science fair presentation

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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

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Page 1: Science  Fair  Presentation

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

Page 2: Science  Fair  Presentation

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 nmRight: Image location URL is http://www.biologycorner.com/bio1/DNA.htmlLeft: Image Source Not Found

Page 3: Science  Fair  Presentation

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 AFMLeft: Image Source Not Found Right: Image Source is http://www.farmfak.uu.se/farm/farmfyskem-web/instrumentation/afm.shtml

Page 4: Science  Fair  Presentation

Mica and Buffer

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

Mica (anionic)

Mg MgMg Mg MgMg MgMg MgMgMg

DNA (anionic)

Mica (anionic)

Mg MgMg Mg MgMg MgMg MgMgMg

AFM image of DNA on mica with buffer AFM images by Alexander Lykoudis

Diagram Drawn By Dr. Koshala Sarveswaran

Page 5: Science  Fair  Presentation

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

Image from www.toyo-adtec.co.jp

Page 6: Science  Fair  Presentation

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

Page 7: Science  Fair  Presentation

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

Si

Silicon

APTES

DNA

Image Drawn By Dr. Koshala Sarveswaran

Page 8: Science  Fair  Presentation

N-Trimethoxysilylpropyl-N,N,N-trimethylammonium chloride

Background of Experiment

This is mixed with APTES in various proportions to see how the DNA reacts…

OMe

N

Si

OMeMeO

MeMeMe

N

EtO

Si

OEtEtO

HH

APTES

Structures Drawn By Dr. Koshala Sarveswaran

Page 9: Science  Fair  Presentation

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

Page 10: Science  Fair  Presentation

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

Page 11: Science  Fair  Presentation

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

Page 12: Science  Fair  Presentation

Experiment 4

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

Without DNA With DNA

Page 13: Science  Fair  Presentation

Experiment 5

DNA mixed with water on a silicon surface covered in N-Trimethoxysilylpropyl-N,N,N-trimethylammonium chloride

Page 14: Science  Fair  Presentation

Experiment 6

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

Without DNA With DNA

DNA

Page 15: Science  Fair  Presentation

Experiment 7

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

Without DNA With DNA

Page 16: Science  Fair  Presentation

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

Page 17: Science  Fair  Presentation

Acknowledgements

Dr. Marya Lieberman

Dr. Thomas Loughran

Dr. Koshala Sarveswaran

Mr. Mark Mankowski

University of Notre Dame, Department of

Chemistry and Biochemistry

Radiation Laboratory

Page 18: Science  Fair  Presentation

Bibliography“Atomic Force Microscopy (AFM).” PHARMACEUTICAL PHYSICAL CHEMISTRY. Uppsala Universitet. 3

March 2007. <http://www.farmfak.uu.se/farm/farmfyskem-web/instrumentation/afm.shtml>

Bernstein, Gary H. et al. “Deposition of DNA Rafts on Cationic SAMs on Silicon [100].” Langmuir 22 (2006): 11279 – 1128.

Chinese Academy of Science. 3 March 2007. <http://cit.iccas.ac.cn/facilities.htm>

Muskopf, Shannan. “DNA – DEOXYRIBONUCLEIC ACID.” The Biology Corner. 3 March 2007. <http://www.biologycorner.com/bio1/DNA.html/>

Seeman, Nadrian. “Nanotechnology and the Double Helix.” Scientific American, Inc. June 2004. 65-75.

“Silicon Wafer.” Toyo Adtec. 3 March 2007. <http://www.toyo-adtec.co.jp/e/siliconwafer.html>