Mixed Monolayers on Silicon for DNA Attachment Goal

1. Mixed Monolayers on Silicon for DNA Attachment Goal • Find right proportions of APTES (aminopropyl triethoxysilane) solution to manipulate with N-Trimethoxysilylpropyl-N,N,N-trimethylammonium chloride in order to… • Loosen the strong hold that pure APTES adhesive has on binding DNA plasmids to a silicon substrate

2. Properties of DNA • DNA is a nucleic acid • A double helix is formed by the hydrogen bonds of the base pairs of two DNA strands • The sugar-phosphate backbone of DNA is negative and so is silicon, so the problem is they repel each other • DNA has a height of around 2 nm and the plasmid has a length when stretched out of around 913 nm

3. The AFM • The AFM stands for the Atomic Force Microscope • It is used to look at the silicon samples with DNA • The sample is analyzed using a computer hooked to the AFM

4. DNA (anionic) Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mg Mica (anionic) Mica (anionic) Mica and Buffer AFM image of DNA on mica with buffer AFM images by Alexi Lykoudis • Mica is bound to silicon using Mg2+ in a buffer solution instead of APTES mixed with the DNA that, like on silicon, sustains its biomolecules • The purpose of DNA on mica is to see how it acts on a different surface from silicon

5. Why DNA on Silicon? • DNA is self-assembling, meaning the strands connect through the base pairs • Therefore they’re easy to make nanostructures with • DNA plasmids are used specifically because they are easy to acquire and easy to use in different concentrations • Silicon is used as a substrate over mica, another substrate because silicon is a semiconductor and thus has more uses

6. How It Happened • The silicon (MEMC Electronic Materials, Inc., Malaysia) was first cut into 1 by 1 cm squares • Then, they are boiled in toluene and cleaned in piranha acid • Afterwards, they bathed in RCA 1 and 2 baths and dried with N2 gas • The APTES or N-Trimethoxysilylpropyl-N,N,N-trimethylammonium chloride was always prepared in 20 µL with 1980 µL of 18 ohm water • The silicon squares were then soaked in APTES, washed in 18 ohm water, and dried with N2 gas • Afterwards, 2 µL of DNA (.1 mg/ µL) was mixed with 18 µL of buffer or 18 ohm water and placed on the silicon surface after which the silicon square was washed with 18 ohm water and then dried with N2 gas

7. DNA APTES Silicon Si Why Mixed Monolayers? • A cationic substance is required to keep the DNA on the silicon • This substance is APTES solution, but it binds the DNA too tightly • As a result, new substances are needed to slightly offset the strong APTES • These are the N-Trimethoxysilylpropyl-N,N,N-trimethylammonium chloride and Propyltriethoxysilane

8. DNA Cl - N APTES CH2 CH2 Silicon CH2 Si Si CH3O CH3O CH3O CH3 CH3 CH3 Background of Experiment N-Trimethoxysilylpropyl-N,N,N-trimethylammonium chloride This is mixed with APTES in various proportions to see how the DNA reacts…

9. Experiments • The first experiment was to mix 2 µL of DNA with 18 µL of buffer on a silicon wafer soaked in 20 µL of APTES and 1980 µL of 18 ohm H2O • In this case, the buffer was only to sustain the biomolecules of the DNA • We know this has to be DNA because all samples are checked with and without DNA • Samples without DNA are all clean, so the particles on the image must be DNA DNA

10. Experiment 2 • This image is with 18 µL of 18 ohm H2O instead of buffer solution on a silicon substrate covered in APTES • This causes the DNA to have a texture more similar to DNA on mica Yellow circular shapes are DNA with the pink being DNA clumped on one another

11. Experiment 3 • The DNA here is mixed with water instead of buffer as well • This was placed on silicon covered with 20 µL of N-Trimethoxysilylpropyl-N,N,N-trimethylammonium chloride

12. Experiment 4 Without DNA With DNA • The fourth experiment here to the right was done with DNA mixed with buffer • The silicon substrate was covered in N-Trimethoxysilylpropyl-N,N,N-trimethylammonium chloride

13. Experiment 5 • DNA mixed with water on a silicon surface covered in N-Trimethoxysilylpropyl-N,N,N-trimethylammonium chloride

14. Experiment 6 Without DNA With DNA • First experiment mixing 4 µL APTES and 16 µL N-Trimethoxysilylpropyl-N,N,N-trimethylammonium chloride on a silicon surface • The image to the right is of DNA with buffer solution

15. Experiment 7 Without DNA With DNA • These images are of silicon samples with 12 µL of N-Trimethoxysilylpropyl-N,N,N-trimethylammonium chloride and 8 µL of APTES • The image to the right is of DNA with buffer solution

16. Discussion and Conclusion • I can only make small, tentative conclusions based only on looking at the image and comparing by sight the different results, as project is not complete • DNA mixed with 18 ohm water tend to be more relaxed and spread out, while samples mixed with buffer solution tend to be stiff and clumped at certain points • My part is a small bit of a much larger project to create nanostructures out of DNA with the goal of putting them to practical use in various fields of science

17. Acknowledgements Dr. Marya Lieberman Dr. Thomas Loughran Dr. Koshala Sarveswaran Notre Dame Department of Chemistry and Biochemistry Radiation Laboratory

18. Bibliography “Atomic Force Microscopy (AFM).” Uppsala Universitet. 2 March 2007 <http://www.liu.edu/CWIS/CWP/library/workshop/citmla.htm> Chinese Academy of Sciences. 2 March 2007 <http://cit.iccas.ac.cn/facilities.htm> “DNA - DEOXYRIBONUCLEIC ACID.” 2 March 2007 <http://www.biologycorner.com/bio1/DNA.htm> Toyo Adtec. November 2006. 2 March 2007. <http://www.toyo-adtec.co.jp/e/siliconwafer.html>