sequence-specific hybridization and forms a highly regular double-helical structure with suitable flexibility. [1][2][3][4] DNA is probably one of the most promising biomolecules for future applications in nanotechnology and materials science.[5] Many 2D and 3D nanostructures with determined shapes and geometries have been reported recently in which DNA is used as the building blocks and mortar. [3,6,7] More excitingly, several types of DNA nanomachines, fuelled with DNA oligonucleotides [8] or other molecules such as intercalators [9] and metal ions, [10] have been constructed. [4,5] During these 10 years of development, substantial progress has been made in the design of DNA-based devices such as tweezers, walkers, and gears, which can perform mechanical functions such as scission, directional motion, or rolling. [11][12][13] The prospects of this field are extraordinarily promising, and several valuable applications of DNA nanomachines as sensors, transporters, and drug-delivery systems have also been reported. [5] For most of the DNA nanomachines constructed so far, oligonucleotides have been generally used as the fuel. In many of these systems, the mechanical motion was usually carried out by hybridization of one DNA fuel molecule to target sequences followed by its removal with another DNA sequence that is completely or partially complementary to the first. [5] Yurke et al. demonstrated the first DNA machine that functioned as "tweezers" fuelled by two strands of DNA with tailored complementarity.[8a] As the energy for operating these DNA nanomachines is produced by a strand-exchange strategy, a DNA duplex is produced as a waste product in every working cycle. Thus, the operating efficiency decreases gradually with the accumulation of "wastes". A new strategy is therefore required to overcome this problem for the further development of DNA nanotechnology.Over the past decade, we have developed a series of photoresponsive DNAs by covalently tethering azobenzene moieties onto the DNA strand. [14][15][16][17][18][19] Hybridization of these photoresponsive DNAs to single-stranded DNA (to form duplexes), RNA (to form DNA-RNA hybrids), or double-stranded DNA (to form triplexes) can be efficiently switched "on" and "off" by simply irradiating with UV and visible light. This is based on the following mechanism: the planar trans-azobenzene intercalates between adjacent base pairs and stabilizes the duplex or triplex structure by stacking interactions, whereas the nonplanar cisazobenzene destabilizes it by steric hindrance.[19] The successful photoregulation of primer elongation, transcription, and RNase H activity have also been demonstrated with photoresponsive DNAs. [20][21][22] Photoregulation efficiency can be amplified by the introduction of multiple azobenzene residues onto the DNA.[23] For example, nine azobenzene groups were introduced onto a DNA strand 20 nucleotides (nt) in length, and the clearcut photoswitching of DNA duplex formation was observed without loss of sequence specificity. Photoregulation of ...

A new photoswitch for DNA hybridization involving para-substituted azobenzenes (such as isopropyl- or tert-butyl-substituted derivatives) with L-threoninol as a linker was synthesized. Irradiation of the modified DNA with visible light led to dissociation of the duplex owing to the destabilization effect of the bulky substituent on the trans-azobenzene. In contrast, trans-to-cis isomerization (UV light irradiation) facilitated duplex formation. The direction of this photoswitching mode was entirely reversed relative to the previous system with an unmodified azobenzene on D-threoninol whose trans form turned on the hybridization, and cis form turned it off. Such reversed and reversible photoswitching of DNA hybridization was directly demonstrated by using fluorophore- and quencher-attached oligonucleotides. Furthermore, it was revealed that the cis-to-trans thermal isomerization was greatly suppressed in the presence of the complementary strand owing to the formation of the more-stable duplex in the cis form.

A photoresponsive DNA nano-pincette was constructed by using azobenzene-modified DNA as materials. When the azobenzene-modified part hybridizes with its complementary sequence on the pincette, the duplex formation closes it. On the contrary, the pincette is opened after the formed duplex dissociates. Based on reversible photoswitching of this DNA hybridization, the pincette involving non-substituted azobenzene can be opened simply by UV light irradiation and closed by visible light irradiation. Interestingly, the operation can be reversed by using para-isopropyl group substituted azobenzene: visible light opens the pincette, and UV light closes it. In both cases, the azobenzene-modified part was attached to the pincette throughout the open/close operation, which makes single molecular operation possible. Furthermore, the operation can be repeated many times without any decrease of the cycling efficiency and no DNA waste was produced.

No abstract

Previously, photoregulation of DNA hybridization was achieved by introducing nonsubstituted azobenzene via a D-threoninol linker: DNA duplex formed (ON) after visible light irradiation (planar trans-form), whereas the duplex dissociated (OFF) after UV light irradiation (non-planar cis-form). In this study, for more efficient photoregulation of DNA functions, the reverse switch that can turn on duplex formation with UV, and turn off it with visible light irradiation was designed. When para-isopropylazobenzene (p-(i)PrAzo) was introduced into DNA via a L-thereoninol linker, the photoswitching direction was completely reversed: the duplex involving non-planar cis-p-(i)PrAzo was much more stable than that involving planar trans-form.