Photoregulated assembly/disassembly of DNA‐templated protein arrays using modified oligonucleotide carrying azobenzene side chains

Hachikubo, You; Iwai, Sosuke; Uyeda, Taro Q.P.

doi:10.1002/bit.22669

Cited by 11 publications

(11 citation statements)

References 29 publications

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“…One‐dimensional photoresponsive DNA‐templated protein arrays using azobenzene‐modified DNA duplex as scaffold were also constructed 53. The fluorescent protein arrays could be modulated by UV‐light irradiation due to the dissociation of the scaffold duplex.…”

Section: Applications Of Azobenzene‐modified Nucleic Acidsmentioning

confidence: 99%

Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology

Li¹,

Wang²,

Liang³

2014

Chemistry An Asian Journal

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Azobenzene has been widely used as a photoregulator due to its reversible photoisomerization, large structural change between E and Z isomers, high photoisomerization yield, and high chemical stability. On the other hand, some azobenzene derivatives can be used as universal quenchers for many fluorophores. Nucleic acid is a good candidate to be modified because it is not only the template of gene expression but also widely used for building well-organized nanostructures and nanodevices. Because the size and polarity distribution of the azobenzene molecule is similar to a nucleobase pair, the introduction of azobenzene into nucleic acids has been shown to be an ingenious molecular design for constructing light-switching biosystems or light-driven nanomachines. Here we review recent advances in azobenzene-modified nucleic acids and their applications for artificial regulation of gene expression and enzymatic reactions, construction of photoresponsive nanostructures and nanodevices, molecular beacons, as well as obtaining structural information using the introduced azobenzene as an internal probe. In particular, nucleic acids bearing multiple azobenzenes can be used as a novel artificial nanomaterial with merits of high sequence specificity, regular duplex structure, and high photoregulation efficiency. The combination of functional groups with biomolecules may further advance the development of chemical biotechnology and biomolecular engineering.

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Section: Applications Of Azobenzene‐modified Nucleic Acidsmentioning

confidence: 99%

Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology

Li¹,

Wang²,

Liang³

2014

Chemistry An Asian Journal

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“…[1][2][3][4][5][6][7][8][9][10][11][12][13][14] The alternative is the use of photoresponsive small molecules that play an intimate role in biochemical processes, as either cofactors or inhibitors. Applying this control strategy to macromolecules such as oligonucleotides and proteins is challenging because their large size and complexity makes it difficult to target a particular area on the macromolecules for modification, although several impressive examples have been reported.…”

mentioning

confidence: 99%

Turning “On” and “Off” a Pyridoxal 5′‐Phosphate Mimic Using Light

Wilson

Branda

2012

Angew Chem Int Ed

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The use of light to reversibly change the structure of biologically relevant molecules and turn "on" and "off" important biochemical functions "on-command" offers the biomedical end-user a non-invasive, rapid, reversible, spatial and temporal tool for research and therapy. Applying this control strategy to macromolecules such as oligonucleotides and proteins is challenging because their large size and complexity makes it difficult to target a particular area on the macromolecules for modification, although several impressive examples have been reported. [1][2][3][4][5][6][7][8][9][10][11][12][13][14] The alternative is the use of photoresponsive small molecules that play an intimate role in biochemical processes, as either cofactors or inhibitors. Not only would these molecular systems be easier to photoactivate and deactivate than their enzyme partners, they would also provide a more "universal" method to regulate biological function because the same cofactor can be involved in more than one operation.We have recently described how two different colors of light can be used to convert a small molecule between two isomeric forms differing by an order of magnitude in their ability to act as an inhibitor for human carbonic anhydrase. [15] While regulating inhibitors is appealing, [16][17][18] applying the same strategy to enzyme cofactors would provide control over a more diverse set of biochemical systems. Cofactors have all the earmarks of a suitable photoresponsive target. They tend to be small in size, structurally simple and easy to modify and study, while still allowing for ultimate control over the enzyme activity. Here, we take a first logical step by using a well-known enzyme cofactor as the inspiration in our design of a proof-of-concept demonstration. We show how our biomimetic system acts as a photoswitchable catalyst for a biochemical reaction. [19] The biologically active form of vitamin B 6 , pyridoxal 5'phosphate (PLP), is a versatile enzyme cofactor responsible for amino acid metabolism in all organisms from bacteria to humans. [20] Its participation in a diverse range of enzymatic reactions including transamination, racemization, decarboxylation, and numerous elimination and replacement processes makes it unrivalled. [21] It is a particularly inspiring cofactor for our proof-of-concept design because it can catalyze many processes without the presence of an enzyme. [22,23] It is also the role-model target of the studies described in this report.The structural features responsible for the action of PLP are the aldehyde and pyridinium functional groups, which are electronically connected to each other through bonds (Scheme 1). This intimate connectivity allows any molecule attached to the aldehyde to "sense" the electron withdrawing nature of the positively charged heterocycle. An example of this is the aldimine generated when an amino acid condenses with PLP (Scheme 1) and it is this Schiff base that is responsible for the enormous range of reactions the cofactor catalyzes. [24] The pyridinium group...

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“…As investigated in a majority of published literature, the actual yield depends on various factors such as the number of azobenzene moieties incorporated, positions and spacing between azobenzene intercalations, and local mismatches of nucleobases surrounding the intercalation site. 71,[85][86][87][88][89][90][91] However, these studies mainly focused on regulating the hybridization of duplex DNA with 'blunt ends', meaning no exposed ssDNA toehold is present to facilitate the dehybridization process. In contrast, our design takes advantage of both the steric hindrance induced by azobenzene and the modulation of effective toehold length to evoke controlled renewability of the seesaw motif cascade reaction network.…”

Section: Discussion On the Yield Of Azobenzene-mediated Dna Dehybridimentioning

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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Photoregulated assembly/disassembly of DNA‐templated protein arrays using modified oligonucleotide carrying azobenzene side chains

Cited by 11 publications

References 29 publications

Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology

Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology

Turning “On” and “Off” a Pyridoxal 5′‐Phosphate Mimic Using Light

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

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