Photonically driven DNA nanomachine with hybrid functions towards cell measurement

Abstract

Physical properties of a cell are often valuable information about the status of the cell, and developing technologies to measure such properties is important to enhance the progress in, for example, diagnosis of diseases. In this paper, we present a photonically driven DNA nanomachine with hybrid functions: providing a physical operation to a cell and reporting the cell's response. The DNA nanomachine can be controlled according to optical signals, and therefore the measurement is achieved locally at designated positions and at desired times. Black hole quenchers (BHQs) are introduced to drive the DNA nanomachine using light. When the DNA nanomachine is irradiated with the light at the excitation wavelength of the BHQs, the thermal energy is produced from the BHQs to drive the DNA nanomachine. To demonstrate a basic functionality, we constructed a DNA nanomachine that transformed between a linear conformation and a hairpin-like conformation depending on the presence or absence of a controlling DNA. This conformation change will be able to provide a force to deform cells as a physical operation. The response of the cell is reported as fluorescence resonance energy transfer (FRET) signals. An experimental result demonstrated that the FRET signal changed according to the presence or absence of the controlling DNA. The method is expected to be useful in measuring the stiffness of a cell.