Biomod/2013/IIT-Madras

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    Home=http://openwetware.org/wiki/Biomod/2013/IIT-Madras
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    Team=http://openwetware.org/wiki/Biomod/2013/IIT-Madras/Team
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    Acknowledgement=http://openwetware.org/wiki/Biomod/2013/IIT-Madras/Acknowledgement
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    References=http://openwetware.org/wiki/Biomod/2013/IIT-Madras/References
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=<center>Acid Artists, IIT Madras</center>=
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==Abstract==
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DNA nano-structures have proved to be very effective tools in solving Structural Biology and Biophysics problems, with potential applications in fields such as Nano-medicine.
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However, since it may not always be desirable to have functioning nano-structures in a given system, a structure which folds into an appropriate configuration based on specific triggers would be more useful. The strand exchange system for actuating DNA nano-structures results in the generation of dsDNA waste products that increase the systems’ toxicity. The time-scale of system response is extremely high owing to diffusional limitations.
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An exciting alternative to this technique is the use of environmental triggers (such as pH, temperature, light). This reduces the response time and results in spatio-temporal homogeneity of system response. As there is no addition of any synthetic intermediate, the system is comparatively “Clean”.
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Our project is a proof-of-concept demonstration of an environmentally triggered DNA nano-structure – specifically, a DNA walker activated by a pH change. This pH-based construct has been designed using a single strand of DNA rich in Cytosine repeats which undergoes a conformational change at a low pH, releasing a walker strand from its bound configuration onto a neighboring strand present on the track.
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This system is a putative candidate for probing systems with varying pH, notably cancer and tumor cell systems.
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Current revision

GC_Ps.jpg


Acid Artists, IIT Madras


Abstract

DNA nano-structures have proved to be very effective tools in solving Structural Biology and Biophysics problems, with potential applications in fields such as Nano-medicine. However, since it may not always be desirable to have functioning nano-structures in a given system, a structure which folds into an appropriate configuration based on specific triggers would be more useful. The strand exchange system for actuating DNA nano-structures results in the generation of dsDNA waste products that increase the systems’ toxicity. The time-scale of system response is extremely high owing to diffusional limitations.

An exciting alternative to this technique is the use of environmental triggers (such as pH, temperature, light). This reduces the response time and results in spatio-temporal homogeneity of system response. As there is no addition of any synthetic intermediate, the system is comparatively “Clean”.

Our project is a proof-of-concept demonstration of an environmentally triggered DNA nano-structure – specifically, a DNA walker activated by a pH change. This pH-based construct has been designed using a single strand of DNA rich in Cytosine repeats which undergoes a conformational change at a low pH, releasing a walker strand from its bound configuration onto a neighboring strand present on the track.

This system is a putative candidate for probing systems with varying pH, notably cancer and tumor cell systems.

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