Biomod/2011/TUM/TNT/Project: Difference between revisions

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<h2>Why DNA Origami?</h2>
<h2>Why DNA Origami?</h2>
The working principle of DNA origami is based on the highly specific interaction behavior of DNA. Because of this specificity, the binding behavior of two strands can be encoded in the base sequence of said strands. By including sequences complementary to two strands on another, a trimolecular system can be created where one strand binds two different ones together. By including more and more complementary sequences on a single strand, increasingly complex configurations can be created. DNA Origami uses this modular behavior to encode the shape of the planned structure in the sequences of the used DNA strands. Designing a new structure is generally done according to the following steps. During the computer-aided design of the structure, a long single stranded DNA called the 'scaffold' is first laid out such that it fills out the shape of the planned structure. Next, short DNA strands called 'staples' are chosen such that they are complementary to partial sequences of the scaffold. By binding to those complementary sequences, the staples force the scaffold into a set conformation, removing degrees of freedom. With each bound staple, more and more helices with fixed relative positions are created. Once all bases of the scaffold are hybridized, the scaffold is forced into one specific shape.<br>
<font color="#CCCCCC">The working principle of DNA origami is based on the highly specific interaction behavior of DNA. Because of this specificity, the binding behavior of two strands can be encoded in the base sequence of said strands. By including sequences complementary to two strands on another, a trimolecular system can be created where one strand binds two different ones together. By including more and more complementary sequences on a single strand, increasingly complex configurations can be created. DNA Origami uses this modular behavior to encode the shape of the planned structure in the sequences of the used DNA strands. Designing a new structure is generally done according to the following steps. During the computer-aided design of the structure, a long single stranded DNA called the 'scaffold' is first laid out such that it fills out the shape of the planned structure. Next, short DNA strands called 'staples' are chosen such that they are complementary to partial sequences of the scaffold. By binding to those complementary sequences, the staples force the scaffold into a set conformation, removing degrees of freedom. With each bound staple, more and more helices with fixed relative positions are created. Once all bases of the scaffold are hybridized, the scaffold is forced into one specific shape.<br>
If the design of an origami contains certain targeted insertions and deletions of base pairs, it is possible to create a built-in twist or curvature [[http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Extras#References Dietz et. al., 2009]]. This work was inspiring because it implies the general idea of an origami's overall shape to be liable to distortions of its microstructure. According to this concept, the above mentioned constraints within the DNA Origami allow the effects of multiple DNA binders to be transported along the structure so that they sum up, amplifying otherwise immeasurable influences. Furthermore, the unparalleled positional control of DNA Origami allows us to place probe molecules on the structure with high accuracy, permitting the observation of minute changes.
If the design of an origami contains certain targeted insertions and deletions of base pairs, it is possible to create a built-in twist or curvature [[http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Extras#References Dietz et. al., 2009]]. This work was inspiring because it implies the general idea of an origami's overall shape to be liable to distortions of its microstructure. According to this concept, the above mentioned constraints within the DNA Origami allow the effects of multiple DNA binders to be transported along the structure so that they sum up, amplifying otherwise immeasurable influences. Furthermore, the unparalleled positional control of DNA Origami allows us to place probe molecules on the structure with high accuracy, permitting the observation of minute changes.


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   <li style="background-color: #cccccc"><a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project"><b>Project</b></a>        
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           <a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project#The_Idea">The Idea</a>|
           <a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project#Project_Specification">Project Specification</a>|
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