutilizelocalparallelismandserialself-assembly 
Win9
;DHHPtilesutilizebothlocalandglobal parallismandserialself-assembly 
WYS9
;andself-assemblyoflinear,hairpin, andbranchedDNAmoleculestogenerateregular,bilinear,andcontext-freelan- guagesmakesuseofglobalparallelismandfreeself-assembly 
WYS98,Eng9
asdotheproposalsofJonoskaetal 
JKS99,JKS9
Ititexpected,butunproven,thatfreeself-assemblyisfaster,morerobustandlesserror-pronethanserialself-assembly.Threemeasuresassistdiscussion: th
dept
ofasuperstructureisthemaximumnumberofself-assemblyreactions experiencedbyanysubstructurethedepthofthegraphofreactionevents,andthe 
size 
ofasuperstructureissimplythenumberoftilesitcontains.Asuperstructure consistingof 
 
tiles,where 
n
,issaidtohav
layers 
.Thedepthsize ofatilingsystemisthemaximumdepthsizeofanysuperstructureitgeneratesLikewiseforthenumberoflayers.Forexample,inatilingsystemwher
AB;
CD;AB 
C
ABCD 
,weknowthatthedepthi
 
2anthesizei
 
4.Again,althoughitneedsfurtherstudy,tilingsystemswithlow depth,smallsize,andfewlayersareconsidereddesirable,motivatingthesearc

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