Optically controlled release of DNA based on nonradiative relaxation process of quenchers

Ogura, Yusuke; Onishi, Atsushi; Nishimura, Takahiro; Tanida, Jun

doi:10.1364/boe.7.002142

Cited by 4 publications

(3 citation statements)

References 31 publications

(31 reference statements)

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“…Optical excitation causes quenchers to generate thermal energy through a non-radiative relaxation process 23 . The energy dissipated from excited quenchers is sufficient to denature 10-bp double-stranded DNA (dsDNA) to two single DNA strands (ssDNAs) 24 . Thus, the bonds between the Y-DNA and the L-DNA in the DNA gel are cleaved by light excitation, and the DNA gels within the irradiation area are decomposed.…”

Section: Resultsmentioning

confidence: 99%

Optical decomposition of DNA gel and modification of object mobility on micrometre scale

Shimomura

Nishimura

Ogura

et al. 2019

Sci Rep

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DNA gels can be engineered to exhibit specific properties through the choice of DNA sequences and modification with dye molecules, and can therefore be useful in biomedical applications such as the detection of biomolecules. State transitions of DNA gels on the micrometre scale can generate a viscosity gradient, which can be used to modify the mobility of micrometre-sized objects. In this paper, we propose a method for changing the viscosity of DNA gels using optical decomposition. The use of light allows for decomposition on the micrometre scale, which can be used to achieve patterned viscosity changes within DNA gels. Decomposition was induced by thermal energy released through non-radiative relaxation of excited quenchers. We demonstrated the decomposition of DNA gels in response to irradiation patterns on the micrometre scale. In addition, as a result of changes in DNA gel viscosity due to decomposition, the mobility of polystyrene beads was shown to increase. This technique could provide a new optical approach for controlling the mobility of micrometre-sized objects.

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Section: Resultsmentioning

confidence: 99%

Optical decomposition of DNA gel and modification of object mobility on micrometre scale

Shimomura

Nishimura

Ogura

et al. 2019

Sci Rep

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“…As a result, the co-contributing effects of TMSD facilitate the circuit regeneration process by ameliorating the issue with unideal yield of azobenzene-mediated DNA dehybridization reported in prior works. 71,72 Our design also provides benets in reducing leaks of seesaw circuit operations due to spurious toehold binding. This not only helps to solve the leakage problem when seesaw circuits scale up, but also makes the seesaw gate regeneration fast and robust.…”

Section: Contributions Of This Workmentioning

confidence: 99%

Renewable DNA seesaw logic circuits enabled by photoregulation of toehold-mediated strand displacement

et al. 2017

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An important achievement in the field of DNA-based computation has been the development of experimental protocols for evaluation of Boolean logic circuits. These protocols for DNA circuits generally take as inputs single-stranded DNA molecules that encode Boolean values, and via a series of DNA hybridization reactions then release ssDNA strands to indicate Boolean output values. However, most of these DNA circuit protocols are use-once only, and there remains the major challenge of designing DNA circuits to be renewable for use with multiple sets of inputs. Prior proposed schemes to make DNA gates renewable suffered from multiple problems, including waste accumulation, signal restoration, noise tolerance, and limited scalable complexity. In this work, we propose a scalable design and in silico verifications for photoregulated renewable DNA seesaw logic circuits, which after processing a given set of inputs, can be repeatedly reset to reliably process other distinct inputs. To achieve renewability, specific toeholds in the system are labeled with photoresponsive molecules such as azobenzene to modulate the effective rate constants of toehold-mediated strand displacement (TMSD) reactions. Our proposed design strategy of leveraging the collective effect of TMSD and azobenzene-mediated dehybridization may provide new perspectives on achieving synchronized and localized control of DNA hybridizations in complex and scalable reaction networks efficiently and economically. Various devices such as molecular walkers and motors could potentially be engineered reusable, be simulated and subsequently implemented using our simplified design strategy.

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“…Although photoinduced DNA hydrogels have already been developed [ 11 ], control of the shape has not been previously achieved without a mould. Here, we design a scheme to form DNA hydrogels based on the controlled denaturation of double-stranded (ds) DNA via a non-radiative relaxation process of optically excited quenchers [ 12 ]. To demonstrate flexible control over the shape, micrometre-sized DNA hydrogels were created by irradiation with specific light patterns.…”

Section: Introductionmentioning

confidence: 99%

Photothermal fabrication of microscale patterned DNA hydrogels

Shimomura¹,

Nishimura²,

Ogura³

et al. 2018

R. Soc. open sci.

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This paper introduces a method for fabricating microscale DNA hydrogels using irradiation with patterned light. Optical fabrication allows for the flexible and tunable formation of DNA hydrogels without changing the environmental conditions. Our scheme is based on local heat generation via the photothermal effect, which is induced by light irradiation on a quenching species. We demonstrate experimentally that, depending on the power and irradiation time, light irradiation enables the creation of local microscale DNA hydrogels, while the shapes of the DNA hydrogels are controlled by the irradiation patterns.

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Optically controlled release of DNA based on nonradiative relaxation process of quenchers

Cited by 4 publications

References 31 publications

Optical decomposition of DNA gel and modification of object mobility on micrometre scale

Optical decomposition of DNA gel and modification of object mobility on micrometre scale

Renewable DNA seesaw logic circuits enabled by photoregulation of toehold-mediated strand displacement

Photothermal fabrication of microscale patterned DNA hydrogels

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