Nucleic Acid Nanotechnology PDF
Preview Nucleic Acid Nanotechnology
Nucleic Acids and Molecular Biology 29 Jørgen Kjems Elena Ferapontova Kurt V. Gothelf Editors Nucleic Acid Nanotechnology Nucleic Acids and Molecular Biology Volume 29 Series Editor JanuszM. Bujnicki International InstituteofMolecular and Cell Biology Laboratory ofBioinformatics and Protein Engineering Trojdena 4 02-109 Warsaw Poland For furthervolumes: http://www.springer.com/series/881 ThiSisaFMBlankPage Jørgen Kjems (cid:129) Elena Ferapontova (cid:129) Kurt V. Gothelf Editors Nucleic Acid Nanotechnology Editors JørgenKjems ElenaFerapontova CenterforDNANanotechnology, CenterforDNANanotechnology, InterdisciplinaryNanoscienceCenter InterdisciplinaryNanoscienceCenter andDepartmentofMolecularBiology AarhusUniversity UniversityofAarhus AarhusC AarhusC Denmark Denmark KurtV.Gothelf CenterforDNANanotechnology, InterdisciplinaryNanoscienceCenter andDepartmentofChemistry AarhusUniversity AarhusC Denmark ISSN0933-1891 ISSN1869-2486(electronic) ISBN978-3-642-38814-9 ISBN978-3-642-38815-6(eBook) DOI10.1007/978-3-642-38815-6 SpringerHeidelbergNewYorkDordrechtLondon LibraryofCongressControlNumber:2013951331 ©Springer-VerlagBerlinHeidelberg2014 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionor informationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped.Exemptedfromthislegalreservationarebriefexcerpts inconnectionwithreviewsorscholarlyanalysisormaterialsuppliedspecificallyforthepurposeofbeing enteredandexecutedonacomputersystem,forexclusiveusebythepurchaserofthework.Duplication ofthispublicationorpartsthereofispermittedonlyundertheprovisionsoftheCopyrightLawofthe Publisher’s location, in its current version, and permission for use must always be obtained from Springer.PermissionsforusemaybeobtainedthroughRightsLinkattheCopyrightClearanceCenter. ViolationsareliabletoprosecutionundertherespectiveCopyrightLaw. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexempt fromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. While the advice and information in this book are believed to be true and accurate at the date of publication,neithertheauthorsnortheeditorsnorthepublishercanacceptanylegalresponsibilityfor anyerrorsoromissionsthatmaybemade.Thepublishermakesnowarranty,expressorimplied,with respecttothematerialcontainedherein. Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Foreword Whatisnucleicacidnanotechnology?Wereadmuchabout“nanotechnology”these days,bothinthetechnicalliteratureandinthepopularpress.Theprefix“nano”in “nanotechnology” means 10−9, a billionth, and implies something very small. In fact, relative to the chemical world, “nano” actually means something that is somewhatlargerthantheusualscale.Abillionthofameteristhelengthofabout half a dozen chemical bonds between atoms, not a single bond. The usual components brought to mind when “nanotechnology” is mentioned are carbon- basedmaterials,suchasfullerenes(buckyballs),carbonnanotubes,orgraphene,or metallic (often gold) and semiconducting nanoparticles, such as CdSe. Except for theparticles,therelationshipofthesespeciesto“nano”isnotimmediatelyobvious. Indeed, except when trying to increase one’s prominence or funding, one doesn’t often describe organic molecules as “nanocomponents,” even though they fit the sizerangeverynicely. So why “nucleic acid” nanotechnology? The nanometer scale is indeed an appropriatescalefortalkingabout“nucleicacids”nanotechnology,becausenucleic acid double helices are about 2 nm wide. However, focusing on size when discussing nucleic acid nanotechnology really leads in the wrong direction. The key quality of nucleic acids is not their size but their information content. This featureiscentraltotherolesofDNAandRNAinbiologicalsystems,anditisthe vitalcomponentthatdistinguishesthemfromtheotherpolymersthatoccurinboth livingandman-madesystems.Althoughthemostprominentaspectofnucleicacids inbiologyistheirabilitytocodeforproteins,RNA,atleast,iswellknowntoform complex tertiary structures from linear molecules. The ability to program the formation from nucleic acids of branched molecules at the secondary structure levelandalsotoprogramtheirintermolecularinteractions(Seeman1982)hasledto anewfieldwhichtodayiscalled“nucleicacidnanotechnology.”Thefieldhasbeen growingsince1982,butitsexpansionhasbeenparticularlydramaticinthetwenty- firstcentury. Thegoalsofnucleicacidnanotechnologyareverybroad,andtheyarecertainly notlimitedtobiologicalapplications.Theinitialtargetofthefieldwastheforma- tionofrobust3Dcrystalstosolvethe“crystallizationproblem”ofmacromolecular v vi Foreword crystallography(Seeman1982).However,whileawaitingtherealizationofthisaim (Zhengetal.2009),numerousothermilestoneshavebeenachieved,andothernew directions have been enunciated. These have included the construction of DNA objects(ChenandSeeman1991),2Dlattices(Winfreeetal.1998),nanomechanical devices(Maoetal.1999),robots(ShermanandSeeman2004),andassemblylines (Gu et al. 2010). IT-related systems have been an intrinsic part of nucleic acid nanotechnologyforover25years(RobinsonandSeeman1987).Adleman’sHam- iltonian Path experiment (Adleman 1994) first brought DNA to the experimental consciousnessofcomputerscientists,andWinfree’sproposalofalgorithmicassem- bly (Winfree 1998) similarly added logical operations to the notion of nanoscale self-assembly. Since its origination in the early 1980s, one of the most important developmentsintheareaisundoubtedlyPaulRothemund’sexpansionofthescale oftargetobjectsthroughtheuseofDNAorigami(Rothemund2006).PengYinet al.’s follow-up of scaffold-free large-object construction nicely complements Rothemund’s advance (Wei et al. 2012). The other key breakthrough in nucleic acid nanotechnology was the development of isothermal strand displacement by Yurkeetal.(2000);asaconsequenceofthisdevelopment,robustsequence-specific (i.e., programmable) devices have been developed (Yan et al. 2002) and signifi- cantly more complex computations have been undertaken successfully (Qian and Winfree2011). The central strength of nucleic acid nanotechnology is its ability to use the chemical information contained in programmed DNA and RNA sequences to organize matter, either DNA itself or other chemical species. We see numerous examples in this volume, which is a compendium of recent advances in the field, including the application of modern instrumentation to the analysis of constructs. However, the book goes beyond these topics, toextend nucleic acid nanotechnol- ogytobiologicalapplicationsaswell. Without the development of single-molecule methods, many of the achievementsofnucleicacidtechnologywouldhaveprovedimpossibletocharac- terize. Inthefirstchapter,LeiLiu,FlemmingBesenbacher,andMingDongusea key nanoscale instrument, the scanning tunneling microscope, to examine the fundamental reaction of nucleic acid nanotechnology and the association of base pairs. Single-molecule experiments are often regarded as another component of “nanotechnology”:Inthesecondchapter,RebeccaBoltEttlinger,MichaelAskvad Sørensen, and Lene Broeng Oddershede apply this force spectroscopy to nucleic acids.Similarly,inthethirdchapter,SofieL.KraghandVictoriaBirkedaldescribe applicationsofsingle-moleculeFRETtoDNAnanotechnology. Fromtheforegoing,itisclearthatself-assemblyisakeycomponentofnucleic acid nanotechnology. In the fourth chapter, Abhijit Rangnekar and Thomas H. LaBeansummarizethelonghistoryofDNAtile-basedself-assembliesandsuggest howthey maybeappliedinthefuture, bothforobjectandlatticeconstruction.In thefifthchapter,AngelaEdwardsandHaoYanprovideanextensiveintroductionof the state of the art of DNA origami and its applications. The sixth chapter, by ChunhuaLiuandAndrewD.Ellington,summarizesrecentdevelopmentsinDNA nanotechnology and addresses its potential applications in drug delivery, analysis Foreword vii and diagnosis, electronics, and photovoltaics, showing how technology can result fromasystemoriginallythoughttoberelevantonlytobiology. TheuseofDNA, fundamentally a nanoscale system, to aid in the construction of molecules on the scale of organic chemistry (DNA-templated synthesis) is treated in the seventh chapter,contributedbyChristianB.Rosen,ThomasTørring,andKurtV.Gothelf. The eighth chapter, by Zhen-gang Wang and Baoquan Ding, discusses the applicationsofDNA-basednanomechanicaldevices. The last section of the book returns DNA to its biological roots but with a nanotechnological slant. The ninth chapter by Eveline Edith Salcher and Ernst Wagner is concerned with the encapsulation of oligonucleotides for therapeutic purposes; it details the nature of the issues involved in this activity. In the tenth chapter, Gu¨nter Mayer, Monika Pofahl, Katia M.U. Scho¨ler, and Silvana Haßel discuss the applications of aptamers for the therapeutic purposes, including modifications and cell targeting. Slaven Garaj discusses the use of nanopores for the central purpose of DNA sequencing in the eleventh chapter; the target here is the least expensive genome, and the chapter covers both the advances and challenges confronting the field. In the final chapter, Alfredo de la Escosura- Mun˜izandArbenMerkoc¸idiscusstheuseofnanomaterialsinDNAsensing,with thegoalofintegratedchiptechnologies. Insummary,JørgenKjems,ElenaFerapontova,andKurtV.Gothelf,theeditors ofthisbook,haveprovidedthereaderwithanaccessibleentrytotheareaofnucleic acid nanotechnology. In addition, they have included developments that go well beyondasimpleintroduction.Theworkinthisfieldwasavailableadecadeagoto those following the output of only a few laboratories. However, it has grown so muchthatitisnolongerpossibleforeventheexpertsintheareatokeepabreastof thedevelopmentsthatareoccurring.Thisvolumewillcertainlyassistinthateffort. NewYork,NY NadrianC.Seeman References Adleman L (1994) Molecular computation of solutions to combinatorial problems. Science 266:1021–1024 ChenJ,SeemanNC(1991)ThesynthesisfromDNAofamoleculewiththeconnectivityofacube. Nature350:631–633 Gu H,Chao J, Xiao SJ,SeemanNC (2010)A proximity-basedprogrammable DNA nanoscale assemblyline.Nature465:202-205 MaoC,SunW,ShenZ,SeemanNC(1999)ADNAnanomechanicaldevicebasedontheB-Z transition.Nature397:144–146 QianL,WinfreeE(2011)ScalingupdigitalcircuitcomputationwithDNAstranddisplacement cascades.Science332:1196–1201 Robinson BH, Seeman NC (1987) The design of a biochip: a self-assembling molecular-scale memorydevice.ProteinEng1:295–300 Rothemund PWK (2006) Scaffolded DNA origami for nanoscale shapes and patterns. Nature 440:297–302 viii Foreword SeemanNC(1982)Nucleicacidjunctionsandlattices.JTheorBiol99:237–247 ShermanWB,SeemanNC(2004)ApreciselycontrolledDNAbipedalwalkingdevice.NanoLett 4:1203–1207 Wei B, Dai M, Yin P (2012) Complex shapes self-assembled from single-stranded DNA tiles. Nature485:623–627 WinfreeE(1998)Algorithmicself-assemblyofDNA.Ph.D.Thesis,Caltech WinfreeE,LiuF,WenzlerLA,SeemanNC(1998)Designandself-assemblyoftwo-dimensional DNAcrystals.Nature394:539–544 YanH,ZhangX,ShenZ,SeemanNC(2002)ArobustDNA mechanical devicecontrolled by hybridizationtopology.Nature415:62–65 YurkeB,TurberfieldAJ,MillsAPJr,SimmelFC,NewmannJL(2000)ADNA-fuelledmolecular machinemadeofDNA.Nature406:605–608 ZhengJ,BirktoftJJ,ChenY,WangT,ShaR,ConstantinouPE,GinellSL,MaoC,SeemanNC (2009)Frommoleculartomacroscopicviatherationaldesignofaself-assembled3DDNA crystal.Nature461:74–77 Preface Fifty-one years passed since James Watson, Francis Crick, and Maurice Wilkins wereawardedtheNobelPrizeinphysiologyormedicinefortheir1953discovery that deoxyribonucleic acid, DNA, consists of two twisted oligonucleotide chains that are held together in an antiparallel fashion by highly specific oligonucleotide base pair interactions. This discovery opened a new era in biology, genetics, medicine,biotechnology,andbiochemistryandprovidedfurtherbasisforstudying andmanipulatingthebiologicalprocesses—molecularbiologyscience.Itdramati- callychangedourunderstandingofthemolecularbasisofgenes,geneticdiseases, andtheinheritancepassageofgeneticmaterialfromonegenerationtoanother. Later, new powerful physical–chemical tools for synthesis, manipulation, and visualizationofnucleoacidsatatomiclevelenabledfunctionalstudiesandcontrol nucleic acids organization and function at a nanoscale level. Now, at the 60th anniversary of the discovery of the double helix, the combination of nucleic acid chemistry and nanotechnology created a new challenging direction of research called Nucleic Acid Nanotechnology, which has tremendously improved our knowledgeandcontrolofbasicbiologicalprocessesandenablednovelbiotechno- logical applications in many fields including food and pharmaceutical industries, medicine,agriculture,forensics,materialengineering,andcomputation.Theneces- sity of a book, where the latest achievements in this rapidly expanding area of researcharesummarized,isevidentandtimely. Thisbookcontains12chapters,writtenbythe leadingworld’sscientists inthe fieldofDNAandRNAnanotechnology.Itrepresentadiversecollectionofreviews devotedtobasicdirectionsinthisarea,fromsinglenucleotidesandsinglenucleic acid molecule studies and characterization to the design and synthesis of more complex DNA- and RNA-based systems and their application in nanomechanics, nanomedicine,andnanobiosensing.Webelievethatthisbookprovidesbothasolid backgroundknowledgeforthosewhoarenotdirectlyinthefieldoftheresearchand advancedknowledgeforthosewhoareinterestedinthemoredetailedandpractical information on the methods and the latest achievements in this field. We are very thankfultoalltheauthorscontributingtothisbookandtoProf.JanuszBujnicki,the Editorofthe“NucleicAcidsandMolecularBiology”series,forchallengingusto ix
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