19th-banner-rev.gif

Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

A Ribosome-Like DNA Nanomechanical Device

The advent of translation was a hallmark development in the evolution of life: It signaled the end of the putative RNA world, because nucleic acids could code for chemical species whose properties were not derived directly from the transcription of their parent molecules. We have built a DNA nanomechanical device that performs the same task, and thus functions in a fashion that is logically equivalent to a ribosome. In response to a DNA signal, it aligns a series of molecules that are then bonded together. We have prototyped this system with DNA, so the products are DNA oligonucleotides of a defined sequence. Thus, in this case, the chemistry of the product is similar to that of the signal molecules, but there is no complementary relationship to the signal sequences. By using DNA molecules to set the states of two DNA PX-JX2 devices (1) independently, we program the synthesis of four different product molecules.


The device (left) consists of a left diamond that is connected to two double diamonds by PX-JX2 devices that are independently programmable. The Arabic numbers in the schematic above represent sticky ends, and the Roman numerals represent numbers for the diamonds. Diamond I contains a site (0) to bind an initiator, and the sticky ends between it can bind a DAE-DX molecule. Depending on the state of the device connecting Diamond I with double-diamond II-III, the sticky ends will be complementary to a DAE-DX molecule whose sticky ends complement 1 and 2 or 1 and 3. Similarly, the gap (on the same side as 0)between double diamond II-III and double diamond IV-V will bind DAE-DX molecules whose sticky ends complement 4 and 6 or 5 and 7 or 4 and 7 or 5 and 6. Thus, four products are possible following ligation, as shown, right, above.



The relationship of the components to the traditional components of the ribosome are indicated above.

Acknowledgement

This research supported by NIGMS, ONR, NSF and Nanoscience Technologies, Inc.

References and Footnotes
  1. Yan, H., Zhang, X., Shen, Z., and Seeman, N. C. Nature 415, 62-65 (2002).

Shiping Liao
Nadrian C. Seeman*

Department of Chemistry
New York University
New York, NY 10003, USA

*Phone: 212-998-8395
Fax: 212-260-7905
Email: ned.seeman@nyu.edu