DNA NANOWIRES USING NANOPARTICLES ECG653 Project Report submitted by GOPI

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1 DNA NANOWIRES USING NANOPARTICLES ECG653 Project Report submitted by GOPI INTRODUCTION: Deoxyribonucleic acid (DNA) has been a key building block in nanotechnology since the earliest work on what is now called DNA-templated self-assembly and it is a relatively inexpensive and ubiquitous material that can be used as a scaffold for constructing nanowires. The paper focuses on the manufacturing of DNA-templated, magnetic nanowires. This is accomplished by synthesizing positively-charged metal nanoparticles that self-assemble along the contours of λ-phage DNA. This self-assembly is achieved through electrostatic interactions between positively-charged metal particles and negatively-charged DNA strands. Three types of magnetic particles were prepared: iron oxide (Fe2O3), cobalt iron oxide (CoFe2O3), and manganese iron oxide (MnFe2O3). These particles were then characterized with ultraviolet-visible spectrophotometry (UV-VIS) and Fourier-Transform Infrared spectroscopy (FT-IR). Future studies will include the fabrication of DNA coated with each type of particle, as well as characterization of the nanowires. Project Description: DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds and the phosphate is negatively charged and therefore the DNA overall has a negative charge. Positively charged nanoparticles are manufactured. Because of the electrostatic attraction the nanoparticles naturally align themselves across the contours of DNA.Three different types of nanoparticles are manufactured these are iron oxide cobolt ironoxide and manganese iron oxide. Fig 1 Nano Particles

2 The Flowchart in Fig 2 represents the steps involved in the manufacture of DNA nanowires. Firstly particles has to be synthesized. Then got to characterize the particles it is done using instrumentation techniques. The next step is to fabricate wire and the way that it is made is by simple method. DNA solution which is actually a buffer solution and when added in the nanoparticles electrostatic attraction bring them together which forms the nanowires. Then we have to characterize the wires using techniques similar to those use for the particles and the final two will constitute what will be the future work. Fig 2 Project Goals This Fig 3 represents the synthesized three different particles iron oxide (Fe2O3), cobalt iron oxide (CoFe2O3), and manganese iron oxide (MnFe2O3), then used ultraviolet visible spectroscopy(uv-vis) in order to analyze the way in which the particles where coating the DNA, Then also used Fourier Transform Infrared spectroscopy(ftir) to look at the coating on the nanoparticles itself. Fig 3 Synthesized Particles

3 Fig 4 is an AFM image or atomic force microscopy image of DNA coated with Ironoxide this DNA is fixed to a surface of clean silicon oxide. The scale on the right from 0-5nm represents the differences in the height on the DNA as you can see the dark red background represents the height of 0nm where as the lighter regions which are yellow represents the coating on DNA and the DNA strands slices to the centre of photograph and the solution used is 1ng DNA and 1ng ironoxide solution. Fig 4 Atomic Force Microscopy Image This picture Fig 5 shows how we manufacture iron oxide, First two pyrrolidinone is combined with fe(acac)2 solution in a flask. Then the flask is heated to 200 degree centigrade at this temperature fe(acac)2 solution is decomposed into two acac solutions as well as positively charged to iron solution. Next heated the flask to 260 degree centigrade at this temperature the iron combined with oxygen already present in the flask to form iron oxide solution. The gray coating around the iron oxide particles is two pyrrolidinone coating and the reason why we have to coat the particle is because otherwise the iron will oxidize the atmosphere and form the particles that would be much too large for our needs. And in order to make manganese and cobolt iron oxide we add manganese and cobolt acac solution instead of iron acac solution. Fig 5 Magnetic Particle Synthesis

4 Here is a photograph Fig 6 of particle synthesizer. In the very middle you can see a flask in which the reaction takes place. In the left you find a vaccum tubing which is used to suck out the oxygen from the flask after the oxygen is sucked out from the chamber it replaced with nitrogen which is neutral gas which will not involve in the reaction. At the top there is cooling mechanism in order to maintain the temperature constant. Fig 6 Particle synthesizer Ultraviolet visible spectroscopy (Fig 7) the word spectroscopy means spectrum and UV-VIS scans through a spectrum of light in particular it utilizes visible to ultraviolet light and the way this works is you have a light source and this light source shines through a sample and the other you have a photo detector which counts the number of photons that are going through from the light source to the detector. Let us say a frequency of 400nm is associated with X amount of photons so if you shine this 400nm of light source through the sample and the photo detector only detects 5% of X so the sample had a 95% absorbance and we have to utilize a quartz crystal because quartz is transparent to ultraviolet rays. Each type of different molecule will absorb a different frequency of light and therefore if u see a peak in UV-VIS graph at a certain frequency then it will correspond the presence of this molecule in a solution. Fig 7 Ultraviolet-visible spectroscopy(uv-vis)

5 DNA has an absorbance at 260nm before we could analyze the DNA coated with particles using the UV-VIS however we need it to analyze the particles themselves to make sure that they do not exhibit any type of signal at 260nm.so here are the results for iron oxide in a buffer solution and the different number represents the concentration of iron oxide as u can see in conclusion is that at 260nm iron oxide indeed has no signal because all of the lines absorbance graph 1 are relatively flat at that area. To the left of 260nm you see that the lines becomes to slope down and slope up and behaves some what radical. Graph 1 Iron Oxide + Buffer Graph 2 and Graph 3 are the results for absorbance s of manganese iron oxide and cobolt iron oxide at varying concentrations. Graph 2 Manganese Iron Oxide + Buffer Graph 3 Cobolt Iron Oxide + Buffer

6 DNA strands coated with iron oxide particles. Graph 4 is the UV-VIS results for this nanowires, In the very middle you can notice the DNA blank line which is represented by dark blue line these are the DNA strands which are not coated by any particles but as we began to coat the DNA with various concentrations of iron oxide particles the results would be rather surprising when 25 micro liters of iron oxide solution added to the DNA the absorbance of the coated newly formed DNA nanowires will lower the pure DNA and when we add 25 micro liters or more then the absorbance increase and become higher than DNA. Graph 4 Iron Oxide + DNA+Buffer We use IR spectroscopy to look at the coating on the particles. It is similar to UV-VIS it scans through spectrum of light. This time it however it utilizes infrared light instead of visible and ultraviolet light., The IR measurements are related to frequencies with which certain bonds vibrate there are different ways with which certain bonds vibrate for instance we have symmetrical stretching asymmetrical stretching and twisting as shown in Fig 8, because each different type of movement absorbs different frequencies of light Fig 8 Different Types of Bond Vibrations

7 Summary: First of all three different types of nano particles are manufactured iron oxide (Fe2O3), cobalt iron oxide (CoFe2O3), and manganese iron oxide (MnFe2O3). Secondly the UV-VIS results gives us insight to the absorbance trends of the ironoxide particles on to the DNA and realized that more is not better when added too many nano particles.finally the IR results verify the particles manufactured are positively charge, That they are able to bond the DNA. The future work will consists in fabricating gaps in the coated DNA strands and making customizable wires. REFERENCES: bcac-c13290a555c4

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