نانوساختار‌های DNA

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DNA asa Nanomaterial Presentation: Sajjad Babaei Ph.D. student of Nano-biotechnology, School of Sciences, Razi Uni. Kermanshah, Iran Lecture: applications of Nano-biotechnology 

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DNA is a biomacromolecule composed of sugar, phosphate and organic bases. It has unique and interesting features. 

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DNA’s structure.1-1 This molecule composed of two chains that coil around each other to form double helix carrying the genetic instructions used in the growth, developm| functioning and reproduction of all known living organisms and many viruse: DNA is a long polymer made from repeating units called 1 two hi chains, bound to each other by hydrogen bonds. The pair of chains has a radi 10 Angstréms (1.0 nanometre). iat ( The backbone of the DNA strand is made from alternating phosphate and sugé deoxyribose) residues. The sugars are joined together by phosphate groups, th form phosphodiester bonds.(which are known as the 3’ and 5’ carbons). The four bases found in DNA are adenine (A), cytosine (C), guanine (G) and thymine (T). These four bases are attached to the sugar-phosphate to form he complete nucleotide The DNA double helix is stabilized primarily by two forces: hydrogen bond: between nucleotides and base-stacking interactions among aromatic nu 

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‎Adenine ©‏ و امه 5 ‎© Hydrogen ‎oye & end ٠ 7 @ Nitrogen AB 5 © Carbon ‎© Phosphorus ‏و ‎Phosphate ۰ ‎deoxyribose ra 5 backbone ~ x ry Pe ‏ع‎ ‏و‎ ‎Minor groove ‎3 ‎8 ‎5 ‎5 ‎3| ‎2 ‏2 ‏ری ‏2 ‎١‏ ۳ کت موزوونی ‏ 3 د 3 ‎5 ۵ ‎ 

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Hydrogen Bonds 8 ‏بو‎ *Here are the two diagrams ‏وم‎ outlining where the hydrogen bonds are within DNA (red lines). N. ‏اج‎ ‎2 ‏م‎ = *Base A and T are held together ‘hymine by two hydrogen bonds ( an O-H 11 and N-H bonds)and bases G and & C are bonded together by three nents hydrogen bonds ( 2 O-H bonds | and 1 N-H bond). 8 b+ 6, 5 ee +The different number of his 8 Hydrogen bonds ensure that the | Ee bases link together correctly Cytosine Guanine 

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Major forms of hydrogen bonds in the DNA structure > In these various forms, the atoms involved in the H-bond are different. » Therefore, it changes the states of syn and anti (Watson-Crick Hoogsteen 

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Base-stacking Interactions >» When this interactions occurs, that two aromatic rings, such as two, plates, are placed nearby on each other. > Interactive periodic rise and fall in electron cloud, creates a force between the rings. » When the electron cloud is thin around one of the ring and a positive charge is created, in that moment, the other one (another ring), has a thick electron cloud which gives it a negative charge. Then a link between the positive and negative charges will be created. » In the next moment, the position of positive and negative areas is) changed. as the result, the connection of the rings will be — continuous. The reason for this is the harmony of electron cloud rise and fall times in the adjacent rings. » This interaction can be flexible and take on the different struct states 

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Base-stacking Interactions Base stacking: an axial view of twist By WONA Thymine 

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DNA has different types fonns 2 A.B) €, DB, ZH, 1 » Creating these forms of DNA depends on the environmental conditions and the presence of some ions and molecules » The presence of these forms is highly depends on humidity » Depending on the environmental conditions, these forms can be transformed into each other For example : B-DNA in an environment with the following features, can change to Z-form : a) high concentration of salt b) adding bromine or methyl to cytosine c) in the presence of regulatory proteins 

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2۸ ZDNA 8 2 267 77 3.03 A 378 5 181 Right handed | Left handed * Extremely rare variant with only 8base pairs per helical * This forms of DNA found in some DNA molecules Comparison of different types of DNA CDNA 9.33 78 232 19 ۸ Right handed D-DNA tum devoid of guanine. BDNA 10 53 337A 20۸ Right handed ADNA 1 202: 2.56 ۸ 23۸ Right handed Characters Base pair per turn of the helix Tilt of pairs (7) base ‘Aaial rise (F) Helical diameter Handedness of the double helix >» B-DNA: Most common ,originally deduced from X-ray diffraction of sodium salt of DNA fibres at 92% relative humidity. » A-DNA: Originally identified by X-ray diffraction of analysis of DNA fibres at 75% relative humidity . » Z-DNA: Left handed double helical structure winds to the left in a zig- zag pattern . » C-DNA: Formed at 66% relative humidity and in presence of Li+ and Mg2+ ions. 

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Structural comparison of different types of DNA 2 se S 15 3 A-DNA ‏مار‎ 97 ف ۵ 

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DNA is the most important biological molecule It has dimensions about nano-meter Known geometric and thermodynamics properties Predictability and programmability of combinations and sequencing properties / Laboratory Benefits : Easy and practical construction, Fixing the mistakes and Easy determination of the features A question ??!! Why do we consider DNA as an important molecule in Nano-biotechnology applications? vvvy » DNA is a bio-database in the all of the living creatures » Self-Assembly Property » Also: Electrical conductivity and Catalytic function 

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DNA Self-Assembly.1-2 this is an important Property » Self-assembly is one of the key approaches that might enable future methods to be developed for building nanostructures and nanodevices » Self-assembly is a process in which a disordered system of pre-existing components forms an organized structure or pattern as a consequence of specific, local interactions among the components themselves, without external direction. Self-assembly processes occur in nature in various forms, from molecular-level protein folding and the formation of lipid bilayers to the establishment of Earth’s entire biological system. 

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Self-assembly » Self-assembly can be classified as either static or dynamic. In static self-assembly, the ordered state forms as a system approaches equilibrium, reducing its free energy. However, in dynamic self- assembly, patterns of pre-existing components organized by specific local interactions are not commonly described as_ "self-assembled" by scientists .These structures are better described as "self-organized", although these terms are often used interchangeably. 

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DNA origami > One of the milestones in DNA nanotechnology was the invention of DNA origami. >» in this technique, long, single-stranded DNA is folded into target shapes with the help of hundreds of short DNA strands called staples. The staple strands are designed to be complementary to particular regions of the long DNA, and thereby guide the folding process. A wide variety of 2D and 3D nano-objects has been made using this technique. 

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Three-dimensional DNA origami 

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single-stranded tile (SST) assembly >» Another important design strategy in DNA nanotechnology is single-stranded tile (SST) assembly. >» in which SSTs — nanometre-scale 2D rectangles or 3D bricks, formed from single-stranded DNA — are designed to interlock with each other through the formation of DNA duplexes at their interfaces. Collections of SSTs are used to form 2D sheets or 3D blocks that can be selectively ‘sculpted’ to create different patterns and shapes, simply by including or omitting specific SSTs. » the sizes of the DNA structures produced in this way are generally comparable to the sizes of origami nanostructures: larger structures have be 

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Wa ROBO ol] | el] a] 10 ‏ناكا ها‎ ‏لانات ل اه‎ ‏لان‎ ‏لال ات دب ما12‎ ‏م‎ ‎2 ‎9 ‏تال‎ ‎[0 ‏تاانا‎ 

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DNA applications as nanomaterial.2 Conductive nano-wire Nano-Architecture Nano-Computer Diagnostic nanomateri: Nano-Machine Molecular Tag Drug delivery ؟ ۳ ۲ ۲ ۲ ۲ ۲ 

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DNA acts as an electron donor and receiver 

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DNA is a conductive Nano-wire » Some researchs have been proven the DNA conductivity . It has down by connecting metal molecules(gold or silver) to the two ends of the DNA-wire. The DNA acts as the electron donor and receiver » Actually the conductivity of DNA is depends on its sequence and conditions of the formation. » DNA can even be used to Photoelectric transmission.(The photoelectric effect is the emission of electrons or other free carriers when light shines on a material). ۲ Any molecular interference in two DNA strands, reduces the conductivity of DNA. This is the basis for using DNA as biosensors 

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2-2. Nano-Architecture » DNA can be used as Nano-Architecture or model in the manufacturing of different materials Two DNA 3-D structures which can be used as templates 

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>» DNA has an important role in Down to Top approachs in nanobiotechnology » Build the networks of DNA molecules or fabrication the wired network of DNA are some examples of this type of DNA’s Nano- applications. ۲ Up to now, scientists have succeeded to fabricate a 4-handed DNA molecule or 2-D Nano-strip and also, Nano-network which in each ends of that, there are 9 strands of DNA. » These capabilities are controllable by the changes at the end of the DNA molecule » Nano network structure of DNA, has the ability of connecting with other materials * Examples of this Application : Production of copper and platinum =~ nano-wires, DNA mutual Interaction with Carbon Nanotubes, DNA nanolithography(DNA as model)... 

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DNA based template General procedure: ¢Fix a DNA strand between two electrical contacts *Exposed to a solution containing some ions eIons bind to DNA and are then form some nanoparticles decorating along the DNA chain DNA bridge ۷ <> electrodes ‏هه‎ (a) (c) 

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In this type of computers, Information converted to the molecules based on chemical reactions. 

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DNA based Nano-Computer » A DNA-Nano computer can carry out massive and fast chemical reactions » In this type of computers, instead of binary numbers (0/1) , four DNA base molecules(A/T/C/G) and their arrangement circumstance, will be the driver of computing. Information will be stored as an array of DNA base molecules. » A large number of the DNA components are needed to solve a complex issue. For this reason, proliferation of prokaryotic organisms such as bacteria is considered » Based on mathematical calculations and modeling, after 30 times of bacterial proliferation, the DNA-computer's speed will be at least 1000 gigabytes which is so great scale compared to binary computers >» There are tow problems : 1. Weaknesses and defects in the design of chemical reactions ee gt ‏ا‎ ۳ ۳ 

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2-4.DNA as Diagnostic nanomaterial » DNA can be used to detect molecules such as antibodies. 2 In this case, method can be used. >» SELEX method volves a series of processes, such as ultaneous genetic __ mutation, natural selection __and ۲ In simultaneous genetic mutation, DNA random sequence is created by placing nucleotides at the different positions (mutation) . Then, the PCR reaction is performed (amplification). Each single-stranded oligonucleotide, creates a 3-D structure. Following that, an oligonucleotide capable to detecting and connecting to the target molecule, will be separated during the natural selection and washing process. The natural selection holds the oligonucleotide that can attach to the target molecule. And the rest of them will be removed during the washinia process 2 

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>» In the next step, the PCR reaction is performed again(amplification). Repeat these three mentioned processes(5-15 times), causes the production of oligonucleotide that has a high tendency to binding with the target molecule. » Eventually, the desired oligonucleotide is selected and sequenced. This oligonucleotide is ۵ » Some of the benefits of Aptamers include: * They can be obtained in the In-Vitro environment * They can be made in according to the desired sequence * Correcting the chemical structure of them, is simple * They have a stable structure and if necessary, their structures are reversible 

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Systematic Evolution of Ligands by Exponential Enrichment a a DNA/RNA- Library S, GG" z= ‏م وج‎ AS 5-15 times 2 2-0 SELEX (Systematic Evolution of Ligands & ۰ by Exponential Enrichment) Sequence <— Identification | Binding Fraction AMPLIFICATION ‏8ص‎ Re 

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DNA as Nano Machine.2-5 » In a study by Li and his colleagues, A nanomachine was designed. This nanomachine is made in a number of different ways . Possible spatial states included these two cases: A) A four-string structure, with extra-threaded links 8) A two-string structure, with Intra-threaded links This nanomachine has the power of dynamic | expansion and contraction, similar to a worm. 0 

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Li and his colleagues DNA- Nanomachine 0 02 ‎ale ۱‏ 5 وم ۷ ‎TE +‏ 2 سس مه 8ه ‎١‏ ۱ ا 

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Another example » York and his colleagues developed the nanomachine that worked with the fuel of the DNA This DNA-nanomachine is made up of three chains(A, B and C), which create the Tweezers-Like structure. At the edge of this structure, a joint part is created between B and C (24 bases). F fragment is another chain that has a complementary sequence with both B and C fragments. For this reason, it can close the edge of the tweezers-like structure. On the other hand, adding another fragment called F’ which is complementary to the F fragment, will release it (the F fragment). Actually, F and F’ act as the fule for this machine 

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York and his colleagues nanomachine op ۴ عر Closed 

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DNA as Molecular Tag.2-6 » DNA can be used as a tag for identification » For example, the DNA identifier is used in the structure of the combined molecular library » New security services use the DNA technology to identify persons. this is known as the DNA-ID card. Some of the customer's DNA, as his identifier, is kept by the security service and this is the password code with DNA ink John Ko «DNA 1D Card 

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2-7.DNA Nanostructures as Drug- Delivery Vehicles DNA molecules can be assembled into custom predesigned shapes via hybridization of sequence-complementary domains. The folded structures have high spatial addressability and a tremendous potential to serve as platforms and active components in a plethora of nanobiotechnological applications. The tailored molecular devices could be used in targeting cells and triggering the cellular actions in the biological environment. The DNA origami is remarkably impressive example of precise engineering and construction at the nanoscale which is important in drug delivery. The attractiveness of the origami method lies in the fact that one can add any desired functionality to the tailored DNA shapes. by assembling other biomolecules and molecular components to them with nanometer scale precision. > 

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۲ The successful delivery of DNA-based structures into cells, ope: new avenues for tackling diverse medical tasks. » Studies have shown that DNA nanostructure is a nice drug carrier to overcome big obstacles existing in cancer therapy such as systemic toxicity and unsatisfied drug efficacy. » Scientists managed to deliver doxorubicin (an anticancer drug and a DNA intercalator) into cells in-vivo, using rod-like DNA origamis and DNA origami triangles as carriers. » Researchers have constructed various DNA polyhedrons, from DNA tetrahedron, DNA octahedron to DNA icosahedron, which can be served as simple carriers in anticancer drugs delivery. '! polyhedron is a three dimensions solid object with many plane faces, typically more than six. >» By adding marker molecules (mAb, Folic acid or even an aptamer), to the DNA nanostructure, it will be a purposeful nano carrier. These marker molecules should have a specific receptors on the target cell surface.(this process named as Active targeting) 

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Targeted drug delivery » Even, we can use the DNA itself as a marker molecule to make purposeful nanocarriers » pay attention: If we use the Aptamer as the marker molecule, we don’t need the chemical modifications of DNA nano carrier. » With targeted drug delivery, the effect of treatment has increased (Enhanced Permeability and Retention (EPR)) » Healthy cells will be safe from the negative effects of the drug. 

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DNA Nanostructure for the Drug-Delivery — E> Cell membrane 2) Ge eee prug rele 3 Endosome ۰ Cytosol ‏م‎ Nucleus 

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Polyhedra Self-Assembled from DNA 

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EB >» DNA nanoribbon is another simple DNA structure and just as the name implies is a double-stranded DNA (dsDNA). » DNA nanoribbon can be generated from simplified DNA origami technology. Using this technology, researchers constructed different nanoribbons to deliver Dox, siRNA, Photosensitizer and so on..(Photosensitizer (Porphyrin, Chlorine) is used in photodynamic therapy) » The major development of DNA nanoribbon in anticancer drug delivery is the construction of targeted or activatable DNA nanoribbon. » Liang and his colleagues, designed a DNA nanoribbon with two components. One component was dsDNA, which was rich in -GC- base pairs for Dox delivery. And the other component was a DNA aptamer named AS1411 which could target cancer cells by binding with nucleolin. Modified with AS1411 aptamer, this drug delivery system showed effectively increased cell uptake and decreased cell efflux of Dox. 

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Multifunctional aptamer-based nanoparticles for targeted drug delivery (X., Liang, X.J., 2016) Aptamer-dsDNA&Drug | 

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Other DNA Nanostructures for drug delivery DNA module assembly nanosystems a DNA nanoflower nanosystems Large-scale DNA origami nanosystems DNA-inorganic nanoparticle hybrid nano. DNA- lipid hybrid nanosystems ‏ممصي فس نا‎ ۲ ۲ ۲ ۲ ۲ ۴ DNA- polymer hybrid 5 DNA nanoflower DNA origami box: 

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This presentation was just a brief and short description of a complex and progressive world,, called DNA-Nanobiotechnology Thank you for your attention Sajjad Babaei 

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