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(Fueling the walker)
(Fueling the walker)
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The CHA reaction has been studied and its kinetics are understood. Using kinetic models we can simulate this reaction. [65]
The CHA reaction has been studied and its kinetics are understood. [65] Using kinetic models we can simulate this reaction.
=2-D representation of DNA forms=
=2-D representation of DNA forms=

Revision as of 20:59, 27 October 2012

Undergraduate DNA nanotechnology research group from the University of Texas at Austin

These genes were made for walkin'...





Motion is a necessary component of life. While this does include the motion of animals and people as they move about, there is also crucial motion which takes place on a cellular level. Cells could not function without the proteins kinesin and myosin [39], which carry cargo to and from our organelles. The movements employed by these proteins are very similar to the way people walk in the fact that they have two “feet” which step forward, one at a time [55]. Because of the crucial role these proteins play in supporting life, we began to wonder if we could create our own molecular walker that could perform similar tasks.

In order for this walker to be comparable to (or even better than) kinesin, it must be autonomous and run on a reusable track. In other words, it should not require an external driver and should not damage the track when taking steps. Other walkers have been created in the past, but none has yet been able to accomplish both of these tasks. There are some that are at least capable of either walking autonomously [2] or of reusing their track [63]. Our walker is able to accomplish both tasks by means of two alterations. The use of two discrete fuel strands which can only interact with the walker system in a specific order allow us to add an excess of fuel while still keeping the walker on the track. We also make use of a nicking enzyme which restores the track to its original form without harming it, allowing it to be reused.

However, our design does sacrifice some functionality by using this system of fuels. Because all molecules are free-floating in solution and have no preference to location, we expect there to be leakage of the walkers to some extent. This is due to the method by which the F1:F2 complex, see below for details, can displace the lagging leg while the leading leg is still in transition to its new foothold. We expect the probability of this occurring to be very low due to the functional breakdown of F1:F2 by the nicking enzyme when the fuels successfully bind to the track.

Design and walking mechanism




The "legs" of the walker are the two toeholds (5'- 2*1* -3' and 5'- 6*4* -3') of W1 and W2. By careful construction of the track, the walker will bind to corresponding toeholds on the first two hairpins (aA, bB) of the track. This is the starting point of the system. When the walker binds to the track, the hairpins will open, exposing a domain that was inaccessible. The fuel F1 binds to this toehold and displaces the lagging leg. We designed the sequence lengths such that when a fuel displaces a leg from the track, there is a smaller chance of the leg retaking its position on the track. This means that the forward intermediate is a more favorable reaction than the reverse. This is what gives the "push" our walker needs to move in one particular direction. This leg will then bind to the next hairpin in line, cA, as it did with the first, now becoming the leading leg by hopping over the other.

The duplex formed by aA and F1 expose a binding domain specific to the second hairpin F2. F2 then displaces F1 from aA, forming a duplex F1:F2. This duplex is free-floating in solution. Because of this, it can bind to bB and displace the now lagging leg, allowing it to bind to dB. Now the walker has taken a full two steps.

Finally a nicking enzyme, Nb.BsmI, specific to a domain formed only when F1:F2 is bound to a hairpin with a B loop will cut the formation. This cut causes the total number of bonds in the duplex to decrease to the point at which they can freely dissociate from the track [cite], becoming waste. This will allow the hairpin bB to return to its initial state, thus regenerating the track.


Fueling the walker




2-D representation of DNA forms





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