Week 6 / DNA Origami / stephany howard

 

 

Paul Rothemund makes DNA origami.  He describes that all life involves computation, and that molecular programs underlie biology.  When someone says that molecular programs underlie biology, they probably mean to say that all living forms have come into existence as a result of a biological, molecular program—computation—that has built its form from a sort of recipe.  Most of us understand that our bodies (and even behavioral traits in humans) have been laid out in a recipe of sorts by the genes we inherit from our parents.  In effect, a computational system that processes information in our nuclei give rise to our physical existence as humans—we are “computer fabricated artifacts”1.  The same goes for all other living organisms. 

Paul Rothemund is a Senior Research Associate at Caltech who has decided to use questions in computer science to better understand molecular and biological computing.  He says:

My interests lie at the interface of computer science, biology, and chemistry. By this I do not mean the application of computer science to solve problems in biology or chemistry such as the protein folding problem. Rather, I am interested in how processes in biology and chemistry can actually act as computers and execute molecular algorithms.2

 

He has noticed that both genetic and computer programs are sensitive to very small mutations or changes in code—an attribute that makes both kinds of computation extremely powerful.  Rothemund also believes that in order to understand any system, one needs to build it from the bottom up.

In his talk at the 2008 Ted conference, he outlines how he created something called DNA Origami in his attempt to understand the way that DNA builds structures—ultimately hoping to enable humans to coopt biological programs in order to build biological computers.  Where synthetic biologists (like Craig Ventor) use cells to build new things, Rothemund and his colleagues take interest in using biomolecules (DNA, RNA, and protein) to build “new languages for building things from the bottom up.”  The first thing that Rothemund has figured out how to do build is shapes and patterns out of DNA:

 

 

 

 

Each smiley face is 1 thousandth the width of a human hair.  The images were built by a relatively simple process (described in Rothemund’s 5 min Ted talk).  Once someone designs a shape or pattern they would like to build out of DNA, a computer program or compiler writes in DNA code the recipe for the molecules needed to make that synthetic form.  These recipes describe the small molecules that when added to the long strand of DNA (like the origami paper), will fold that strand into a desired shape (an origami object).   

 

 

Once this recipe is written, it is sent out (via email) to a company that uses a DNA synthesizer creates small bits of DNA (staples), in the form of a seed.  When appropriately watered, this seed essentially grows into the object / pattern desired.  During this process, the small bits of DNA (staples) attach to a long strand of DNA (found in the M13 virus), and fold that long strand into a desired shape or pattern (eg. smiley face).

           

The idea is that eventually we’d be able to build things like cell phones:

 

     

 

And Rothemund describes, “It turns out that nano-artwork is just what you need to make nano-circuits.”  And they’ve been able to make a single functioning switch out of DNA.  A functional computer needs half a billion switches, but they’re on their way to building a functioning biological computer with parts 1/10th the size of a normal computer.  We can only imagine the ramifications of having computers this small. 

 

stephany howard


2 Rothemund’s bio, website: http://www.dna.caltech.edu/~pwkr/

 

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