Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

A Robust Sequence-Dependent Rotary DNA Nanomechanical Device

DNA nanotechnology entails the construction of objects, arrays and devices that utilize unusual motifs. Previously, we have reported a rotary two-state DNA nanomechanical that is based on the B-Z transition of DNA. The B-Z transition is activated by the presence or absence of high ionic strength or by small molecule effectors, such as Co(NH3) 6Cl3, that facilitate it. Were N such devices to be incorporated into a 2D or 3D array, there would only be two states, that corresponding to B-DNA and that corresponding to Z-DNA, except perhaps for a small amount of nuance. It is desirable to be able to produce more structural states within the array, ideally at least 2N states.

Here, we report a sequence dependent DNA nanomechanical device that appears capable of leading to this goal. The device is based on a new motif, paranemic crossover DNA (PX-DNA), a four-stranded structure related to parallel double crossover molecules, except that every possible crossover takes place. Eliminating two crossovers leads to a molecule, termed JX2, in which one pair of ends are switched, while the others remain the same. Thus, in the drawing on the left, the two top ends of the PX molecule are labeled A and B, and the bottom ends are labeled C and D. The top ends of the JX2 molecule are labeled A and B in the same order, but now C and D, on the bottom, are seen to be reversed. The transition between the two states takes place by replacing single strands that set the state to be PX or JX2. The device is robust, in that it can be cycled without the formation of any detectable by-products, such as dimers. We demonstrate operation of the device by using atomic force microscopy.

This research supported by NIGMS, ONR, NSF/DARPA, USAF and NSF.

Hao Yan, Xiaoping Zhang and Nadrian C. Seeman*

Department of Chemistry, New York University, New York, NY 10003, USA
ph: 212-998-8395; fx: 212-260-7905,email: ned.seeman@nyu.edu.