Biomod/2012/Titech/Nano-Jugglers/Methods/Design of photoresponsive DNA

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==3-1.Design of photoresponsive DNA==
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==3.1. Design of photoresponsive DNA==
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:&nbsp;&nbsp;&nbsp;&nbsp;We incorporated 4 azobenzene units into photoresponsive DNA<sup>[1]</sup> strand so that we can quickly dissociated DNA duplex.{Photo-switchable DNA 5'-AATXACXCCXAGXCC-3' (X=Azobenzene)}
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:&nbsp;&nbsp;&nbsp;&nbsp;We incorporated 4 azobenzene units into photoresponsive DNA<sup>[1]</sup> sequence S<sup><small>*</small></sup> so that we can quickly dissociated DNA duplex. We called it as Photoresponsive DNA sequence S<sup><small>*</small></sup>.[5'-AATXACXCCXAGXCC-3' (X=Azobenzene)]
:{|
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|width="150px"|[[Image:BIOMOD-TNJ-azobenzen5.png|left|150px]]
|width="150px"|[[Image:BIOMOD-TNJ-azobenzen5.png|left|150px]]
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photoresponsive DNA<br>
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Photoresponsive DNA sequence S<sup>*<sup><br>
*5’ -(HS)-AATxACxCCxAGxCC-3’ (x=azobenzene)
*5’ -(HS)-AATxACxCCxAGxCC-3’ (x=azobenzene)
1.We incorporated 4 azobenzene units into 11 bases DNA so that we can quickly dissociated DNA duplex.
1.We incorporated 4 azobenzene units into 11 bases DNA so that we can quickly dissociated DNA duplex.
|width="150px"|[[Image:BIOMOD-TNJ-azobenzen7.png|left|150px]]
|width="150px"|[[Image:BIOMOD-TNJ-azobenzen7.png|left|150px]]
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cDNA of photoresponsive DNA<br>
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Photoresponsive DNA sequence S<br>
*5’-(HS)-GGCTGGGTATT-3’
*5’-(HS)-GGCTGGGTATT-3’
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1.This 11 bases DNA are a complementary sequence of DNAⅰ(photoresponsive DNA).
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1.This 11 bases DNA are a complementary sequence of photoresponsive DNA sequence S<sup>*<sup>.
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:&nbsp;&nbsp;&nbsp;&nbsp;And then, we confirmed that photoresponsive DNA could hybridize stably at consistent temperature. For verifying hybridization, we use the value of absorbance.<br>
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:&nbsp;&nbsp;&nbsp;&nbsp;And then, we confirmed that photoresponsive DNA could hybridize stably. For verifying hybridization, we used the value of absorbance.<br>
:&nbsp;&nbsp;&nbsp;&nbsp;In spectroscopy, a relational expression about absorbance can be expressed as follows.
:&nbsp;&nbsp;&nbsp;&nbsp;In spectroscopy, a relational expression about absorbance can be expressed as follows.
:[[Image:Math.png|center|200px]]
:[[Image:Math.png|center|200px]]
:&nbsp;&nbsp;&nbsp;&nbsp;(Abs: absorbance, ε: the absorption coefficient, c: strength, d: length of a visual leg )  
:&nbsp;&nbsp;&nbsp;&nbsp;(Abs: absorbance, ε: the absorption coefficient, c: strength, d: length of a visual leg )  
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:&nbsp;&nbsp;&nbsp;&nbsp;The value of Abs is proportional to the concentration of corresponding materials. If photoresponsive DNA formed duplex, the concentration of ssDNA decrease, onthe other hand the concentration of dsDNA increase. Reserchin these corresponding values, we could determine whether they formed duplex or not.<br>  
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:&nbsp;&nbsp;&nbsp;&nbsp;The value of Abs is proportional to the concentration of corresponding materials. When photoresponsive DNA formed duplex, the concentration of ssDNA decreases, on the other hand, the concentration of dsDNA increases. From the reserches of these corresponding values, we could determine whether they formed duplex or not.<br>
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:Reference
:[1]Hiroyuki Asanuma, Xingguo Liang, Takayuki Yoshida, and Makoto Komiyama,;CHEMBIOCHEM  2, 39-44(2001)
:[1]Hiroyuki Asanuma, Xingguo Liang, Takayuki Yoshida, and Makoto Komiyama,;CHEMBIOCHEM  2, 39-44(2001)
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::::::::::>>back to [[Biomod/2012/Titech/Nano-Jugglers/Results#3-1.Design_of_photoresponsive_DNA|Result]]
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::::::::::>>back to [[Biomod/2012/Titech/Nano-Jugglers/Results#3.1._Design_of_photoresponsive_DNA|Results]]

Current revision


3.1. Design of photoresponsive DNA

    We incorporated 4 azobenzene units into photoresponsive DNA[1] sequence S* so that we can quickly dissociated DNA duplex. We called it as Photoresponsive DNA sequence S*.[5'-AATXACXCCXAGXCC-3' (X=Azobenzene)]

Photoresponsive DNA sequence S*

  • 5’ -(HS)-AATxACxCCxAGxCC-3’ (x=azobenzene)

1.We incorporated 4 azobenzene units into 11 bases DNA so that we can quickly dissociated DNA duplex.

Photoresponsive DNA sequence S

  • 5’-(HS)-GGCTGGGTATT-3’

1.This 11 bases DNA are a complementary sequence of photoresponsive DNA sequence S*.

    And then, we confirmed that photoresponsive DNA could hybridize stably. For verifying hybridization, we used the value of absorbance.
    In spectroscopy, a relational expression about absorbance can be expressed as follows.
    (Abs: absorbance, ε: the absorption coefficient, c: strength, d: length of a visual leg )
    The value of Abs is proportional to the concentration of corresponding materials. When photoresponsive DNA formed duplex, the concentration of ssDNA decreases, on the other hand, the concentration of dsDNA increases. From the reserches of these corresponding values, we could determine whether they formed duplex or not.
Reference
[1]Hiroyuki Asanuma, Xingguo Liang, Takayuki Yoshida, and Makoto Komiyama,;CHEMBIOCHEM 2, 39-44(2001)
>>back to Results

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