Information Directed Molecular Technology: Programming Nucleic Acid Self-Assembly

May 21, 2009
11:00am-12:00pm
EE Conference Room 1300 Mudd
Speaker: Peng Yin, California Institute of Technology

Abstract

This talk will describe my work and plans on engineering information directed self-assembly of nucleic acid (DNA/RNA) structures and devices, and on exploiting such systems to do useful molecular work, e.g. templating nanomaterials and devices, and probing and programming biological processes for biomedical applications.

Specifically, I will first present a rudimentary programming language that enables user-friendly design of the dynamic behavior of synthetic nucleic acid systems (Yin et al, Nature, 451:318, 2008). The language is based on the graphical abstraction of a DNA hairpin motif, which physically implements a programmable kinetic trap. A high level molecular program specifies the connection of such kinetic traps on a free energy landscape, and defines the system's reaction pathway and dynamic behavior. A variety of molecular programs were experimentally executed: the catalytic formation of DNA branch junctions, a cross catalytic circuit, the triggered growth of a binary molecular "tree", and the autonomous unidirectional motion of a DNA "walker". In a related work, the abstraction of a 42 base single-stranded DNA motif is used to direct the self-assembly of molecular tubes with mono disperse, programmable circumferences (Yin et al, Science, 321:824, 2008).

The above work builds the foundation for my future research in three complementary directions. First, I will develop a new paradigm in synthetic molecular self-assembly, which I call developmental self-assembly.

Here, a synthetic molecular structure grows isothermally in a kinetically controlled fashion, like a living organism develops from a genome. This paradigm is fundamentally different from and conceptually more powerful than the dominant self-assembly paradigm based on thermal annealing. Second, I will engineer synthetic nucleic acid nano-devices to probe and program biology. Such devices sense and process molecular cellular information, and produce observable signals or actuate biological responses. By serving as in situ molecular instrumentation and therapeutic tools, they promise transformative biomedical applications. Third, I will develop the molecular foundation for molecular programming, with the ultimate goal to transform molecular engineering into computer programming.

The above work and plans will bring us closer to the vision of information directed molecular technology: by programming a user-friendly molecular controller, humans freely specify and realize their functional needs in the molecular world.

Biography

Peng Yin is a senior postdoctoral scholar of Bioengineering and Computer Science at Caltech's systems biology and synthetic biology center, the Center for Biological Circuit Design. At Caltech, he primarily works with Prof. Niles Pierce and Prof. Erik Winfree. Before joining Caltech, he obtained a Ph.D. in Computer Science under Prof. John Reif and a M.Sc. in Molecular Cancer Biology, both from Duke University. Before coming to Duke, he graduated from Peking University with a B.Sc. in Biochemistry and Molecular Biology and a Bachelor in Economics.

His paper "Programming Biomolecular Self-Assembly Pathways" (Yin, Choi, Calvert, Pierce, Nature, 451:318, 2008) was highlighted in The Year in Nature 2008, which features Nature editors' 22 favorites in 2008. This paper and his other recent paper "Programming DNA Tube Circumferences" (Yin, Hariadi, Sahu, Choi, Park, LaBean, Reif, Science, 321:824, 2008) can be accessed from his homepage at http://pengyin.org/. He was chosen, together with N.A. Pierce and R.M. Dirks, as a finalist for Feynman Prize in Nanotechnology in 2008.


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