Download AFM image of DNA on mica with buffer

Mixed Monolayers on Silicon for DNA
Attachment Goal

Find right proportions of APTES (aminopropyl
triethoxysilane) solution to manipulate with NTrimethoxysilylpropyl-N,N,N-trimethylammonium
chloride in order to…
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Loosen the strong hold that pure APTES
adhesive has on binding DNA plasmids to
a silicon substrate
Properties of DNA
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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

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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
AFM image of DNA on mica with buffer
AFM images by Alexi Lykoudis
DNA (anionic)
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MgMg Mg MgMgMg MgMg Mg MgMg
MgMg Mg MgMgMg MgMg Mg MgMg
Mica (anionic)
Mica (anionic)
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
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
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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 NTrimethoxysilylpropylN,N,N-trimethylammonium
chloride and
Propyltriethoxysilane
DNA
Si
APTES
Silicon
Background of Experiment
N-Trimethoxysilylpropyl-N,N,Ntrimethylammonium chloride
Cl CH3
CH3
CH3
N
DNA
CH2
CH2
CH2
Si
This is mixed
with APTES in
various
proportions to
see how the
DNA reacts…
Si
APTES
Silicon
CH3O
CH3O CH3O
Experiments
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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
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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
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The DNA here is mixed
with water instead of
buffer as well
This was placed on
silicon covered with 20
µL of NTrimethoxysilylpropylN,N,Ntrimethylammonium
chloride
Experiment 4
Without DNA
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With DNA
The fourth experiment here to the right was done
with DNA mixed with buffer
The silicon substrate was covered in NTrimethoxysilylpropyl-N,N,N-trimethylammonium
chloride
Experiment 5
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DNA mixed with water
on a silicon surface
covered in NTrimethoxysilylpropylN,N,Ntrimethylammonium
chloride
Experiment 6
Without DNA
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With DNA
First experiment mixing 4 µL APTES and 16 µL NTrimethoxysilylpropyl-N,N,N-trimethylammonium
chloride on a silicon surface
The image to the right is of DNA with buffer solution
Experiment 7
Without DNA
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With DNA
These images are of silicon samples with 12 µL of NTrimethoxysilylpropyl-N,N,N-trimethylammonium chloride and
8 µL of APTES
The image to the right is of DNA with buffer solution
Discussion and Conclusion
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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
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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.toyoadtec.co.jp/e/siliconwafer.html>