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

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

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

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 Alexi Lykoudis

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

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

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

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

Background of Experiment

N

CH2

CH2

CH2

Si

CH3O CH3O CH3O

CH3 CH3 CH3

Cl -

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

Si

Silicon

APTES

DNA

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

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

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

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

Experiment 5

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

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

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

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

Acknowledgements

Dr. Marya Lieberman

Dr. Thomas Loughran

Dr. Koshala Sarveswaran

Notre Dame Department of Chemistry and Biochemistry

Radiation Laboratory

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>