Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

A Robust Sequence-Dependent Three-State DNA Nanomechanical Device

We have reported a robust sequence-dependent two-state DNA rotary device that operates in a four-step machine cycle (1). This device operates by the addition of a pair of 'set strands', and then their removal by 'unset strands', which act as fuel. These strands induce the interconversion between two robust topological motifs, Paranemic Crossover (PX) DNA and its topoisomer JX2 DNA. The difference between the two states is that one end of the device is rotated relative to the other by 180°. The operation of the rotary device is shown in the left portion of the drawing. A major motivation for developing the sequence-dependent two-state device is that a set of N different two-state devices inserted into a larger superstructure can lead to 2N distinct structural states. Devices with three states would lead to 3N distinct states when they are incorporated into a larger superstructure. Consequently, the two-state device has been extended to a three-state device.

A second reason to add another state is to add more number of motions to the nano machine. The presence of a third state leads to two different motions. These are a pure translation, and a screw-translation, as shown in the diagram. The third state is called Branched Crossover(BX). BX has the same frame structure as the other two states PX and JX2. New set strands are used to pull apart the set strand region to give rise to a BX structure. The three-state device has been cycled by the addition of set and fuel strands that direct the structure. The formation of the three states as well as the intermediate frame structures are demonstrated cleanly by gel electrophoresis. All possible transitions between the devices have been shown electrophoretically. The three different states have been observed by AFM; to do this, we by form one dimensional arrays with large trapezoidal markers whose orientations are visible. FRET studies are being conducted to measure the extent of the contraction between the JX2 state and the BX State.

Banani Chakraborty
Ruojie Sha
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

Note that the same molecule acts as an intermediate for all transitions. This device will lead to more control and more flexibility of motions in DNA nanotechnology, hastening the advent of a DNA-based nanorobotics.


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).