Nucleic Acid Nanotechnology

340 Pages·2014·9.06 MB·English

by  Lei Liu

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
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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
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assemblyline.Nature465:202-205
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transition.Nature397:144–146
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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