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DNA Nanotechnology and its Biological Applications
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without entirely redesigning the nanostructure By autonomous we mean that the. steps are executed with no exterior mediation after starting We discuss various. such programmable molecular scale devices that achieve various capabilities. including computation 2D patterning amplified sensing and molecular. 13 1 Introduction, 13 1 1 DNA Nanotechnology and its use to Assemble Molecular Scale. The particular molecular scale devices that are the topic of this article are known. as DNA nanostructures As will be explained DNA nanostructures have some. unique advantages among nanostructures they are relatively easy to design. fairly predictable in their geometric structures and have been experimentally. implemented in a growing number of labs around the world They are constructed. primarily of synthetic DNA A key principle in the study of DNA nanostructures is. the use of self assembly processes to actuate the molecular assembly Since. self assembly operates naturally at the molecular scale it does not suffer from. the limitation in scale reduction that so restricts lithography or other more. conventional top down manufacturing techniques Other surveys of DNA. nanotechnology and devices have been given by LaBean 1 Mao 2 Reif 3. and Seeman 4, In attempting to understand these modern developments it is worth recalling that. mechanical methods for computation date back to the very onset of computer. science for example to the cog based mechanical computing machine of. Babbage Lovelace stated in 1843 that Babbage s Analytical Engine weaves. algebraic patterns just as the Jacquard loom weaves flowers and leaves In. some of the recently demonstrated methods for biomolecular computation. described here computational patterns were essentially woven into molecular. fabric DNA lattices via carefully controlled and designed self assembly. In general nanoscience research is highly interdisciplinary In particular DNA. self assembly uses techniques from multiple disciplines such as biochemistry. physics chemistry and material science as well as computer science and. mathematics We will observe that many of these self assembly processes are. computational based and programmable and it seems likely that a variety of. interdisciplinary techniques will be essential to the further development of this. emerging field of biomolecular computation,13 1 2 The Topics Discussed in this Article. While a high degree of interdisciplinarity makes the topic quite intellectually. exciting it also makes it challenging for a typical reader For this reason this. article was written with the expectation that the reader has little background. knowledge of chemistry or biochemistry We define a few relevant technical. terms in subsection 13 2 1 In subsection 13 2 2 we list some known enzymes. used for manipulation of DNA nanostructures In subsection 13 2 3 we list some. reasons why DNA is uniquely suited for assembly of molecular scale devices. In many cases the self assembly processes are programmable in ways. analogous to more conventional computational processes We will overview. theoretical principles and techniques such as tiling assemblies and molecular. transducers developed for a number of DNA self assembly processes that have. their roots in computer science theory e g abstract tiling models and finite state. transducers Computer based design and simulation are also essential to the. development of many complex DNA self assembled nanostructures and systems. Error correction techniques for correct assembly and repair of DNA self. assemblies are also discussed, The area of DNA self assembled nanostructures and robotics is by no means. simply a theoretical topic many dramatic experimental results have already. been demonstrated and a number of these will be discussed The complexity of. these demonstrations has been increasing at an impressive rate even in. comparison to the rate of improvement of silicon based technologies This article. discusses the accelerating scale of complexity of DNA nanostructures such as. the number of addressable pixels of 2D patterned DNA nanostructures and. provides some predictions for the future, Molecular scale devices using DNA nanostructures have been engineered to.
have various capabilities ranging from i execution of molecular scale. computation ii use as scaffolds or templates for the further assembly of other. materials such as scaffolds for various hybrid molecular electronic architectures. or perhaps high efficiency solar cells iii robotic movement and molecular. transport and iv exquisitely sensitive molecular detection and amplification of. single molecular events and v transduction of molecular sensing to provide. drug delivery,13 2 Introductory Definitions,13 2 1 A Brief Introduction to DNA. Single stranded DNA denoted ssDNA is a linear polymer consisting of a. sequence of DNA bases oriented along a backbone with chemical directionality. By convention the base sequence is listed starting from the 5 prime end of the. polymer and ending at the 3 prime end these names refer to particular carbon. atoms in the deoxyribose sugar units of the sugar phosphate backbone the. details of which are not critical to the present discussion The consecutive. nucleotide bases monomer units of an ssDNA molecule are joined through the. backbone via covalent bonds There are 4 types of DNA bases adenine thymine. guanine and cytosine typically denoted by the symbols A T G and C. respectively These bases form the alphabet of DNA the specific base sequence. comprises DNA s information content The bases are grouped into. complementary pairs G C and A T, The most basic DNA operation is hybridization where two ssDNA oriented in. opposite directions can bind to form a double stranded DNA helix dsDNA by. pairing between complementary bases DNA hybridization occurs in a buffer. solution with appropriate temperature pH and salinity A dsDNA helix is. illustrated in Figure 13 1, Figure 13 1 Structure of a DNA double helix Created by Michael Str ck and released under the GNU. Free Documentation License GFDL, Since the binding energy of the pair G C is approximately half again the. binding energy of the pair A T the association strength of hybridization. depends on the sequence of complementary bases and can be approximated by. known software packages The melting temperature of a DNA helix is the. temperature at which half of all the molecules are fully hybridized as double helix. while the other half are single stranded The kinetics of the DNA hybridization. process is quite well understood it occurs in a random zipper like manner. similar to a biased one dimensional random walk, Whereas ssDNA is a relatively flexible molecule dsDNA is quite stiff over.
lengths of less than 150 or so bases and has the well characterized double helix. structure There are about 10 5 bases per full rotation on this helical axis The. exact geometry of the double helix depends slightly on the base sequence in a. way readily computed by existing software A DNA nanostructure is a multi. molecular supramolecular complex consisting of a number of ssDNA that have. partially hybridized as designed along their sub segments. 2 2 Manipulation of DNA, In addition to the hybridization reaction there are a wide variety of known. enzymes and other proteins used for manipulation of DNA nanostructures that. have predictable effects Interestingly these proteins were discovered in natural. bacterial cells and tailored for laboratory use These include. Restriction enzymes can cut double strand break or nick single. strand break a DNA backbone at specific locations determined by. short base sequences, Ligase enzymes can heal or repair DNA nicks by forming covalent. bonds in the sugar phosphate backbone, Polymerase can extend an ssDNA by covalently coupling further. complementary bases as dictated by a template ssDNA thus. forming a longer sequence of dsDNA, Besides their extensive use in other biotechnology procedures the above. reactions together with hybridization are often used to execute and control DNA. computations and DNA molecular robotic operations The restriction enzyme. reactions are programmable in the sense that they are site specific only. executed as determined by the appropriate DNA base sequence The latter two. reactions using ligase and polymerase require the expenditure of energy via. consumption of ATP molecules and thus can be controlled by ATP. concentration, 13 2 3 Why use DNA to Assemble Molecular Scale Devices.
There are many advantages of DNA as a material for building things at the. molecular scale, a From the perspective of design the advantages are. The basic geometric and thermodynamic properties of dsDNA are well. understood and can be modeled by available software systems The. structure of a large number of more complex DNA nanostructures can be. predicted by a number of prototype software systems from details like the. sequence composition temperature and buffer conditions which are the. key relevant parameters, Design of DNA nanostructures can be assisted by software To design a. DNA nanostructure or device one needs to design a library of ssDNA. strands with specific segments that hybridize to and only to specific. complementary segments on other ssDNA There are a number of. software systems for this combinatorial sequence design task and for. design of DNA nanostructures with desired structures. b From the perspective of experiments the advantages are. The chemical synthesis of ssDNA is now routine and inexpensive a test. tube of ssDNA consisting of any specified short sequence of bases 150. can be obtained from commercial sources for modest cost about half a. US dollar per base at this time it will contain a very large number. typically at least 1012 identical ssDNA molecules The synthesized. ssDNA can have errors premature termination of the synthesis is the. most frequent error but can be easily purified by well known techniques. e g electrophoresis as mentioned below, The assembly of DNA nanostructures is a very simple experimental. process in many cases one simply combines the various component. ssDNA into a single test tube with an appropriate buffer solution at an. initial temperature above the expected melting temperature of the most. stable base pairing structure and then slowly cools the test tube below the. melting temperature, The assembled DNA nanostructures can be characterized by a variety of. techniques One such technique is electrophoresis It provides information. about the relative molecular mass of DNA molecules as well as some. information regarding their assembled structures depending on what type. of electrophoresis denaturing or native respectively is used Other. techniques like Atomic Force Microscopy AFM and Transmission. Electron Microscopy TEM provide images of the actual assembled DNA. nanostructures on 2D surfaces, 13 3 Adelman s Initial Demonstration of a DNA based Computation.
13 3 1 Adleman s Experiment, The field of DNA computing began in 1994 with a laboratory experiment. described in 5 6 The goal of the experiment was to find within a given. directed graph a Hamiltonian path which is a path that visits each node exactly. once To solve this problem a set of ssDNA was designed based on the set of. edges of the graph When combined in a test tube and cooled they self. assembled into dsDNA Each of these DNA nanostructures was a linear DNA. helix that corresponded to a path in the graph If the graph had a Hamiltonian. path then one of these DNA nanostructures encoded the Hamiltonian path By. conventional biochemical extraction methods Adelman was able to isolate only. DNA nanostructures encoding Hamiltonian paths and by determining their. sequence the explicit Hamiltonian path It should be mentioned that this. landmark experiment was designed and experimentally demonstrated by. Adleman alone a computer scientist with limited training in biochemistry. 13 3 2 The Non Scalability of Adelman s Experiment. While this experiment founded the field of DNA computing it was not scalable in. practice since the number of different DNA strands needed increased. exponentially with the number of nodes of the graph Although there can be an. enormous number of DNA strands in a test tube 1015 or more depending on. solution concentration the size of the largest graph that could be solved by his. method was limited to at most a few dozen nodes This is not surprising since. finding the Hamiltonian path is an NP complete problem whose solution is likely. to be intractable using conventional computers Even though DNA computers. operate at the molecular scale they are still equivalent to conventional. computers e g deterministic Turing machines in computational power This. experiment taught a healthy lesson to the DNA computing community which is. now well recognized to carefully examine scalability issues and to judge any. proposed experimental methodology by its scalability. 13 3 3 Autonomous Biomolecular Computation, Shortly following Adleman s experiment there was a burst of further experiments. in DNA computing many of which were quite ingenious However almost none. of these DNA computing methods were autonomous and instead required many. tedious laboratory steps to execute In retrospect one of the most notable. aspects of Adleman s experiment was that the self assembly phase of the. experiment was completely autonomous it required no exterior mediation the. bulk of the labor was in the non autonomous molecular sorting steps The. strategy can be termed generate and sort since all possible answers are created. and incorrect solutions are subsequently discarded Maximizing molecular. autonomy makes an experimental laboratory demonstration much more feasible. as the scale increases The remaining article mostly discusses autonomous. devices for bio molecular computation based on self assembly. 13 4 Self Assembled DNA Tiles and Lattices,13 4 1 Computation By Self Assembly. The most fundamental way computer science ideas have impacted DNA. nanostructure design is via the pioneering work by theoretical computer scientists. on a formal model of 2D tiling due to Wang in 1961 which culminated in a proof. by Berger in 1966 that universal computation could be done via tiling assemblies. Winfree 7 was the first to apply the concepts of computational tiling assemblies. to DNA molecular constructs His core idea was to use tiles composed of DNA to. perform computations during the process of self assembly where only valid. solutions to the computation are allowed to assemble To understand this idea. we will need an overview of DNA nanostructures as presented in the next. subsection 4 2,13 4 2 DNA Nanostructures, Recall that a DNA nanostructure is a multi molecular complex consisting of a. number of ssDNA that have partially hybridized along their sub segments The. field of DNA nanostructures was pioneered by Seeman 4. Particularly useful types of motifs often found in DNA nanostructures include. Stem Loops and Sticky Ends as illustrated below,Figure 13 2 A Stem Loop and a Sticky End.
Figure 13 2A illustrates a stem loop where ssDNA loops back to hybridize on. itself that is one segment of the ssDNA near the 5 end hybridizes with another. segment further along nearer the 3 end on the same ssDNA strand The. shown stem consists of the dsDNA region with sequence CACGGTGC on the. bottom strand The loop in this case consists of the ssDNA region with sequence. TTTT Stem loops are often used as markers for visualizing programmed. patterning on DNA nanostructures, Figure 13 2B illustrates a sticky end where unhybridized sDNA protrudes from. the end of a double helix The sticky end shown ATCG protrudes from dsDNA. CACG on the bottom strand Sticky ends are often used to combine two DNA. nanostructures together via hybridization of their complementary ssDNA The. Figure 13 2B shows the antiparallel nature of dsDNA with the 5 end of each. strand pointing toward the 3 end of its partner strand. Figure 13 3 A Holliday Junction Image created by Miguel Ortiz Lombard a CNIO Madrid Spain and. used with permission, Figure 13 3 illustrates a Holliday junction where two adjacent DNA helices form a. junction with one strand of each DNA helix blue and red crossing over to the. other DNA helix Holliday junctions are often used to tie together various parts of. a DNA nanostructure,13 4 2 DNA Tiles and Lattices, A DNA tile is a DNA nanostructure that has a number of sticky ends on its sides. which are termed pads A DNA lattice is a DNA nanostructure composed of a. group of DNA tiles that are assembled together via hybridization of their pads. Generally the strands composing the DNA tiles are designed to have a melting. temperature above those of the pads ensuring that when the component DNA. molecules are combined together in solution first the DNA tiles assemble and. only then as the solution is further cooled do the tiles bind together via. hybridization of their pads A number of prototype computer software systems.


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