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             <li class='has-sub'><a href="http://openwetware.org/wiki/Biomod/2014/experiment.html"><span>Project</span></a>
             <li class='has-sub'><a href="http://openwetware.org/wiki/Biomod/2014/experiment.html"><span>Project</span></a>
           <ul>
           <ul>
               <li><a href="http://openwetware.org/wiki/Biomod/2014/experiment.html#strand replacement reaction"><span>Strand Replacement Reaction</span></a></li>
               <li><a href="http://openwetware.org/wiki/Biomod/2014/experiment.html#Three-arm locker"><span>Three-arm Locker</span></a></li>
                     <li><a href="http://openwetware.org/wiki/Biomod/2014/experiment.html#synthesis of au-dna-cy3"><span> Synthesis of AU-DNA-CY3</span></a></li>
                     <li><a href="http://openwetware.org/wiki/Biomod/2014/experiment.html#Gold nanoparticle based photosensor"><span> Gold Nanoparticle Based Photosensor</span></a></li>
                     <li><a href="http://openwetware.org/wiki/Biomod/2014/experiment.html#dna origami"><span>DNA Origami</span></a></li>
                     <li><a href="http://openwetware.org/wiki/Biomod/2014/experiment.html#dna origami"><span>DNA Origami</span></a></li>
                 </ul>
                 </ul>
             </li> 
             </li> 
        
        
             <li class='active'><a href="http://openwetware.org/wiki/Biomod/2014/result.html"><span>Protocol</span></a>  
            <li class='active'><a href="http://openwetware.org/wiki/Tianjin_protocol"><span>Protocol</span></a>
    </li>
 
             <li class='active'><a href="http://openwetware.org/wiki/Biomod/2014/future.html"><span>Future Work</span></a>  
    </li>
    </li>
            
            
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</ul>
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==Background==
==Background==
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Advantages of light
<big>DNA Origami</big>
 
A revolution in cancer therapy has taken place by the emerging use of laser light to achieve controlled and confined thermal damage in the tumor tissue. Laser, the acronym for light amplification by the stimulated emission of radiation, is an optical source that emits photons in a coherent and narrow beam. Laser light has the characteristics of monochromaticity, coherence, and collimation. These properties provide a narrow beam of high intensity, which transmits deep down into the target location with minimal power loss and great precision.
 


In recent years, the near infrared (NIR) laser (in the region of 650-1100 nm) mediated photothermal therapy has attracted increased attentions. NIR laser irradiation can induce hyperthermia damage of cancer cells and tumor organ with deep tissue penetration but minimal skin absorbance. NIR is selected in our project due to its low expenditure, abundant source as well as excellent controllability. Additionally, we choose NIR laser as the photothermal trigger also because its irradiation possesses minimal invasiveness and precise spatial-temporal selectivity since its therapeutic effect happens only at the specific site where both light-absorbent and localized photo-irradiation coexist.  
The unique structural motifs and molecular recognition properties of DNA make it a promising template for building nanostructures. Using a long single-stranded DNA as a template, a novel strategy, the so-called DNA origami method, has been developed for the preparation of various two-dimensional (2D) and three-dimensional (3D) nanostructures with defined size which is predictable, precise, controllable and efficient.<br><br>


[[Image:fig02.gif|thumb|550px|center|Fig 1.DNA origami and its applications.<br>]]


Properties of gold nanoparticles (GNPs)
DNA origami is an excellent plantform for the nanopatterning and a variety of functional biomolecules and nanoparticles can be assembled onto the DNA origami nanoscaffolds, to obtain complicate nanodevices with special functions which can be used to facilitate imaging, targeted delivery, and controlled release of therapeutic compounds. As described, DNA origami possess the capability of transporting molecular payloads to cells, sensing cell surface inputs for conditional, triggered activation, and reconfiguring its structure for payload delivery. DNA origami structures can also be used as molecular pegboards with a resolution of 4–6 nm, and they been widely used in the assembly of hetero-elements such as proteins and nanoparticles. Therefore, DNA origami has shown great potential in nanotechnology.<br>


Nanomedicine is currently an active field because new properties emerge when the size of a matter is reduced from bulk to the nanometer scale. These new properties, including optical, magnetic, electronic, and structural properties, make nano-sized particles (generally 1–100 nm) very promising for a wide range of biomedical applications such as targeted therapy. Plasmonic (noble metal) nanoparticles distinguish themselves from other nanoplatforms by their unique surface plasmon resonance (SPR). A special property of these plasmonic nanoparticles is their heat generation resulting from optical stimulation.
<big>Advantages of light</big>


[[Image:%E5%85%89%E7%85%A7%E5%8A%A8%E7%94%BB.gif|thumb|550px|center|Fig 1.<br>]]
A revolution in cancer therapy has taken place by the emerging use of laser light to achieve controlled and confined thermal damage in the tumor tissue. Laser, the acronym for light amplification by the stimulated emission of radiation, is an optical source that emits photons in a coherent and narrow beam. Laser light has the characteristics of monochromaticity, coherence, and collimation. These properties provide a narrow beam of high intensity, which transmits deep down into the target location with minimal power loss and great precision. <br>


Among plasmonic nanoparticles, gold nanoparticles (GNPs) are most extensively investigated because of their inertness, low cytotoxicity, ready multi-functionalization and long history of medical use. GNPs are also attractive due to their facile synthesis, excellent biocompatibility as well as strongly enhanced and tunable optical properties to convert NIR light into local heat. Gold nanoparticles exhibit NIR activated photothermal activity due to their geometry dependent SPR. This SPR, resulting from photon confinement to a small particle size, enhances all the radiative and nonradiative properties of GNPs. Hence GNPs have immense potential for the selective laser photothermal therapy of cancer due to their ability to efficiently convert surface plasmon resonance-enhanced absorbed light into localized heat and thus offering multiple modalities for biological and medical applications.
<big>Properties of gold nanoparticles (GNPs)</big>


Nanomedicine is currently an active field because new properties emerge when the size of a matter is reduced from bulk to the nanometer scale. These new properties, including optical, magnetic, electronic, and structural properties, make nano-sized particles (generally 1–100 nm) very promising for a wide range of biomedical applications such as targeted therapy. Plasmonic (noble metal) nanoparticles distinguish themselves from other nanoplatforms by their unique surface plasmon resonance (SPR). A special property of these plasmonic nanoparticles is their heat generation resulting from optical stimulation. <br><br>


DNA Origami
[[Image:fig01.gif|thumb|550px|center|Fig 2.The photothermal property for gold nanoparticle.<br>]]


Nucleic acids have been used as building blocks for the bottom-up assembly of intricate suprastructures due to their inherent chemical and biological addressability,structural precision, and efficiency of synthesis. As a novel self-assembly method developed in recent years, DNA
Among plasmonic nanoparticles, gold nanoparticles (GNPs) are most extensively investigated because of their inertness, low cytotoxicity, ready multi-functionalization and long history of medical use. GNPs are also attractive due to their facile synthesis, excellent biocompatibility as well as strongly enhanced and tunable optical properties to convert light into local heat. Gold nanoparticles exhibit light activated photothermal activity due to their geometry dependent SPR. This SPR, resulting from photon confinement to a small particle size, enhances all the radiative and nonradiative properties of GNPs. Hence GNPs have immense potential for the selective laser photothermal therapy of cancer due to their ability to efficiently convert surface plasmon resonance-enhanced absorbed light into localized heat and thus offering multiple modalities for biological and medical applications. <br>
origami is one of the greatest progress in the field of DNA nanotechnology and DNA self-assembly. In this method, a long scaffold strand (single-stranded DNA from the M13 phage genome, ~7,429 nucleotides long) was folded with the help of hundreds of short ‘staple’ strands into defined two- and three-dimensional (2D and 3D) shapes. Moreover, the nanostructures by DNA origami are predictable, precise, controllable and efficient. The merits also include relatively low requirements for the experimental conditions and operation skills.  
[[Image:那张图.jpg|thumb|550px|center|Fig 3.The the therapy use of gold nanoparticle and DNA origami.<br>]]


A variety of functional biomolecules and nanoparticles can be assembled onto the DNA origami nanoscaffolds, to obtain complicate nanodevices with special functions which can be used to facilitate imaging, targeted delivery, and controlled release of therapeutic compounds. As described, DNA origami possess the capability of transporting molecular payloads to cells, sensing cell surface inputs for conditional, triggered activation, and reconfiguring its structure for payload delivery. DNA origami structures can also be used as molecular pegboards with a resolution of 4–6 nm, and they been widely used in the assembly of heteroelements such as proteins and nanoparticles. Therefore, DNA origami has shown great potential in nanotechnology.


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==Motivation==
==Motivation==
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Use light instead of strand displacement reaction to open DNA origami:


Generally strand displacement reaction is used to open DNA origami. In that process two strands with partial or full complementarity hybridize and displace one or more pre-hybridized strands.  This mechanism allows for the kinetic control of reaction pathways. However, we need to add the substitutive stand to start the process. If we use DNA origami to transport drugs in vivo, it’s difficult and unsafe to add single-stranded DNA to human body to open DNA origami. So we want to open DNA origami in a physical way.
DNA origami is also emerging as a strong candidate for drug delivery in living systems. For its high compatibility to so many kinds of molecules, such as functional biomolecules and nanoparticles which can be linked to the DNA origami scaffolds, to obtain complicated functional nano-devices. Besides, it's capability to fold structures of 2-dimentional or 3-dimentional makes it will get more circumstances to apply. What’s more, the high rate of development and the endless potential of DNA origami make it worth researching.


Why light?
But the methods of opening an origami box or changing the structure of it is limited in the addition of ssDNA to open by strand replacement or chemical methods to break, which limits the  applications of  origami especially in vivo. So, a physical way without adding anything to achieve the goal is what we need and search for. We choose light. But why?  


We want to use light to open DNA origami because light control has many advantages.
We want to use light to open DNA origami because light control has many advantages.
1. Light is low expenditure and easy to get.


1. Light is low expenditure and easy to get
2. It is convenient to control the intensity of light.


2. It is convenient to control the intensity of light
3. Light for therapeutic could cause less damage on tissue.  


3. Light won’t damage human body
In fact, in treatment, only light will produce sufficient power to penetrate the specific site with less energy loss. And, light has already been used into medical treatment field for many years, such as photothermal therapy. Then, the next question is how to change the light into heat, and the traditional way of photothermal therapy may answer this question.


In fact, for treatment, only light will produce sufficient power to penetrate  the appropriate site with less energy loss. And, light has already been used into medical treatment field for many years, such as photothermal therapy.  
A type of nanomaterial with strong light absorption comes into the sight of us, which is named gold nanoparticle (Au NP). Au NP has immense potential for the selective laser photothermal therapy of cancer cells due to its photo-thermal activity. It can convert light into heat, and leads to a temperature increase, which serves as our opening trigger.


And we use visible or near infrared light for inflammation, edema and preventing tissue damage. Besides, the basic phenomena that is reflection, refraction and absorption occurs when matter is exposed to light. Hemoglobin and water, the major absorbers of visible and near-infrared light (NIR light), respectively, have their lowest absorption coefficient in the NIR region around 650–900 nm. So, we choose the NIR light to reduce the loss in energy.
And as all we know, origami is locked by complementary DNA sequence, which is difficult to totally separate by heating and restoring to room temperature. So that means our origami box have a large possibility to reclose after its open. To overcome this problem, we design three-arm DNA lock to “intelligently” control the open and close of origami by displacement, and it will be showed in the next part.
 
Our design’s  performance objectives:
All in all, by creating and utilizing these principle or design, we want to grant this device with the following control characteristics:
Achieving controlled release of the encapsulated cargo with spatial and temporal control remains a challenge. By taking advantage of Au nanoparticles and different strand-displacement reaction, we hope the realization of a controlled-release formulation  might be an important part of our design.
Local release of drugs. Traditional drugs are transported to every corner in human body, and may attack all the cells including the normal ones,such as the low specificity of anticancer drugs. However, our device is supposed to release at a specific location in human body under control.
 
 
<big>Selective release of drugs</big>
 
We want to give our device a DNA logical gate, which enable the device to selectively release specific drugs aimed at curing different cells under different conditions.
 
<big>Physical control</big>


We can design a GNP-DNA origami complex in response to light cues.The controlled release of cargo is achieved by varying light intensity of optical stimulation on Au nanoparticles modified on DNA origami. We prospect that the generated heat by GNPs can break the hydrogen bonds of double-strand DNA. The lock is realised by a special strand-displacement reaction which will not be able to reform its native structure once unzip.  
We replace traditional control methods of adding chemicals with a physical trigger to make our device tunable for future modification, which has never done before.


We gain the inspiration on the beautiful honeycomb which is one of the nature's most effective structures , for the reason that the hexagonal honeycomb uses the least amount of bees wax and forms the biggest capacity. And for the other design, what is particularly worth mentioning here is that it looks like the gate of Tianjin University.


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==Calculation==
==Calculation==
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Equation of △T
<big>Equation of △T</big>


WHEN
WHEN
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[[Image:2014-08-18_201722.jpg]]
[[Image:2014-08-18_201722.jpg]]


Corrected equation of △T
<big>Corrected equation of △T</big>


The fact is that the particle is located close to the interface between two homogeneous media. They are lying on a glass substrate and immersed in water. So the equation has to be corrected by a correction factor b. And κ should be replaced by κeff = κ/b
The fact is that the particle is located close to the interface between two homogeneous media. They are lying on a glass substrate and immersed in water. So the equation has to be corrected by a correction factor b. And κ should be replaced by κeff = κ/b
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[[Image:2014-08-18_201908.jpg]]
[[Image:2014-08-18_201908.jpg]]


Calculation of σabs
<big>Calculation of σabs</big>


1、when R≤15nm
1、when R≤15nm
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[[Image:2014-08-18_202827.jpg]]
[[Image:2014-08-18_202827.jpg]]


According to the formulas got above, the dependence amongst the intensity, wave length of the illumination, the size of the nanoparticle and the local temperature increase around a nanoparticle become quantative. Then we are able to select the light source needed for certain temperature increase. For instance, if we use a laser whose wave length is 520nm and intensity is 2.7×10<sup>5</sup>W/cm<sup>-2</sup> to irradiate a 40nm-gold nanoparticle, the local temperature of the nanoparticle will be 70°C.
==References==
[1] Rajendran A, Endo M, Katsuda Y, et al. Programmed two-dimensional self-assembly of multiple DNA origami jigsaw pieces[J]. ACS nano, 2010, 5(1): 665-671.<br><br>
[2] Huang X, Jain P K, El-Sayed I H, et al. Plasmonic photothermal therapy (PPTT) using gold nanoparticles[J]. Lasers in medical science, 2008, 23(3): 217-228.<br><br>
[3] Weissleder R. A clearer vision for in vivo imaging[J]. Nature biotechnology, 2001, 19(4): 316-316. <br><br>
[4] Pinheiro A V, Han D, Shih W M, et al. Challenges and opportunities for structural DNA nanotechnology[J]. Nature nanotechnology, 2011, 6(12): 763-772.<br><br>
[5] Baffou G, Berto P, Bermúdez Ureña E, et al. Photoinduced Heating of Nanoparticle Arrays[J]. ACS nano, 2013, 7(8): 6478-6488.<br><br>
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Background

<html></a></html> DNA Origami

The unique structural motifs and molecular recognition properties of DNA make it a promising template for building nanostructures. Using a long single-stranded DNA as a template, a novel strategy, the so-called DNA origami method, has been developed for the preparation of various two-dimensional (2D) and three-dimensional (3D) nanostructures with defined size which is predictable, precise, controllable and efficient.

Fig 1.DNA origami and its applications.

DNA origami is an excellent plantform for the nanopatterning and a variety of functional biomolecules and nanoparticles can be assembled onto the DNA origami nanoscaffolds, to obtain complicate nanodevices with special functions which can be used to facilitate imaging, targeted delivery, and controlled release of therapeutic compounds. As described, DNA origami possess the capability of transporting molecular payloads to cells, sensing cell surface inputs for conditional, triggered activation, and reconfiguring its structure for payload delivery. DNA origami structures can also be used as molecular pegboards with a resolution of 4–6 nm, and they been widely used in the assembly of hetero-elements such as proteins and nanoparticles. Therefore, DNA origami has shown great potential in nanotechnology.

Advantages of light

A revolution in cancer therapy has taken place by the emerging use of laser light to achieve controlled and confined thermal damage in the tumor tissue. Laser, the acronym for light amplification by the stimulated emission of radiation, is an optical source that emits photons in a coherent and narrow beam. Laser light has the characteristics of monochromaticity, coherence, and collimation. These properties provide a narrow beam of high intensity, which transmits deep down into the target location with minimal power loss and great precision.

Properties of gold nanoparticles (GNPs)

Nanomedicine is currently an active field because new properties emerge when the size of a matter is reduced from bulk to the nanometer scale. These new properties, including optical, magnetic, electronic, and structural properties, make nano-sized particles (generally 1–100 nm) very promising for a wide range of biomedical applications such as targeted therapy. Plasmonic (noble metal) nanoparticles distinguish themselves from other nanoplatforms by their unique surface plasmon resonance (SPR). A special property of these plasmonic nanoparticles is their heat generation resulting from optical stimulation.

Fig 2.The photothermal property for gold nanoparticle.

Among plasmonic nanoparticles, gold nanoparticles (GNPs) are most extensively investigated because of their inertness, low cytotoxicity, ready multi-functionalization and long history of medical use. GNPs are also attractive due to their facile synthesis, excellent biocompatibility as well as strongly enhanced and tunable optical properties to convert light into local heat. Gold nanoparticles exhibit light activated photothermal activity due to their geometry dependent SPR. This SPR, resulting from photon confinement to a small particle size, enhances all the radiative and nonradiative properties of GNPs. Hence GNPs have immense potential for the selective laser photothermal therapy of cancer due to their ability to efficiently convert surface plasmon resonance-enhanced absorbed light into localized heat and thus offering multiple modalities for biological and medical applications.

Fig 3.The the therapy use of gold nanoparticle and DNA origami.


<html><a name="motivation"></html>

Motivation

<html></a></html>

DNA origami is also emerging as a strong candidate for drug delivery in living systems. For its high compatibility to so many kinds of molecules, such as functional biomolecules and nanoparticles which can be linked to the DNA origami scaffolds, to obtain complicated functional nano-devices. Besides, it's capability to fold structures of 2-dimentional or 3-dimentional makes it will get more circumstances to apply. What’s more, the high rate of development and the endless potential of DNA origami make it worth researching.

But the methods of opening an origami box or changing the structure of it is limited in the addition of ssDNA to open by strand replacement or chemical methods to break, which limits the applications of origami especially in vivo. So, a physical way without adding anything to achieve the goal is what we need and search for. We choose light. But why?

We want to use light to open DNA origami because light control has many advantages.

1. Light is low expenditure and easy to get.

2. It is convenient to control the intensity of light.

3. Light for therapeutic could cause less damage on tissue.

In fact, in treatment, only light will produce sufficient power to penetrate the specific site with less energy loss. And, light has already been used into medical treatment field for many years, such as photothermal therapy. Then, the next question is how to change the light into heat, and the traditional way of photothermal therapy may answer this question.

A type of nanomaterial with strong light absorption comes into the sight of us, which is named gold nanoparticle (Au NP). Au NP has immense potential for the selective laser photothermal therapy of cancer cells due to its photo-thermal activity. It can convert light into heat, and leads to a temperature increase, which serves as our opening trigger.

And as all we know, origami is locked by complementary DNA sequence, which is difficult to totally separate by heating and restoring to room temperature. So that means our origami box have a large possibility to reclose after its open. To overcome this problem, we design three-arm DNA lock to “intelligently” control the open and close of origami by displacement, and it will be showed in the next part.

All in all, by creating and utilizing these principle or design, we want to grant this device with the following control characteristics: Local release of drugs. Traditional drugs are transported to every corner in human body, and may attack all the cells including the normal ones,such as the low specificity of anticancer drugs. However, our device is supposed to release at a specific location in human body under control.


Selective release of drugs

We want to give our device a DNA logical gate, which enable the device to selectively release specific drugs aimed at curing different cells under different conditions.

Physical control

We replace traditional control methods of adding chemicals with a physical trigger to make our device tunable for future modification, which has never done before.


<html><a name="calculation"></html>

Calculation

<html></a></html> Equation of △T

WHEN

1、the NPs are far enough（ interdistance is at least 4 or 5 times larger than the NP diameter ）

2、the NPs are in a homogeneous medium

The temperature increase on the surface of a spherical gold NP can be calculated by using the following equation.

Corrected equation of △T

The fact is that the particle is located close to the interface between two homogeneous media. They are lying on a glass substrate and immersed in water. So the equation has to be corrected by a correction factor b. And κ should be replaced by κeff = κ/b

r is the distance from the center of a particle. We want to calculate the temperature increase on the surface. So r= R, radius of a NP.

Calculation of σabs

1、when R≤15nm

2、when R>15nm

The previous formalism becomes inappropriate and the Mie theory has to be used. Within this model, the σabs is equal to

According to the formulas got above, the dependence amongst the intensity, wave length of the illumination, the size of the nanoparticle and the local temperature increase around a nanoparticle become quantative. Then we are able to select the light source needed for certain temperature increase. For instance, if we use a laser whose wave length is 520nm and intensity is 2.7×105W/cm-2 to irradiate a 40nm-gold nanoparticle, the local temperature of the nanoparticle will be 70°C.

References

[1] Rajendran A, Endo M, Katsuda Y, et al. Programmed two-dimensional self-assembly of multiple DNA origami jigsaw pieces[J]. ACS nano, 2010, 5(1): 665-671.

[2] Huang X, Jain P K, El-Sayed I H, et al. Plasmonic photothermal therapy (PPTT) using gold nanoparticles[J]. Lasers in medical science, 2008, 23(3): 217-228.

[3] Weissleder R. A clearer vision for in vivo imaging[J]. Nature biotechnology, 2001, 19(4): 316-316.

[4] Pinheiro A V, Han D, Shih W M, et al. Challenges and opportunities for structural DNA nanotechnology[J]. Nature nanotechnology, 2011, 6(12): 763-772.

[5] Baffou G, Berto P, Bermúdez Ureña E, et al. Photoinduced Heating of Nanoparticle Arrays[J]. ACS nano, 2013, 7(8): 6478-6488.

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