Biomod/2012/IIT-Madras/AcidArtists/Project

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Controlled Activation of a structure

The functionality of a structure is not always desirable. To accomplish this, we need a device similar to an electronic logic gate, that is switched on only under certain conditions. An analogous concept on the nanoscale is DNA Logic Gates.

Relation with an electrical logic gate

• Input wires - Single stranded “input” DNA Molecules
• Output Wires - Single stranded DNA Molecule released due to interaction of Input DNA Strand with gate complex
• Gate Complex - Corresponds to a partially double stranded DNA Complex (Gate Complex), consisting of 2 strands. The base strand, and the bound output strand
• Signal - Concentration of Strands
• Current flowing in a wire = Exposed toehold domain of a strand. A DNA strand having an exposed toehold domain is called as “Active”

http://openwetware.org/images/b/bd/Acid_artists_1.png

The strands are colour coded to illustrate different domains involved in binding.

Why do both interact ?

For 2 DNA strands to interact, we need complementary sequences on each. This implies, that input and one of the strands in the Gate Output complex have complementary sequences.

Moreover, the structure of the base must permit release of the Output DNA Strand from the complex. Displacement of the output must occur. To be precise, strand displacement reaction must occur.

Consider displacement of one strand from another, without using toeholds. For example, consider the displacement of the green strand by the red one. It is a very slow and stochastic process depending on random collisions between both species.

How do we make this process faster?

This can be accelerated, if we have a method of localising the red strand near the double stranded complex. This will facilitate the easy branch migration of the input strand, releasing the output strand in the process. Each step in branch migration is reversible. It also increases the probability of a collision being effective. This is achieved through a toehold.

A toehold is a short single stranded DNA, that is complementary to a part of the input strand.

Thus toehold mediated strand displacement reaction forms the basis for DNA Logic Gates.