Construction of Molecular Robots from Microtubules for Programmable Swarming.

Swarm robotics has been attracting much attention in recent years in the field of robotics. This chapter describes a methodology for the construction of molecular swarm robots through precise control of active self-assembly of microtubules (MTs). Detailed protocols are presented for the construction of molecular robots through conjugation of DNA to MTs and demonstration of swarming of the MTs. The swarming is mediated by DNA-based interaction and photoirradiation which act as processors and sensors respectively for the robots. Furthermore, the required protocols to utilize the swarming of MTs for molecular computation is also described.

Development of Red-Shifted and Fluorogenic Nucleoside and Oligonucleotide Diarylethene Photoswitches.

The reversible modulation of fluorescence signals by light is of high interest for applications in super-resolution microscopy, especially on the DNA level. In this article we describe the systematic variation of the core structure in nucleoside-based diarylethenes (DAEs), in order to generate intrinsically fluorescent photochromes. The introduction of aromatic bridging units resulted in a bathochromic shift of the visible absorption maximum of the closed-ring form, but caused reduced thermal stability and switching efficiency. The replacement of the thiophene aryl unit by thiazol improved the thermal stability, whereas the introduction of a benzothiophene unit led to inherent and modulatable turn-off fluorescence. This feature was further optimized by introducing a fluorescent indole nucleobase into the DAE core, resulting in an effective photoswitch with a fluorescence quantum yield of 0.0166 and a fluorescence turn-off factor of 3.2. The site-specific incorporation into an oligonucleotide resulted in fluorescence-switchable DNA with high cyclization quantum yields and switching efficiency, which may facilitate future applications.

Development of High-Performance Pyrimidine Nucleoside and Oligonucleotide Diarylethene Photoswitches.

Nucleosidic and oligonucleotidic diarylethenes (DAEs) are an emerging class of photochromes with high application potential. However, their further development is hampered by the poor understanding of how the chemical structure modulates the photochromic properties. Here we synthesized 26 systematically varied deoxyuridine- and deoxycytidine-derived DAEs and analyzed reaction quantum yields, composition of the photostationary states, thermal and photochemical stability, and reversibility. This analysis identified two high-performance photoswitches with near-quantitative, fully reversible back-and-forth switching and no detectable thermal or photochemical deterioration. When incorporated into an oligonucleotide with the sequence of a promotor, the nucleotides maintained their photochromism and allowed the modulation of the transcription activity of T7 RNA polymerase with an up to 2.4-fold turn-off factor, demonstrating the potential for optochemical control of biological processes.