self - assembly is a remarkable 
 process that nature uses to organize 
 chemical systems composed of nonliving components into living , biological 
 systems .
nature accomplishes this incredible feat by adding information 
 to matter and by guiding the self - assembly process to create functional 
 structures . toward the goal of engineering biomimetic ,
bioinspired , 
 or biokleptic components that can communicate , regulate , and actuate 
 in artificial molecular networks , information - coding polymers such 
 as dna , rna , and proteins have been used as ideal building blocks 
 in the assembly of designer nanoarchitectures .
this perspective will 
 concentrate on the most recent and inspiring advances in structural 
 dna nanotechnology and present an outlook of the future of this rapidly 
 expanding field .
more comprehensive reviews that provide very detailed 
 descriptions of the state of the art in this field can be found elsewhere 
 in the literature .
dna , nature s molecule of choice for storing and transmitting 
 genetic information , is an excellent nanoscale building block because 
 of its specific three - dimensional ( 3d ) conformation , chemical addressability , 
 and predictable watson  crick base - pairing .
structural dna nanotechnology , 
 derived from seeman s innovative proposal that dna could be 
 used as a physical material for the self - assembly of nanoscale structures ( figure 1 ) , has developed 
 with astounding speed over the past 30 years .
the most significant 
 underlying concept is the application of immobile , branched dna junctions , 
 together with sequence - specific sticky end associations , to create 
 self - assembling arrays , objects , and devices ( figure 1a ) .
structural foundations of structural dna nanotechnology and representative 
 examples ( each panel described left to right ) .
original 
 proposals to use immobile dna junctions to create self - assembling 
 arrays ( a ) and self - assembled 3d dna lattices 
 ( b ) as scaffolds to organize macromolecules into crystalline lattices .
( c ) dna nanostructure motifs used to create periodic 
 2d arrays and 3d crystal ( top , helical structures of the motifs ; bottom , 
 afm images of the assembled 2d arrays and optical image of the 3d 
 crystal ) : double - crossover dna tile , 44 
 dna tile , 64 dna tile , and tensegrity triangle dna tile .
( d ) polyhedral dna nanostructures : molecular models of a dna cube , dna tetrahedron , dna dodecahedron , and dna biprism .
( e ) algorithmic self - assembly based on double - crossover 
 tiles : sierpinski triangles and binary 
 counter .
( f ) dna origami nanostructures 
 ( top , schematic drawings of the structures ; bottom , corresponding 
 afm or tem images ) : 2d dna origami smiley face , 3d dna origami in the shape of a gear , curved single - layer 3d origami in the shape of a vase , and dna origami gridiron .
( g ) complex nanostructures produced using the single - stranded 
 dna tile strategy .
images reproduced with permission : 
 ( c ) ref ( 13 ) , 1998 
 nature publishing group ( npg ) ; ref ( 14 ) , 2003 american association for the advancement 
 of science ( aaas ) ; ref ( 15 ) , 2006 american chemical society ( acs ) ; ref ( 16 ) , 2009 npg ; ( e ) ref ( 28 ) , courtesy of p. rothemund ; 
 ref ( 29 ) , 2005 acs ; 
 ( f ) ref ( 32 ) , 2006 
 npg ; ref ( 37 ) , 2009 
 aaas ; ref ( 38 ) , 2011 
 aaas ; ref ( 114 ) , 2013 
 aaas ; and ( g ) ref ( 45 ) , 2012 npg ; ref ( 46 ) , 2012 aaas . over the past several decades
, 
 researchers have established a collection 
 of convenient methods to construct dna nanostructures that exhibit 
 significant geometric and topological complexity .
designing and predicting 
 the 3d conformation of these nanostructures is now routine thanks 
 to several user - friendly software interfaces that have been developed .
a number of 2d and 3d lattices assembled from small , repeating dna 
 nanostructure motifs were produced ( figure 1c ) , and several discrete polyhedral 
 objects were constructed from fixed numbers of dna junction motifs ( figure 1d ) . in 2009 , seeman s group 
 was the first to assemble 3d dna crystals from deliberately designed 
 sticky - end connections ( figure 1c , right ) rather than through simple , nonspecific 
 base stacking .
they used self - assembling tensegrity triangle motifs 
 to create 3d crystals with various unit dimensions .
this work represents 
 a milestone in fulfilling seeman s original vision of using 
 3d dna lattices as hosts to organize guest protein molecules and facilitate 
 protein crystallography ( figure 1b ) .
several researchers encoded algorithms into 
 dna nanostructure components to direct the assembly of particular 
 2d lattice arrays and had some initial success ( figure 1e ) ; however , scaling - up algorithmic 
 assembly to realize more complex patterns remains a challenge , mainly 
 because of the errors that accumulate during assembly .
if error correction 
 mechanisms could be implemented , it would 
 represent a ground - breaking advance in this field . in 2006 , 

the dna origami method 
 uses a number of short single - stranded dna ( ssdna ) oligonucleotides 
 to direct the folding path of a long ssdna  scaffold  
 strand .
rothemund used genomic ssdna from the m13 phage as the scaffold 
 strand ( 7249 nucleotides ) and designed a set of short  staple  

strands to selectively bind to distant regions of the scaffold and 
 fold it into a predesigned shape .
this 
 assembly method results in near - quantitative yield for most 2d designs 
 ( figure 1f ) , even with unpurified staples . 

several groups successfully extended dna origami fabrication to 3d and to the assembly of twisted and 
 curved 3d objects ( figure 1f ) .
other research groups have focused their attention on 
 scaling - up dna origami using the following methods : edge - to - edge base - stacking 
 interactions between individual origami units , sequence - specific sticky end cohesion between individual 
 units ,  super origami  , and use of longer scaffolds for origami construction .
more recently , yin and co - workers synthesized a variety of 
 1d , 2d , and 
 3d dna nanostructures from single - stranded 
 dna 
 tiles ( ssts ) .
the platform that they developed is based on a series 
 of interlocking local connections between ssts .
collections of ssts 
 form 2d sheet or 3d block canvases that can be selectively engraved 
 to create different shapes and patterns by simply including or omitting 
 specific ssts ( figure 1 g ) .
natural biological 
 devices are designed to operate in dynamic conditions , responding 
 to subtle biological cues to realize their functions .
the structural 
 properties of dna that allow it to serve as a versatile construction 
 material have been exploited to create dynamic nanodevices ( figure 2a ) ranging from small switchable structures and reconfigurable systems to structures that display complex movements such as rolling , rotating , and walking .
( d ) dna assembly line : dna 
 walker will transport gold nanoparticles to a different product formation 
 station with instructions from dna strand displacement .
protein molecular motors transform chemical energy into mechanical 
 energy to facilitate a variety of biological functions from cell division , 
 transport , and motility to enzymatic activity .
dna nanotechnologists 
 have long envisioned programming dna walker molecules to mimic the 
 ability of natural motor proteins to walk along intracellular tracks 
 and achieve controlled motion .
imparting directionality to dna walkers 
 could be realized by means of successively additng dna fuels , by coordinating 
 conformational changes between different components of the walker , 
 by leading the walker through selective track modifications , or by 
 pairing their motion to unidirectional reaction cycles .
researchers 
 have already demonstrated unidirectional motion by dna walkers through 
 prescribed tracks and landscapes ( figure 2b , c ) . on the basis of this 
 technology
, it is possible to develop walkers that are programmed 
 to travel a certain path by encoding the directions into the nucleotide 
 sequences of the walker itself and into the corresponding landscape . 

for example , seeman s group reported a dna - based robot that 
 manufactured structures on a nanoscale assembly line ( figure 2d ) .
their dna walker traveled 
 through three fixed modules that were individually programmed to selectively 
 incorporate a gold nanoparticle into the final product , resulting 
 in eight possible outcomes .
recently , researchers demonstrated that 
 dna walkers can also be used to mediate multistep organic synthesis , pointing to the possibility of programming chemical 
 reactions with dynamic dna nanodevices .
as structural dna nanotechnology 
 transitions from adolescence into 
 adulthood , the need to demonstrate potential applications is of the 
 utmost importance .
we must improve our ability to engineer and program 
 complex molecular systems and prove that designer dna nanostructures 
 can be employed in real - world applications .
if we continue to exploit 
 the programmability of dna nanostructures to accurately template functional 
 molecules , materials , and probes , we will be able to organize these 
 external elements into practical devices and engineer molecular sensors , 
 circuits , and actuators .
inorganic nanomaterials such as quantum 
 dots , nanowires and nanorods , and metal nanoparticles have attracted 
 much attention because of their unique optical and electronic properties 
 that can be used in solar cells , phototransistors , laser diodes , light - emitting 
 diodes , and other optoelectronic devices . however , a better understanding of the photophysical behavior of 
 these materials is necessary to use them in such devices .
researchers 
 have successfully used dna nanoscaffolds to organize metallic nanoparticles , 
 semiconductor nanocrystals ( figure 3a ) , and organic chromophores into well - defined architectures .
these hybrid dna nanostructure complexes have enabled systematic 
 investigation of distance - dependent interactions between photonic 
 elements . in one example ,
liedl and co - workers constructed 
 a spiral , nanoscale staircase on which gold nanoparticles were arranged 
 at regular intervals and with chiral geometries ( figure 3a ) .
this work demonstrates 
 how dna scaffolding can be used to control the precise structural 
 arrangement of metal nanoparticles , enabling researchers to tailor 
 surface plasmon resonance and the interaction with visible light . 
 in another example
, dna nanostructures were used to organize various 
 organic chromophores into artificial light - harvesting complexes with 
 control over cascading , unidirectional energy transfer .
representative examples of dna nanostructure - directed 
 assembly 
 of inorganic and protein molecules ( top , schematics ; bottom , corresponding 
 tem or afm images ) .
( a ) left to right : gold nanoparticles organized 
 by a 2d dna tile array , gold nanorod 
 dimers with controlled angles between the nanorods organized by dna 
 origami , dna origami - directed quantum 
 dot architectures , and dna origami - directed 
 gold nanoparticles in a chiral arrangement and the induced circular 
 dichromic effect .
( b ) left to right : 
 organization of streptavidin proteins by a 2d dna nanoarray , protein arrays templated by a 2d dna nanostructure 
 through aptamer 
protein interactions , and orthogonal snap - tag- and his - tag - mediated decoration of dna 
 origami .
images reproduced with permission : 
 ( a ) ref ( 69 ) , 2006 
 acs ; ref ( 70 ) , 2011 
 acs ; ref ( 71 ) , 2012 
 acs ; ref ( 72 ) , 2012 
 npg ; and ( b ) ref ( 14 ) , 2003 aaas ; ref ( 79 ) , 2007 acs ; ref ( 80 ) , 2010 wiley . as we previously mentioned , 
 one of the initial goals of structural 
 dna nanotechnology was to use 3d dna lattices as hosts to organize 
 guest protein molecules and facilitate protein crystallography .
although 
 this vision has yet to be realized , scientists have already begun 
 to use dna nanostructures as chaperones to align and organize protein 
 molecules using different strategies , including ligand 
streptavidin ) interactions , aptamer  target interactions , and ligand - engineered ( tagged ) protein interactions ( figure 3b ) . shih and 
 co -
workers recently designed dna origami nanotube liquid crystals 
 to provide the appropriate  alignment environment  for 
 determining the previously unknown structure of a membrane protein 
 by nuclear magnetic resonance ( nmr ) .
turberfield 
 and co - workers used periodic 2d dna tile arrays as templates to arrange 
 proteins and subsequently used cryo - em to solve their structures .
proteins , some of nature s most 
 powerful agents , are large 
 macromolecules that perform a wide assortment of functions required 
 to sustain life , including metabolic catalysis , dna replication , and 
 molecular transport . in order to better understand the governing dynamics 
 in complex protein systems ,
we need control over the number , orientation , 
 and arrangement of the constituents .
nucleic acid scaffolds afford 
 this level of control , and researchers have already used rna and dna 
 platforms to engineer a number of enzyme cascades ( figure 4a ) . for example
, silver and co - workers used a bacterial host to transcribe 
 rna and assemble intracellular rna nanoscaffolds for spatial organization 
 of metabolic elements for hydrogen production .
willner and co - workers organized a glucose oxidase and 
 horseradish peroxidase enzyme cascade by 2d dna lattices .
more recently , yan and co - workers conducted 
 substrate channeling in a multienzyme cascade by using an artificial 
 dna swinging arm .
representative examples 
 of dna nanostructure - directed assembly 
 of protein molecules for functional structures .
( a ) upper left , assembly 
 and disassembly of holoenzymes mediated by dna strand displacement ; upper right , glucose oxidase ( yellow ) and horseradish 
 peroxidase ( red ) enzyme cascade organized by 2d dna lattices ; lower left , substrate channeling in a multienzyme 
 cascade by an artificial dna swinging arm ; and lower right , glucose oxidase ( yellow ) and horseradish peroxidase 
 ( red ) enzyme cascade organized on dna origami with distance control .
( b ) rectangular dna origami travels on a cellular 
 actin network through the binding and action of myosin lever arms .
( c ) molecular tug - of - war between two motor proteins 
 displayed from a 12-helix dna bundle .
dna origami scaffolds have also 
 been used to organize motor proteins 
 and study their spatially dependent motility ( figure 4b ) .
understanding how motors cooperate 
 productively , and compete antagonistically , is important for understanding 
 how intracellular transport is regulated .
researchers recently demonstrated 
 this  molecular tug - of - war  by displaying different 
 numbers of dynein and kinesin motor proteins from a dna origami structure . by controlling the number , distance , and orientations 
 of the two types of biological motors
, they were able to systematically 
 study coordinated motor behavior ( figure 4c ) .
structural dna nanotechnology has also emerged as a useful tool 
 for biological and medicinal applications ( figure 5 ) .
the intrinsic biocompatibility , nanoscale dimensions , programmability , 
 and ability for functionalization of dna nanostructures are virtually 
 unrivaled by existing techniques . in particular , the addressable configuration 
 of dna origami lends itself to detection of gene expression and single nucleotide polymorphism .
the sugiyama group developed dna origami frames 
 and rulers to investigate biomolecular interactions such as 
 protein  dna binding events and homologous recombination processes 
 in real time at the single molecule level ( figure 5a ) .
further , the spatial addressability and multivalent 
 properties of dna nanostructures make them promising vehicles for 
 targeted drug delivery . for example , douglas and co - workers demonstrated 
 a barrel - shaped nanorobot that releases fab antibody fragments in 
 the presence of target cells . in their 
 system ,
two ssdna aptamer locks are opened by specific markers present 
 on the surface of cells ( figure 5b ) .
after 
 opening , the payload molecules inside the barrel are exposed , inducing 
 a particular cellular signaling pathway .
anderson and co - workers used 
 a dna tetrahedron to deliver small interfering rna in vivo to target and suppress gene expression in a mouse model ( figure 5c ) .
yan , chang , and co - workers used a dna tetrahedron to coassemble 
 model antigens and cpg adjuvants into nanoscale complexes with precise 
 control of the valency and spatial arrangement of each component ( figure 5d ) .
dna 
 complexes induced stronger and longer - lasting antibody responses against 
 the antigen , without stimulating a reaction to the dna nanostructure 
 itself , as compared to an unstructured mixture of antigen and cpg 
 molecules .
more recently , amir et al . showed that dna origami robots 
 can dynamically interact with each other and perform logic computations 
 in a living animal , opening up opportunities to develop smart theranostic 
 nanodevices ( figure 5e ) .
( a ) dna origami 
 frames to investigate protein  dna binding events in real time 
 at the single molecule level .
( b ) barrel - like 
 dna nanorobot programmed to be open in the presence of target cells 
 and expose fab antibody fragment cargo .
( c ) six sirna duplexes and folic acid tags ( gray ) chaperoned by 
 a dna tetrahedron are injected into mice ; the tetrahedra bind to tumor 
 cells by targeting folate receptors expressed on the tumor cell surface .
cpg odn adjuvant molecules ( curved yellow ribbons ) 
 and the model streptavidin antigen ( red ) bind specifically to b cells 
 and are subsequently presented to t cells to activate b cell response 
 and antibody production .
( e ) three different 
 drugs carried by a dna nanorobot can be released in a programmed fashion 
 by undergoing complex dna computation in a living cockroach .
image ( e ) reproduced with permission from ref ( 99 ) , 2014 npg .
the interdisciplinary nature of dna nanotechnology 
 crosses the 
 traditional boundaries of physics , chemistry , biology , and engineering 
 and allows scientists to connect and integrate their unique perspectives 
 in pursuit of solutions to the most pressing problems in medicine , 
 technology , and more . from the earliest dna junction motifs to the 
 most recently developed dna nanostructures of incredible complexity , 
 the field has started to explore various novel applications , including 
 directed material assembly , structural biology , biocatalysis , dna 
 computing , nanorobotics , disease diagnosis , and drug delivery , as 
 we mentioned briefly in the previous section .
each of these applications 
 is made possible by the ability of dna nanostructures to direct molecular 
 species with nanoscale precision while maintaining the utmost structural 
 integrity .
dna nanotechnology is progressing with such incredible 
 speed that it is becoming more and more difficult to predict from 
 which areas the next breakthroughs will occur .
next , we are merely 
 providing our opinion about the critical challenges that the field 
 faces and which directions we believe researchers should pursue to 
 help structural dna nanotechnology reach its full potential .
we have divided 
 the remaining outlook into three main areas : design 
 and assembly , which will include discussions 
 of dynamic , developmental , quasicrystal lattice , 3d periodic crystal 
 lattice , scaffolded , surface - mediated , algorithmic , and topological 
 assembly ; future applications , which will 
 include discussions of structural dna nanotechnology for molecular 
 scaffolds , sensors , robotics , and computing ; and from nano to angstrom technology , in which we conceive of 
 potential directions the field might explore over the longer term .
george whitesides 
 once wrote ,  although much of current understanding of self - assembly 
 comes from the examination of static systems , the greatest challenges , 
 and opportunities , lie in studying dynamic systems .
perhaps the most 
 important justification for studying self - assembly is its central 
 role in life .   
dynamic 
 self - assembly processes underlie many forms of adaptive and intelligent 
 behaviors in natural systems ; however , very little is known about 
 the principles that govern them .
one of the most intriguing , dynamic 
 self - assembly processes in living cells is the polymerization of cytoskeletal 
 biopolymers such as microtubules .
microtubule polymerization is characterized 
 by two unique phenomena , referred to as tread - milling and dynamic instability .
tread - milling is said to occur with the net addition of 
 tubulin monomers at one end of the microtubule and simultaneous net 
 loss of tubulin at the opposite end .
dynamic instability is characterized 
 by switching between phases of relatively slow and rapid shortening 
 of the microtubules at their ends .
although these phenomena were once 
 thought to be incompatible , it is now known that both behaviors coexist 
 in near - steady - state conditions in cells .
it would be quite interesting if we could use the desirable 
 properties of dna nanostructures to recapitulate these phenomena and 
 ultimately dissect the governing dynamics of microtubule polymerization 
 ( figure 6a ) .
dna tiles could be designed such 
 that the rate of assembly equaled the rate of disassembly , resulting 
 in steady - state tread - milling and fixed - length nanotubes .
further , 
 if tiles with bi- or tridirectional growth were utilized , the resulting 
 arrays would have defined shapes .
the intrinsic conformational flexibility 
 and rigidity of different dna building blocks could be exploited to 
 mimic dynamic instability , where polymerization of flexible dna tiles 
 can be induced through seeded growth on a rigid tile and depolymerization 
 of the flexible tiles can be initiated by removing the rigid tile 
 protection cap .
when the association and dissociation reactions reach 
 equilibrium , the input of additional rigid tiles will catalyze the 
 polymerization of released flexible tiles . studying the association 
 and dissociation kinetics of model dna tile species with variable 
 flexibility is absolutely essential to recreating this or similar 
 dynamic self - assembling systems .
schematic illustrations of ( a ) dynamic 
 dna self - assembly with simultaneous 
 joining in one end and dissociation in the other end , ( b ) developmental 
 dna self - assembly , in which the assembly process may grow into different 
 final products in response to different external cues , ( c ) an example 
 of a possible quasicrystal ( 2d penrose tiling ) using dna tile self - assembly , 
 and ( d ) self - replication of dna nanostructures .
the creation 
 of new life depends on a set of extraordinary developmental processes 
 including stem cell growth , differentiation , and morphogenesis .
these 
 processes rely on nature s ability to precisely control the 
 spatial and temporal relationship between cellular components and 
 signaling pathways .
it would be extremely interesting if we could 
 create synthetic dna systems that mimic this kind of spatiotemporal 
 development .
dna tiles have the potential to develop into unique patterns 
 through instructions embedded in the building blocks or by external 
 stimuli such as fuel strands that trigger new growth pathways ( figure 6b ) .
metastable dna nanostructures could be designed 
 and used to serve as nucleation seeds and/or catalysts to increase 
 the growth and development of particular pathways .
multivalency and/or 
 cooperativity within dna nanostructures could be exploited for nucleation 
 and initiation of alternative assembly paths .
for example , pierce and co - workers recently reported the dynamic assembly 
 of dna nanostructures through a seeded cascade of hybridization chain 
 reactions based on toehold - mediated strand displacement .
strand displacement circuits have also been 
 used to trigger dna tile assembly and control their growth into dna 
 tubes .
there are several key challenges 
 to implementing toehold - mediated strand displacement in dynamic dna 
 systems , including leakage , slow reaction rates , and the necessity 
 for high salt conditions .
zhang and co - workers reportedly designed toehold 
 exchange probes and optimized the specificity of dna hybridization 
 so that their system can detect single - base changes . designing robust self - assembling dna platforms to mimic 
 developmental systems will also certainly require a thorough understanding 
 of the thermodynamics and kinetics of dna self - assembly . in 
 2011 ,
the nobel prize in chemistry was awarded to dan shechtman for 
 his discovery of quasicrystals , a finding that fundamentally changed 
 how chemists understand solid matter .
prior to his report , scientists believed that the atoms in a crystal 
 were always packed into symmetric patterns that repeated periodically . 

we have since come to understand that it is possible to form packed 
 crystals from nonrepeating patterns , an arrangement of molecules now 
 referred to as  quasicrystalline  .
the distinctive properties 
 of quasicrystals , as well as their unique structures , have intrigued 
 scientists ever since their discovery ; however , very little 
 is currently known about the properties exhibited by synthetic and 
 naturally occurring quasicrystals .
scientists have yet to determine 
 what guides quasiperiodic rather than periodic growth and what factors 
 result in the unique properties that quasicrystals display .
one of the biggest challenges facing researchers today is the lack 
 of plausible systems from which to assemble quasicrystals and enable 
 further studies .
dna platforms are promising candidates for the controlled , 
 programmable growth of synthetic quasicrystals ( figure 6c ) .
interacting dna building blocks can potentially be programmed 
 to assemble into 2d and 3d quasicrystal patterns , allowing us to investigate 
 the still unknown mechanisms of quasicrystal growth and providing 
 a means to organize other materials for engineering pursuits .
realizing 3d dna 
 lattices as hosts to organize guest protein molecules 
 and facilitate protein crystallography necessitates that 3d dna crystals 
 can themselves be reliably assembled and characterized .
researchers 
 successfully demonstrated the assembly of a 3d dna crystal in which 
 the triangular unit tiles were connected by sticky ends and solved 
 its structure to 4  resolution using x - ray crystallography .
however , most dna crystals only diffract to 
 710  , leaving scientists 
 trying to determine why rationally designed dna crystals do not diffract 
 with better resolution
. there are several possible explanations , including 
 defects that arise during crystallization , impurities in the synthetic 
 dna , and the presence of bulky solvent molecules in the large cavities 
 of the dna lattices .
crystal defects may be caused by the limited 
 rigidity of dna unit motifs , where any over- or under - twisting of 
 the tiles causes inter - tile mismatches that are detrimental to the 
 integrity of the crystal lattice .
we surmise that imparting flexibility 
 to certain domains of the dna building blocks may allow the unit tiles 
 to more reliably accommodate their neighbors and reach a lower energy 
 state for crystal lattice formation , thereby improving the overall 
 quality of the crystal .
the sleiman group pioneered dna junctions 
 with metal complex modifications that combine rigidity within the 
 core of the junction with intrinsic flexibility in the arms .
this type of modified dna unit motif has the 
 potential to improve the quality of dna crystals but has yet to be 
 exploited for crystallization applications .
reducing the volume 
 of solvent present in the lattice cavities 
 by inserting sequence - specific binding proteins may improve the diffraction 
 quality , but sequence - independent methods to orient proteins within 
 the dna cavities still need to be developed .
this strategy is particularly 
 attractive , as some have already demonstrated that rna - binding proteins 
 are useful chaperones for rna crystallization .
piccirilli and co - workers 
 derived rna - specific antibodies using synthetic phage display libraries 
 and showed that the antibody fragments promoted crystallization of 
 rna molecules . similarly , dna tile binding 
 antibodies could be identified through in vitro evolution 
 and used for coassembly of the dna units and proteins into designed 
 3d crystals .
recent developments in free electron laser ( fel ) 
 x - ray nanocrystallography 
 have the potential to revolutionize the field of structural biology 
 by providing highly focused coherent x - ray beams with a peak brilliance 
 that is 10 higher than the x - ray beams at the most powerful 
 synchrotron facilities .
obtaining high - quality 
 diffraction patterns using fel x - ray requires micrometer - sized nanocrystals ; 
 it might be possible to program the growth of 3d dna lattices into 
 finite nanocrystals with suitable dimensions by designing a 3d box 
 that acts as a scaffold to nucleate the growth of a periodic lattice 
 of dna tiles .
growing 3d crystals with designed crystal morphologies 
 and dimensions is undoubtedly an interesting topic in itself .
the development 
 of scaffolded dna origami represents a milestone in structural dna 
 nanotechnology .
while the complexity 
 and robustness of 2d and 3d dna origami objects has increased over 
 the past few years , researchers still lack basic understanding of 
 the thermodynamics and kinetics of scaffolded assembly .
understanding 
 the minutia of dna origami formation will allow us to guide the design 
 of more complex dna nanostructures , optimize annealing protocols , 
 and manipulate functionalized dna nanostructures more effectively . 

structurally speaking , we are still a long way from being able to 
 weave a scaffold strand along arbitrary paths within a dna origami 
 structure , although some progress has been made in this direction . 

recently , yan and co - workers developed a novel strategy to fold gridiron - like 
 dna origami structures . in that work
, 
 interconnected four - arm junctions were used as vertices within a network 
 of dna fragments , and measured distortion of the junctions from relaxed 
 conformations allowed the scaffold strand to traverse through individual 
 vertices in several directions . despite this initial success , interlacing 
 the scaffold strand through the vertices of multiarm junctions remains 
 a challenge that , if achieved , would dramatically improve our ability 
 to form aperiodic tiling patterns and polyhedral 3d structures using 
 the dna origami technique .
besides increasing complexity , scaling 
 up the size of dna origami and reducing the cost of staple strand 
 synthesis are also important issues facing dna nanotechnologists . 

various strategies to address these limitations have been explored , 
 including the use of longer single - stranded scaffolds , double - stranded scaffolds , origami of origami ( super - origami ) , and enzymatic production of staple strands on microarray 
 chips , which has the added benefit of 
 greater fidelity than chemical synthesis .
dna origami 
 has shown great success in directing the assembly of nanoelectronic 
 and photonic elements and has been used as a lithographic mask to 
 etch nanoscale patterns on silicon and graphene substrates . for practical device applications ,
it is highly 
 desirable to achieve robust patterning of self - assembled dna nanostructures 
 on inorganic surfaces , and several groups have developed unique strategies 
 to organize dna origami nanostructures on solid substrates .
the next logical step is to generate chemically functional surface 
 features to facilitate patterning of dna origami nanostructures into 
 spatially addressable arrays .
surface - mediated assembly may be the 
 key to scaling - up dna nanostructure assemblies into wafer - size arrays . 

researchers have already shown that mica and silicon dioxide surfaces 
 will mediate the assembly of small dna tiles into millimeter - range 
 periodic 2d lattices .
the buffer conditions , 
 especially the concentration and species of the ions present , may 
 play a critical role in surface - mediated diffusion of dna nanostructures , 
 an important factor that remains to be explored
. it would also be interesting to use fluidic 2d surfaces 
 such as lipid bilayers to improve the surface - mediated diffusion of 
 dna nanostructures . in mathematics 
 and computer science
however , if you look beyond their traditional 
 context in mathematics , you will see that algorithms can be used to 
 describe the process of self - assembly in the natural world .
consider 
 the self - assembly of lipids into membranes , or viral proteins into 
 capsids , or even just amino acids into intricately folded protein 
 structures , each process involves the spontaneous , or automatic , assembly 
 of small components into larger , more complex structures .
the process 
 by which these structures grow can be described as algorithmic . in 
 each example , a limited number of molecular building blocks grow into 
 higher order structures by following the growth rules encoded into 
 the building blocks themselves .
dna tiles are information - rich building 
 blocks ideally suited for implementing algorithmic self - assembly . 
 originally proposed by winfree , algorithmically self - assembled dna 
 nanostructure patterns have been experimentally demonstrated .
for 
 example , winfree and co - workers showed that dna double - crossover tiles 
 could be programmed to compute and grow into sierpinski triangle and binary counter - assemblies .
they also showed that prescribed dna origami displaying 
 sticky - end - capture probes function as effective nucleation seeds to 
 grow algorithmic arrays while suppressing spurious nucleation , which 
 is a major source of errors during algorithmic assembly .
the design of novel nucleation frames could 
 improve the fidelity and robustness of algorithmic assemblies of dna 
 tiles .
other errors arise from sticky end mismatches between different 
 tiles that share certain sticky end sequences .
the kinetics of tile  tile 
 association between the algorithmic building blocks should be carefully 
 investigated to promote the desired computations and reduce any undesirable 
 mismatches .
also , tile sets could be expanded beyond the typical double - crossover 
 dna tiles to more complex or optimal geometries to facilitate multivalent 
 and cooperative binding between the tiles and allow for improved understanding 
 of the constraints that limit the scope of algorithmic assembly . in biological 
 systems
, there is a clear relationship between the 
 specific structure of a biomolecule and its function . in particular , 
 biopolymers are important molecules whose structure supports the organization 
 and functionality of cells .
the topology of biopolymers can be exploited 
 to facilitate tasks such as packing information - bearing dna molecules 
 into tiny compartments within cells .
molecular topology is a fascinating 
 and technically challenging topic that dna nanotechnology is ideally 
 suited to examine .
seeman and co - workers were the first to show that 
 topological structures such as knots and borromean rings could be 
 self - assembled from dna by combining right - handed b - form and left - handed 
 z - form dna together to create positive and negative nodes .
yan and co - workers later used the dna origami 
 method to construct mbius strip topological structures that 
 could be reconfigured into catenanes and twisted topological ribbons 
 through toehold - mediated strand displacement .
more recently , willner and co - workers developed strategies to interlock 
 dna rings into multiring catenanes .
weizmann 
 and co - workers just reported the assembly of complex knots and links 
 by specifically configuring four - way dna junctions . despite these interesting examples , the area of dna - based 
 topological nanostructures is underdeveloped compared to the geometric 
 structures that have been reported over the past decade .
new construction 
 strategies and topological targets should be identified to push the 
 frontiers of dna - based molecular topology forward .
self - replication 
 is an astounding process by which a molecule in 
 a dynamic system makes an identical copy of itself .
biological cells , 
 provided they have a suitable environment , reproduce by cell division . 
 during cell division , linear dna autonomously undergoes replication 
 by enzyme - mediated processes and is transmitted to offspring .
it is 
 a considerable challenge to design and construct autonomous structures 
 that mimic the action of nucleic acid polymerases and are capable 
 of replicating entire synthetic dna systems nonenzymatically ( figure 6d ) .
the first development in this direction was 
 reported by seeman s group in 2011 .
they constructed a seven - tile seed and successfully generated several 
 generations of progeny in a step - by - step manner .
winfree and co - workers 
 recently showed that mechanically induced scission of 2d dna crystals 
 can accurately replicate self - assembled dna nanopatterns by creating 
 new fronts of crystal growth .
however , 
 constructing autonomous self - replicating systems that do not require 
 external manipulation remains a significant challenge .
pierce and 
 co - workers demonstrated autocatalytic dna duplex formation by way 
 of a cross - catalytic circuit , yet extending 
 this concept to independent formation of sophisticated dna nanopatterns 
 needs additional development .
the successful 
 design and assembly of the dna nanosystems discussed above will undoubtedly 
 lead to many new opportunities and innovative applications .
the information - rich 
 character of self - assembling dna nanostructures in particular will 
 create many new frontiers for the application of designer dna nanostructures 
 as molecular scaffolds , sensors , computers , and robots . in the following 
 sections we will discuss the potential of dna nanostructures to serve 
 as scaffold for functional nanoelectronic and nanophotonic devices , 
 to regulate protein interactions , and to create sense  compute  actuate 
 elements for molecular medicine .
however , these examples are in no 
 way limiting , and the field has already demonstrated a tendency to 
 grow in unexpected directions , surprising even the sagest of researchers .
one of the most obvious applications of a 
 dna nanostructure is to direct the assembly of other , less controllable 
 materials , as was discussed in the previous sections .
we have seen 
 several examples of spatially addressable dna origami structures being 
 used to organize nanoelectronic and photonic components .
however , 
 we have not yet seen concrete examples of dna nanostructures in functional 
 nanoelectronic and photonic devices , where bottom - up , dna - directed 
 assembly is interfaced with top - down , lithographic methods of micro- 
 and macroscale patterning .
the latest developments in surface - mediated 
 self - assembly and site - specific control of chemical properties could 
 enable more precise arrangement of these nanophotonic or nanoelectronic 
 elements into regular , large - scale patterns that can be integrated 
 with macroscopic systems .
dna - directed assembly of complex protein 
 arrays is another area 
 of development to watch for in the future .
enzymes , marvels of natural 
 evolution , are intramolecular organizations of proteins that 
 are capable of recognition , capture , and activation of molecules and 
 regulation of biochemical processes .
these protein complexes act as 
 the central functional components of metabolism and reproduction in 
 living systems .
the binding sites for 
 substrates and cofactors are chemically specific , while the active 
 sites are stereospecific and highly sensitive to conformational rearrangement . 
 inspired by nature
, researchers have pursued a variety of strategies 
 to regulate and control the catalytic activities of enzymes , as well 
 as to understand the mechanism of enzyme function and pathways .
compared to most conventional techniques , dna nanotechnology is 
 a highly efficient and controllable strategy to achieve structural 
 programmability and reconfigurability through rational design and 
 construction .
assembling enzymes and cofactors on dna nanostructure 
 scaffolds has already allowed researchers to probe the essential parameters 
 for modulating catalysis , such as intermolecular distance and 
 relative spatial position .
one example of controlling the activity 
 of an individual enzyme using dna was reported in 2013 , where the 
 authors achieved mechanical regulation of the enzyme luciferase by 
 attaching a dna spring . in the same 
 year
an even loftier and more valuable goal 
 is to engineer highly programmed 
 cascading enzyme pathways on dna nanostructure platforms with control 
 of input and output sequences . achieving this goal not only would 
 allow researchers to mimic the elegant enzyme cascades found in nature 
 and attempt to understand their underlying mechanisms of action but 
 also would facilitate the construction of artificial cascades that 
 do not exist in nature ( figure 7a ) .
( b ) design and implementation of theranostic nanodevices on targeted 
 cell surfaces that carry out functions such as compute , sense , release 
 signal , trigger activation , and deliver therapeutic molecules across 
 the cell membrane . one major challenge in 
 integrating multiple proteins into dna nanostructures 
 is to precisely define their relative orientation and position .
a 
 set of reliable and general methods for site - specific conjugation 
 of proteins with oligonucleotides must be established in order to 
 accommodate the diversity of proteins of interest . in an ideal system
, 
 a single protein with multiple coupling sites would be conjugated 
 to unique dna sequences to enable absolute orientational control of 
 the protein relative to the dna nanostructure . in this way ,
the active 
 sites of the enzymes , in a multienzyme cascade for example , could 
 be precisely oriented to facilitate substrate 
intermediate  product 
 transfer , and the overall enzymatic activity of the cascade could 
 be optimized .
a far - reaching goal of structural dna nanotechnology 
 is to develop smart molecular machines that perform sense  compute  actuate 
 mechanisms based on intrinsically information - rich dna molecules and 
 structures ( figure 7b ) .
for example , the development 
 of  smart molecular doctors  would revolutionize the 
 field of personalized medicine .
a smart molecular doctor would have 
 the same responsibilities as a real ( human ) doctor , including diagnostic 
 and therapeutic roles , but would operate entirely at the cellular 
 level . directly treating individual diseased cells to cure them on 
 the single - cell level offers
improved therapeutic efficiency and fewer 
 side effects since smaller drug doses are required compared to conventional 
 therapies .
other targeted drug delivery systems based on multifunctional 
 liposomes , polymersomes , and nanoparticles have already been developed .
dna is an attractive material for theranostic 
 applications , not only because of its inherent design modularity , 
 structural programmability , and biocompatibility but also because 
 dna molecules of a particular sequence or with certain modifications 
 can selectively bind , distinguish , and communicate with target cells 
 to trigger drug release .
researchers have made strides toward constructing 
 dna - based drug containers and dna nanostructures that can be embedded 
 into lipid bilayers , particularly after 
 the establishment of the dna origami method .
the first dna origami 
 box with a responsive lid that recognized a specific oligonucleotide 
 key and subsequently opened was reported in 2009 .
more recently , researchers developed a dna nanobarrel with 
 two single - stranded aptamer locks that were opened by the presence 
 of target cells in vitro . performing dna computation directly on the surface of cells , 
 or 
 in cellular environments ,
recently , rudchenko , stojanovic , and 
 colleagues engineered dna strand displacement cascades that detected 
 the presence of certain cell markers on the surface of cells . in another report ,
hemphill and deiters successfully 
 engineered oligonucleotide logic gates to detect specific microrna 
 inputs in live mammalian cells . as more 
 complex and robust dna - based computing systems
are developed , it may 
 be possible to integrate them into cellular systems to control and 
 trigger cellular functions such as gene expression or to interfere 
 with the metabolic pathways .
recently , 
 researchers reported the construction of a consensus network that 
 distinguishes between two different input signals and reports the 
 majority signal . by combining dna computation - based 
 target cell detection with reconfigurable dna - based drug containers , 

it may be possible to create a dna nanorobot that can interface and 
 communicate with living cells ( figure 7b ) .
there are a number of critical issues that must be addressed before 
 dna nanorobots can be used for drug delivery in vivo .
researchers must find a way to protect dna nanostructures from 
 degradation by the intra- and extracellular nucleases and liver 
 metabolism over long periods .
compact dna nanostructures generally 
 display relative stability against dna nucleases for a short time 
 ( a few hours ) . in the future
it will be important 
 to increase resistance to biodegradation by using methods such as 
 chemical cross - linking of selected dna strands or designated dna backbone 
 modifications . identifying the mechanisms by which dna nanostructures 
 enter cells without being damaged , and escape endosomal processing , is also a critical point .
the biggest obstacles to transforming 
 dna nanostructures from mere 
 curiosities into real - world solutions are the cost of synthetic dna , 
 small production scales , typically low yield of complex 3d structures , 
 and sensitivity of dna to ionic strength , temperature , and nucleases . 

researchers have already begun to address these issues by optimizing 
 origami design and folding strategies to increase assembly yields and shorten assembly times and by developing suitable purification strategies for 
 large - scale synthesis .
it is also important 
 to develop biocompatible conditions for efficiently folding dna nanostructures , 
 rather than by thermal annealing under high magnesium concentrations .
living cells are information - rich , sophisticated machines that 
 display angstrom - level organizational precision . although dna nanostructures 
 are exquisitely programmable , they are only able to regulate biological 
 molecules at a relatively coarse level compared to nature .
if we want 
 additional control , we must push the boundaries of nanoscale fabrication 
 to the angstrom level .
in contrast to dna , rna and proteins have more 
 refined architectures with angstrom - level features .
these aspects 
 of their organization have attracted increasing attention in the past 
 decade .
methods for engineering 
 designed proteins and nanostructured complexes using proteins have 
 also begun to emerge .
the progress of characterization 
 techniques such as cryo - em , x - ray diffraction , and nmr supports the 
 development of angstrom technology . in particular , the most recent 
 developments in cryo - em techniques allow crystallization - free structural 
 determination of large - sized proteins that is comparable to x - ray 
 methods . using dna origami frames both 
 as structural hosts and as references , the structure of dna and rna 
 binding proteins may now be determined to angstrom - level resolution 
 by cryo - em .
this advance will provide 
 researchers with atomic - level structural information ( in conjunction 
 with the structural solutions obtained from x - ray crystallography ) 
 that can be fed back into the design pipeline , elevating the field 
 to unimaginable heights ( figure 8) . from nano- 
 to angstrom - level control : engineering molecular toolboxes 
 composed of dna , rna , peptide , and protein molecules and their unnatural 
 derivatives to extract new design rules and create complex , self - assembling 
 structures with angstrom - level spatial control . in summary ,
after more than 30 years of growth , structural 
 dna 
 nanotechnology is transitioning from adolescence into adulthood .
the 
 field is crossing the boundaries of physics , chemistry , biology , and 
 engineering and is poised to generate unique approaches and solutions 
 to real - world challenges in science and technology . in the next phase 
 of structural dna nanotechnology , novel interactions between dna , 
 rna , and proteins could be used to facilitate angstrom technology , 
 representing the major challenges and opportunities in molecular design , 
 assembly , computing , and programming .
living cells are information - rich , sophisticated machines that 
 display angstrom - level organizational precision . although dna nanostructures 
 are exquisitely programmable , they are only able to regulate biological 
 molecules at a relatively coarse level compared to nature .
if we want 
 additional control , we must push the boundaries of nanoscale fabrication 
 to the angstrom level .
in contrast to dna , rna and proteins have more 
 refined architectures with angstrom - level features .
these aspects 
 of their organization have attracted increasing attention in the past 
 decade .
methods for engineering 
 designed proteins and nanostructured complexes using proteins have 
 also begun to emerge .
the progress of characterization 
 techniques such as cryo - em , x - ray diffraction , and nmr supports the 
 development of angstrom technology .
in particular , the most recent 
 developments in cryo - em techniques allow crystallization - free structural 
 determination of large - sized proteins that is comparable to x - ray 
 methods . using dna origami frames both 
 as structural hosts and as references , the structure of dna and rna 
 binding proteins
this advance will provide 
 researchers with atomic - level structural information ( in conjunction 
 with the structural solutions obtained from x - ray crystallography ) 
 that can be fed back into the design pipeline , elevating the field 
 to unimaginable heights ( figure 8) . from nano- 
 to angstrom - level control : engineering molecular toolboxes 
 composed of dna , rna , peptide , and protein molecules and their unnatural 
 derivatives to extract new design rules and create complex , self - assembling 
 structures with angstrom - level spatial control . in summary ,
after more than 30 years of growth , structural 
 dna 
 nanotechnology is transitioning from adolescence into adulthood .
the 
 field is crossing the boundaries of physics , chemistry , biology , and 
 engineering and is poised to generate unique approaches and solutions 
 to real - world challenges in science and technology . in the next phase 
 of structural dna nanotechnology , novel interactions between dna , 
 rna , and proteins could be used to facilitate angstrom technology , 
 representing the major challenges and opportunities in molecular design , 
 assembly , computing , and programming .
 over 
 the past three decades dna has emerged as an exceptional molecular 
 building block for nanoconstruction due to its predictable conformation 
 and programmable intra- and intermolecular watson  
 crick 
 base - pairing interactions . 
 a variety of convenient design rules and 
 reliable assembly methods have been developed to engineer dna nanostructures 
 of increasing complexity . 
 the ability to create designer dna architectures 
 with accurate spatial control has allowed researchers to explore novel 
 applications in many directions , such as directed material assembly , 
 structural biology , biocatalysis , dna computing , nanorobotics , disease 
 diagnosis , and drug delivery . 
 this perspective discusses the state 
 of the art in the field of structural dna nanotechnology and presents 
 some of the challenges and opportunities that exist in dna - based molecular 
 design and programming . 
Introduction
Recent Developments in Structural DNA Nanotechnology
Frontiers of Structural DNA
Nanotechnology
From Nano to Angstrom Technology