The DNA Origami Protocol - Research Paper Example

 “What to make with DNA origami” Abstract DNA nanotechnology where by the single molecules are put together and folded to form shapes that are complex which are used in assembling the nanostructures. The DNA nanotechnology is part of the DNA origami. The DNA has a number of limitations in the percentage of the chemicals which enable it to be optical and electronically. I doing so, the DNA molecules will act as templates in order to come up with a new functional property. Sometimes, some of the components can be incorporated into the DNA nanostructures in order to be imaged. The components can be large nanocomponents like nanoparticles and biomolecules. The chemical reactions that happen along with the single molecules can be done on the DNA origami and be imaged by the force of microscopy. During the experiments, other organic materials can be formed like chemo electives that form successive cleavages that form bonds which show of the ability of the experiments to have the chemical modifications of the nanostructures and the address potential. With the DNA Origami, the major use of its components to have the ability to fold to create Super materials that is very important. The origami is able to fold create a tiny colorful bits of papers. The scientists who study DNA origami are on exposing all the codes concerning the nanoscopic materials that have amazing properties. Introduction DNA origami is the folding of the DNA in order to form a double or triple nanoscale shapes. This becomes more important in the field of Bioengineering because of the nature of the DNA nature. The nature of the DNA becoming a polymer creates interesting characteristics that the chemists become addicted to. The polymer has the characteristics of forming sequences that are complemented and it favors the chemistry nature in the field of bioengineering. This makes the molecules of the DNA to be binding to each other making them to flow to the same consequence assembling them to form shapes that are intricate and they are structured to form the nanoscale. The DNA molecules form one weave together binding them together creating a complex scaffold that is nanomachinery. The process of DNA nanoengineering that is not easy to the chemists and it remains to be a dream to them. The researchers have collected the segments of the DNA to form sheets and tubes. Having a design of such structures has been a problem since it takes months and years. This takes time because the researchers concentrate on beginning from scratch. The researchers also use the short segments which have a 150 base pair making the manufacture. The design of the DNA synthesizers is reduced in terms of size and complexity. It is also in questions that the designers need to create a smaller stuff that is very complicated in such an easy way that is not costly. The sheets of the DNA folded can be grouped in the same sequence that will be used in the binding of the molecules. The DNA can make the bio molecules Creating of the DNA origami is helpful in the development of the metamaterials because it is just like baking a new cake without bearing in mind of the ingredients. When the right ratio of the ingredients is applied, complex structures will be created and many of the people will appreciate. “A primer to scaffolded DNA origami” AND “Folding DNA to create nanoscale shapes and patterns” With the arrangement of the DNA origami, a practical guide is given to their formation creating a prediction over the objects to be formed. This will also give the conditions needed for the formation of the objects with their expected structure. Scaffolded DNA origami has arrangement a collection of nucleotides and sub nanometer. When developing a DNA origami, one is assumed to be creating a blueprint for a building. The specifics of each of the bricks forming the building should be known and be specified by the expert. Just like the double bricks, the double helical DNA is formed by the single oligonucleotides which are formed from the long scaffold molecule that is stranded. They form threads that are staple strands that have a sequence. In the creation of the DNA origami objects there is special software that creates them called caDNAno and it is an open source application. In the formation of the DNA origami, there are domains that are adjacent forming interhelix connections that have junctions. The connections are normally by crossovers that are not parallel to the staple or the strand that is a double helical domain. DNA that has a double helical domain is always protruding within the crossovers. The expanding depends on the crossovers distances between them. With the single DNA layer, it forms an out interhelical domain. Examples that are used in the design of the scaffolded Origami are the AFM images that are formed between the middle and bottom. An AFM image is an image that is formed from the crystallized DNA origami which has been formed from the copies of the single shaped layer made by the single cross shaped layer. Another images formed are the container like objects. In the object, there is a segment that is created from the two strands of the DNA origami creating a continuous strand. One of the first step when creating the DNA origami is to incorporate the scaffold into all the domains which will make the DNA Origami objects. Incase one uses a circular scaffold in the DNA origami creation it is recommended to make it end at the starting point. The scaffold element can also be in a linear form and this will be the solution of routing the circular scaffold. For the sake of understanding and clarity, the multilayer objects can be created from a three dimensional scaffold which can be transformed into a two dimensional layer and this can be treated differently in regard to the strands that will be used in the DNA origami creation. In the packing of the DNA origami, there should be rules used in the cross over spacing. In the space filling one can decide to use the multilayer approach or the single layer used for helix. For the single layer, the yields can be seen within a period of few hours. With the multi layers, it can take some time because of the structure being used in the formation of the DNA origami and this differs from one object to another. There are computational tools which are used in the three dimensional structures designs. This saves the cost used in the creation of the structures because of the omission of the oligonucleotides which is not available in the synthesis. The tools have got a value which is used in the design of the complex objects that make twisted objects that are attractive. With the computer Aided engineering, the three dimensional DNA origami can be used to make creative objects that are attractive. Folding the DNA to form the shapes that are nanoscale with patterns that are attractive is a challenge. The ability of the atoms and molecules to form their organization attributes depends on their intrinsic properties. The main purpose of the structure creation is to create nanostructures that are complex and of high quality and match the required style. With the as semblance of the DNA molecules, it is easy for them to form a two dimensional shape. This will come out with the possible ways of folding the DNA molecules to form the two dimensional. This is achieved by the use of the process of raster filling the scaffold and collecting all the strands that hold the scaffold into place. This will form a DNA structure that will have a diameter of 100 nm with the required shapes of squares with the best resolution. The oligonucleotides can be used as a 6nm having which will enable the patterns to be programmed and form patterns that are attractive. At the end the whole DNA structure can be use to come up with an assembly that is large forming the helix designs and lattices of triangles. The design of the DNA origami is created following steps that are necessary. In the past two steps are done by the use of the hand and the other three steps are done by the use of the computer. Building the geometric mode of the DNA origami is the first step which will come up with the right shape required. The second step is where a single scaffold nucleotide is folded both sides by the use of the raster pattern to create a helix pattern. There is also a creation of the crossovers which is formed from the formation of the scaffold form one helix to another. During the DNA origami folding the scaffold can create crossovers at some points of the helices forming a twist. For the scaffold to exist from one helix to another, the distance in between the crossovers must be of an even number. The path of the fold is always compatible with the circular scaffold. When both the folding path and the geometric model have been created, the lengths of the DNA and the offsets which are there in form of the units’ represent the DNA origami. The inputs are all put in a computer program for documentation. This assists a lot during the retrieval of the information instead of assuming the measurements which may affect the DNA origami being created. The third step is the staple strands design which gives compliment to the scaffold and creates the crossover period. For the structures assembled the helix bend towards the crossovers making only the phosphate to be created. The bending does not affect the structure of the DNA origami such greatly. When two of the staples of the DNA origami join together they form a backbone nick which appear at the top and bottom sides of the helix. The last step is that the staples are banded to form a larger scaffold domain in order to attain higher energy and temperatures. “Challenges and opportunities for structural DNA nanotechnology” Structural DNA nanotechnology has many opportunities and technical challenges which face it. Over the past 30 years, DNA molecules have been used to build a variety of nanoscale devices and structures. One of the challenges facing Structural DNA nanotechnology is that the finer structure control has a weakness due to lack of quantitative tools for analyzing defect occurrence in DNA nanostructures which are complex. Test structures need designed effects which are magnified in order to form cumulative small folding errors so as to produce geometries which are deviated hence easy to use molecular imaging. More complex DNA nanostructure designs to be made in future are not effectively experienced since there is a difference between an individual macromolecular complex such as a ribosome and a cell. Another challenge is that DNA molecules in nanostructure, are difficult to synthesize and mechanically fragile. Therefore they cannot link together to form larger superstructures in order to form design of super-tile interfaces which can be optimized in order to improve yield. Another challenge facing structural DNA nanotechnology is the positioning of hetero elements for functionality. Nanotechnology does not fully have the ability to construct actuators and machines which are sophisticated. Hetero elements like proteins and nanoparticles may lift DNA nanotechnology into a new inappropriate dimension of functional potential. Integration of hetero elements into DNA structures precisely controls over position and orientation of the demanded molecules. Proteins integration has been a challenge since coupling of oligonucleotides that are converted to different functionalities to specific positions on the protein. An effective method need to be developed in order to accommodate the guest proteins of interest diversity concerning structural DNA nanotechnology. Another challenge is that ineffective biocompatibility of DNA nanostructures and their potential for function in cells has been experienced. This has been portrayed by nanostructures not genetically encoded for assembly and cellular expression in structural DNA nanotechnology context. DNA nanotechnology structures involving single-stranded development methods is a great challenge because it does not create the desired variable segments according to the intended overall structure or function. There is also a challenge of not creating DNA nanostructures towards compatible and bioactive structures. The gene-encoded molecules in DNA nanotechnology structures are not appropriately linked to protein production. Organization of the DNA structures and its functionalism with fullerene molecules and single-walled carbon non-tubes requires more unconventional approaches in order to pay an effective attention in the future about it. Another long-term challenge facing structural DNA nanotechnology is that the DNA nanostructure field may not generate an artificial cell. Therefore the functional behavior provided by DNA becomes ineffective and inconvenient in the structural DNA nanotechnology. Biostructural DNA nanotechnology is limited in such a way that it has no ability to assemble nanostructures in vivo since they lack proper stability. Therefore this becomes a challenge facing structural DNA nanotechnology. The ability of DNA to transport charge over long distances along its bases to support oxidation is not supported because DNA structures have got fragile molecules which cannot stretch or enlarge. An opportunity in the structural DNA nanotechnology which is technological emerges when there is commercial availability of affordable arrays. For example, small amounts of each the tens of thousands of unique oligonucleotides sequences are largely printed at a current price of less than US$0.001 per base in the structural DNA nanotechnology. There are many large reductions in cost of enzymatic amplification which can enable a huge production of gram to kilogram quantities of DNA nanostructures which are complex. An opportunity which entails the primary source of scaffold in relation to DNA origami has a reliance on the 7kb genome of M13 in structural DNA nanotechnology context. “Folding DNA into Twisted and Curved Nanoscale Shapes” Strands of DNA may either be twisted or curved into Nanoscale Shapes through folding. Multiple combined curved elements may be formed in order to build up many different types of complex nanostructures like square-toothed gears and wireframe beach balls. Complex higher-order structures to form multiple double-helical segments which are connected through a lot of turn regions can be engineered by the sequence of molecules of DNA. Shapes of nanoscale of the 1- to 100-nm (1-4) have been used in constructing two-dimensional (2D) crystals (5), 3D wireframe polyhedral (12-17) and nano tubes (6¬-11). A very powerful method to direct the self-assembly of the custom-shaped, planar arrays of anti parallel helices and megadalton-scale of the multiple kilo base “scaffold strand” has been introduced. In this case, a single staple strand can pair with many scaffold-strand segments in order to achieve the intended strategy of switching. With a strategy of extended DNA origami to 3D nano construction it can be conceptualized as anti parallel helices (19) by stacking corrugated sheets. In order to produce a variety of 3D shapes, the arrangement, individual lengths and number of helices may be tuned so as to help the design process (20) through graphical software development. By doing this, the design spaces of accessible DNA-origami shapes are expanded in order to increase the diversity of nanostructures curvature and designed twists in relation to nanoscale. The numbers of base pairs in selected subsets of array cells in order to realize DNA shapes have been systematically adjusted to bend curve or bend along helix-parallel axes in context. Deletion of a pair base results in a local tensile strain for a certain fragment and over winding which in turn causes an exertion of a pull and left-handed move or stretch along the nanoscale. Constructive reinforcement, bend deformations and compensatory global twists can be implemented through the destructive cancellation process. The bundle experiences some deletions or insertions which are only distributed once. The bundle with only deletions is taken to be analogous to the architecture of coiled coils of proteins. They therefore over wind to the left-handed helices from 3.6 to 3.5 amino acids per turn and apply enforcement through heptads-repeat phasing hence a global twist which is left-handed. A model system of a 10-row, 6-helix-per-row (10-by-6) bundle composed of 60 which are tightly interconnected with DNA double helices. Polymerization bundles for ribbons with locally under twisted DNA have nodes which consistently move upwards at an 80 degrees counterclockwise rotation. An identification which is unequivocal to global twist lays to the left hand side in relation DNA structures. Some of the ribbons constructed from bundles with over twisted local DNA contain ribbon nodes which consistently move downward hence revealing global left-handed twists have been developed. Through measuring the distance between consecutive nodes for multiple ribbons, twist frequency has been quantified. There has also been a plot of global twist per turn for each version of the 10-by-6 bundles versus initially imposed double-helical twist density in relation to nanoscale. There have been different architectures which bring out twists which are global hence vary in absolute magnitude along the nanostructure scale. Double helical twist density should be properly considered when developing a design of DNA nanostructure in order to avoid global twist deformations which are unwanted in the system. It has also been developed whereby DNA nano tubes are assembled from oligonucleotides-based tiles which have double-helical twist densities deviating from 10.5bp per turn (21, 22) in nanoscale context. Bend angles which range from 30 degrees to 180 degrees as well as radii of curvature which bend sharply to 6nm can go to an extent of having a nucleosome (23) that is resulted from extreme bending of DNA. “Self-assembly of DNA into nanoscale three-dimensional shapes” Self- assembly of molecular complex structures from simple components in the DNA has been developed. The DNA has largely proved to be important building blocks which help in constructing certain objects in two-dimensional nano tubes and three-dimensional nano polyhedra wireframe. The design of three-dimensional DNA origami contains staple strands which are blue, white and orange and scaffold that is grey. Both the staple strands and the scaffold run parallel to the z-axis in order to form an unrolled two-dimensional schematic in relation to the shape which is targeted. Staple crossovers bridging different layers portrayed as semicircular arcs are formed due to the phosphate linkages which crossover between adjacent helices. The assignment and steps to follow when creating a design of staple sequences meant for the shapes is aided by rendering strand diagrams in Adobe Illustrator manually. This can be done by writing ad hoc programs of the computer in order to produce sequences which are staple corresponding to those designed diagrams in context. Staple helices are prone to crossovers which are restricted in order to form intersections between every third layer of a stack of planes orthogonal to the axes of the helices and intersections between blocks in self-assembly mechanism. A target of three-dimensional shape in relation to assembly uses the honeycomb-pleat-based strategy in conceptualizing the strand of scaffold into an array of anti parallel helices whereby m + 1 has got a preferred attachment angle to helix m of +_ 120 degrees. This is compared to the attachment of helix m – 1 to helix m (Fig. 1b, c) in context. Complementary staple strands often wind in an anti parallel direction around the strands of the scaffold so as to assemble B-form double helices which are effectively assigned initial parameters of the geometrical diameter of 2.0 nm, 34.3 per base-pair mean twist and 0.34nm per base-pair rise in context. TEM and Gel analysis of folding conditions for three-dimensional DNA origami has been established and developed. In this analysis, through self-assembly system, there are a variety of cylindrical models of various shapes corresponding to scaffold sequences which include stacked cross, monolith and two versions of genie bottle. The same shape is achieved through folding under the conditions which are identical in order to give out superior and quality yields in respect to scaffold sequence of a M13-base. With the PEGFP-N1 sequence of scaffold, success to some folding has been achieved when staple concentrations and much higher scaffold are applied. Methodology “Engineered Nanoparticles for Targeted Drug Delivery” In the creation of the nanostructures and devices, the advancement of the nanostructure which are designed by using the DNA origami techniques. There have been large structures of the DNA origami being designed by the use of the programmed DNA. Some of the shapes can be customized in order to have nanoscale devices like the biological antennae. In the methodology the research will look at the creation of the nanoscale antennae designed from the bio structure which is the scaffold. In the conductivity of the antennae, is achieved by the use of the nanoparticles which are formed as a result of the coating of the DNA. This can be achieved also by the conductions of the polymers which form the structures of the polymers. The methodology covers the design of the nano antennas with their characteristics. This study and nano antennas creation can assist in the diagnostic and delivery of the drugs. The technology and improvement of the nanotechnology with the techniques has led to forming structures that have sound and thermal properties. The nanotechnology is heavily applied in the sensors creation technology. This is one of the best researches made by the medical science and technology experts. Some time back, the research has been affected by lack of enough fabrication which is responsible for the structures which have electrical properties. There are several properties realised from this field including lithography, particle scanning and many more. The use of the nanotechnology and the drug delivery of the mechanisms with the origami techniques have led to the evolution of the study. In the methodology there are the following processes needed for the construction of the antennas. Nanoscale antenna design The focus is on the spiral antennae because it has independence over the radiation property which displays patterns that are impedance. This goes along with the size of the antennas which are spiral by the use of the dielectric material. DNA Origami There are a number of spiral antennas being created that are accompanied with the mathematical models used in the technology. Below is the design of the nanoscale antennae. Spiral antennae design With the design techniques of the DNA origami, the protection of the single strand DNA to form more attractive shape designs is positively boosted. This promotes the structures of the nanoscale in the bioengineering sector. With this also the design achieves the creation of curved and circular structures in the design. They protrude patterns that are important in the sector of the design. The nanotechnology also gives the chemical assemble of the structures to have a good foundation of creation. With the electromagnetic phenomena of the structure depicted by the plasmonic mono particle creates an impact into the design. Design of the antennae The sensors have the ability to have the nanotechnology and the nanoparticles which is used in the research field. The use of the nano tubes and the wires are used in the development of the microwave. The antenna has a number of turns with angles which form radiations that are consistent. The antennae always radiate at a circumference that has the length of the wavelength. Scaling Effect In the phase velocity, there is a lot happening at the antenna. There are techniques involved in the process including the slow wave structure. The inductive and capacitive loading with the high dielectric to get new wave propagation that is slow in connection with a few sizes of the antennae. The scaled antennae can be fabricated by the scaffold of the DNA. One of the characters in the antennae is that it experiences low magnetic propagation of the propagation. Some of the spirals can exhibit different frequencies depending on the phase. The characters of the spirals are the same depending on the scale of the nanometer regime. The DNA Origami protocol The protocol is found from the techniques of the DNA origami with the process of assembling the nanoscale three dimensional designs. The protocol has been formed from the uses of the DNA origami process. Conclusion The paper has got a good explanation of the design of the antennae with the DNA scaffold. The antennas are used in the nano carriers where by they are used in the engineering field. The antennas can be used in the drug delivery and its diagnostics. The capability of the antennas to respond to the required frequencies, they are able to be used at the communication and control of the nano particles. In the process it will be very easy to identify the toxic substances in the body of the nano particles. On the same centrally, it is not easy to monitor traditionally the drug being delivered to the body. The introduction of the nanoscale antennae which delivers the medicine and allows the communication to the researchers has been a solution to this. References Andre, V. Pnheiro & Dongran Han. (2011). Challenges and opportunities for structural DNA nanotechnology. Published online on 6th November 2011: DOI: 10.1038/NNANO.2011.187 Breland, M. B. Patel & Hassan. (2013). Engineering Nanoparticles for Targeted Drug Delivery. U.S.A: University of Bridgeport. Castro, E. & Kilchherr, F. (2011). A primer to scaffolded DNA origami.Nature America: Dietz, H. (2009). Folding DNA into Twisted and Curved Nanoscale Shapes. NewYork: American Association for the Advancement of Science. Science ( print ISSN 0036-8075; online ISSN 1095-9203. Paul W. K. Rothemund. (2006). Folding DNA to create nanoscale shapes and patterns. VOL 440. Paul W. K. Rothemund. (2006). What to make with DNA origami. VOL 464. Shawn M. Douglas & Hendrik Dietz. (2009). Self assembly of DNA into nanoscale three dimensional shapes. VOL 459. Read More