Biomod/2014/HKBUteam/experimentalresults: Difference between revisions

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<h4>Mass-spectrometry</h4>
<b>Mass-spectrometry</b>
1. Control group 1: Single-stranded DNA A2<br>
 
 
1. Control group one: MS-Single stranded DNA A2<br>


[[Image:Mass_Spectrometry_Control_Single-stranded_DNA_A2.png|500px|For MS-single stranded DNA A2 control ]]
[[Image:Mass_Spectrometry_Control_Single-stranded_DNA_A2.png|500px|For MS-single stranded DNA A2 control ]]


2. Control group 2: Single-stranded DNA A3<br>
2. Control group two: MS-Single stranded DNA A3<br>


[[Image:Mass_spectrometry_Single-stranded_DNA_A3_.png‎|500px|For MS-single stranded DNA A3 control ]]
[[Image:Mass_spectrometry_Single-stranded_DNA_A3_.png‎|500px|For MS-single stranded DNA A3 control ]]


3. conjugated group<br>


3. Conjugated group<br>
[[Image:Exp1.2.jpg|720px|thumb|alt=Example alt text|For MS-single stranded DNA A2 ,a minor peak at 10120 shows the conjugation of A2 and chlorambrucil.<br>For MS-single stranded DNA A3 , a minor peak at 7043 shows the conjugation of A3 and folic acid.<br>For MS-single stranded DNA A6 , a peak at 11171 shows the conjugation of A6 and carbon nanodots<br>]]
 
[[Image:Exp1.2.jpg|720px|For MS-single stranded DNA A2 , a minor peak at 10120 shows the conjugation of A2 and chlorambrucil.<br>
 
For MS-single stranded DNA A3 , a minor peak at 7043 shows the conjugation of A3 and folic acid.<br>
 
For MS-single stranded DNA A6 , a peak at 11171 shows the conjugation of A6 and carbon nanodots. ]]


For MS-single stranded DNA A2 ,a minor peak at 10120 shows the conjugation of A2 and chlorambrucil.<br>
For MS-single stranded DNA A3 , a minor peak at 7043 shows the conjugation of A3 and folic acid.<br>
For MS-single stranded DNA A6 , a peak at 11171 shows the conjugation of A6 and carbon nanodots<br>


<h4>DNA extraction after folding of DNA origami</h4>
<h4>DNA extraction after folding of DNA origami</h4>
Gel photo :
Gel photo :


[[Image:expresultSection1_4.jpg|400px|
[[Image:expresultSection1_4.jpg|400px|]] <br>
Left: GeneRuler DNA Ladders, Samples, Modified Primers A2, A3 ]] <br>
(GeneRuler DNA Ladders, Samples, Modified Primers A2, A3) <br>
 


<h4>Nanodrop Reading</h4>
<h4>Nanodrop Reading</h4>
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260/230 : 0.86
260/230 : 0.86




Line 59: Line 50:
Hep G2 Treatment
Hep G2 Treatment


[[Image:expresultSection1_5.jpg|230px]] [[Image:expresultSection1_6.jpg|230px]]  [[Image:expresultSection1_7.jpg|230px]]
[[Image:expresultSection1_5.jpg|230px]]
[[Image:expresultSection1_6.jpg|230px]]   
[[Image:expresultSection1_7.jpg|230px]]




Hep G2 Control
Hep G2 Control


[[Image:expresultSection1_8.jpg|230px]] [[Image:expresultSection1_9.jpg|230px]]  [[Image:expresultSection1_10.jpg|230px]]
[[Image:expresultSection1_8.jpg|230px]]
[[Image:expresultSection1_9.jpg|230px]]   
[[Image:expresultSection1_10.jpg|230px]]


Excitation wave lengths: 405nm
Excitation wave lengths: 405nm
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<b>Conjugation condition</b>
<b>Conjugation condition</b>


Single strand DNA to folic acid/carbon nanodots/chlorambrucil Ratio
Single strand DNA, A2 and A3 conjugated with chlorambrucil and folic acid respectively in ratio 1:1. Mixtures were vortexed at room temperature for 4 hrs.
 
1:1
 
RTP
 
Mixture was vortex for 4 hrs




In-Complete route
In-Complete route


Folic acid and chlorambrucil were first conjugated and folded, carbon nanodots were added afterwards.
Folic acid and chlorambrucil were first conjugated and folded, carbon nanodots were added afterwards at ration 1:1.  




<h4>Mass-spectrometry</h4>
<b>Mass-spectrometry</b>


1. Control group 1 & 2 refer to Trial 1<br>
1. Control group 1 & 2 refer to Trial 1<br>
Line 102: Line 91:


For MS-single stranded DNA A3 , a minor peak at 7043 shows the conjugation of A3 and folic acid.<br>
For MS-single stranded DNA A3 , a minor peak at 7043 shows the conjugation of A3 and folic acid.<br>


<h4>DNA extraction after folding of DNA origami</h4>
<h4>DNA extraction after folding of DNA origami</h4>


Gel photo :
Gel photo :
[[Image:expresultSection2_3.jpg|400px|
[[Image:expresultSection2_3.jpg|400px|]]
Left: GeneRuler DNA Ladders, Samples, Modified Primers A2, A3]]
(GeneRuler DNA Ladders, Samples, Modified Primers A2, A3)<br>




Line 121: Line 111:
Hep G2 Treatment
Hep G2 Treatment


[[Image:expresultSection2_4.jpg|230px]] [[Image:expresultSection2_5.jpg|230px]] [[Image:expresultSection2_6.jpg|230px]]
[[Image:expresultSection2_4.jpg|230px]]
[[Image:expresultSection2_5.jpg|230px]]  
[[Image:expresultSection2_6.jpg|230px]]




Hep G2 Control
Hep G2 Control


[[Image:expresultSection2_7.jpg|230px]]  [[Image:expresultSection2_8.jpg|230px]] [[Image:expresultSection2_9.jpg|230px]]
[[Image:expresultSection2_7.jpg|230px]]   
[[Image:expresultSection2_8.jpg|230px]]  
[[Image:expresultSection2_9.jpg|230px]]


Excitation wave lengths: 405nm
Excitation wave lengths: 405nm
Line 152: Line 146:
2. Conjugated group<br>
2. Conjugated group<br>


[[Image:Exp3.jpg|720px|thumb|alt=Example alt text|For MS-single stranded DNA A2 , a peak at 10193 shows the conjugation of A2 and chlorambrucil.
[[Image:Exp3.jpg|720px|thumb|alt=Example alt text|For MS-single stranded DNA A2 , a peak at 10193 shows the conjugation of A2 and chlorambrucil.<br>For MS-single stranded DNA A3 , a peak at 7043 shows the conjugation of A3 and folic acid.<br>]]
 
For MS-single stranded DNA A3 , a peak at 7043 shows the conjugation of A3 and folic acid. ]]




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1st Trial

Conjugation condition

Single strand DNA, A2 and A3 conjugated with chlorambrucil and folic acid respectively in ratio 1:1. Mixtures were vortexed at room temperature for 4 hrs.


In-Complete route

Folic acid and chlorambrucil were first conjugated and folded, carbon nanodots were added afterwards at ration 1:1.


Mass-spectrometry


1. Control group one: MS-Single stranded DNA A2

For MS-single stranded DNA A2 control

2. Control group two: MS-Single stranded DNA A3

For MS-single stranded DNA A3 control

3. conjugated group

Example alt text
For MS-single stranded DNA A2 ,a minor peak at 10120 shows the conjugation of A2 and chlorambrucil.
For MS-single stranded DNA A3 , a minor peak at 7043 shows the conjugation of A3 and folic acid.
For MS-single stranded DNA A6 , a peak at 11171 shows the conjugation of A6 and carbon nanodots


DNA extraction after folding of DNA origami

Gel photo :


(GeneRuler DNA Ladders, Samples, Modified Primers A2, A3)


Nanodrop Reading

DNA concentration : 0.8 ng/ul

260/280 : 1.34

260/230 : 0.86


Confocal Microscopy

Hep G2 Treatment


Hep G2 Control

Excitation wave lengths: 405nm

Emission wave lengths: 460 – 560nm

2nd Trial

Conjugation condition

Single strand DNA, A2 and A3 conjugated with chlorambrucil and folic acid respectively in ratio 1:1. Mixtures were vortexed at room temperature for 4 hrs.


In-Complete route

Folic acid and chlorambrucil were first conjugated and folded, carbon nanodots were added afterwards at ration 1:1.


Mass-spectrometry

1. Control group 1 & 2 refer to Trial 1

2. Conjugated group

For MS-single stranded DNA A2 , a minor peak at 10120 shows the conjugation of A2 and chlorambrucil. For MS-single stranded DNA A3 , a minor peak at 7043 shows the conjugation of A3 and folic acid.

For MS-single stranded DNA A2 , a minor peak at 10120 shows the conjugation of A2 and chlorambrucil.

For MS-single stranded DNA A3 , a minor peak at 7043 shows the conjugation of A3 and folic acid.


DNA extraction after folding of DNA origami

Gel photo : (GeneRuler DNA Ladders, Samples, Modified Primers A2, A3)


Nanodrop Reading

DNA concentration : 2.3 ng/ul

260/280 : 1.28

260/230 : 0.52

Confocal Microscopy

Hep G2 Treatment


Hep G2 Control

Excitation wave lengths: 405nm

Emission wave lengths: 460 – 560nm

3rd Trial

Conjugation condition


Single strand DNA, A2, A3 and A6 conjugated with chlorambrucil, folic acid and carbon nanodots respectively in ratio 1:10. Mixtures were vortexed at 37 for 4 hrs.


Complete route

All substituent was conjugated and folded simultaneously


Mass-spectrometry

1. Control group 1 & 2 refer to Trial 1

2. Conjugated group

Example alt text
For MS-single stranded DNA A2 , a peak at 10193 shows the conjugation of A2 and chlorambrucil.
For MS-single stranded DNA A3 , a peak at 7043 shows the conjugation of A3 and folic acid.


DNA extraction after folding of DNA origami

Gel photo :


Nanodrop Reading

DNA concentration : 5.5 ng/ul

260/280 : 2.65

260/230 : 1.12


Confocal Microscopy

Hep G2 Treatment


Hep G2 Control

HK-1 Treatment


HK-1 Control

Excitation : 405nm

Emission : 460 – 560nm


Emission Spectrum

Hep G2 HK-1

AFM photo

Discussion:
The Atomic force microscopy image has a low resolution and the structure of the functionalized DNA origami
can hardly be identified which may due to the following reasons:

  1. The DNA origami samples is not dried up completely which increase the adhesive force of the AFM instrument
  2. The DNA origami samples was clustered on the mica platform
  3. The scan size of AFM is restricted from 1 to 5 nm so many area attached with the DNA was not examined properly
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