Photoisomerization Quantum Yield of Azobenzene-Modified DNA Depends on Local Sequence

Yan, Yunqi; Wang, Xin; Chen, Jennifer I. L.; Ginger, David S.

doi:10.1021/ja403249u

Cited by 49 publications

(72 citation statements)

References 29 publications

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“…Azobenzenes are the moste xplored photoswitches for the regulation of duplex stabilityb ecause they are easily synthesized,t he isomeric forms show pronouncedc hangesi ns hape and polarity,a nd they have good photochemical properties (i.e.,f atigue resistance, switching amplitude, thermal stability) depending on the substitution pattern. [7,9,[21][22][23][52][53][54] Many acyclic linkers( see references [5,9,11,21] for reviews) have been reportedt oi ncorporate azobenzenes, for example, 2,2-bis(hydroxymethyl)propionic acid, [55][56][57] d-threoninol (tAzo), [58,59,7] or glycol. [60,61] Nevertheless, elevated temperatures [62,63] were necessary for ac omplete trans-to-cis photoisomerization after duplex formation in many of thesea pplications.A sa ne xception, ag lycol scaffold introduced by Liang and co-workers was demonstrated to induce complete isomerization at room temperature, [60] but elevated temperatures werer equired for strand displacement.…”

Section: Introductionmentioning

confidence: 99%

Azobenzene C‐Nucleosides for Photocontrolled Hybridization of DNA at Room Temperature

Goldau

Murayama

Brieke

et al. 2015

Chemistry A European J

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Herein, we report the reversible light-regulated destabilization of DNA duplexes by using azobenzene C-nucleoside photoswitches. The incorporation of two different azobenzene residues into DNA and their photoswitching properties are described. These new residues demonstrate a photoinduced destabilization effect comparable to the widely applied D-threoninol-linked azobenzene switch, which is currently the benchmark. The photoswitches presented herein show excellent photoswitching efficiencies in DNA duplexes - even at room temperature - which are superior to commonly used azobenzene-based nucleic acid photoswitches. In addition, these photoswitching residues exhibit high thermal stability and excellent fatigue resistance, thus rendering them one of the most efficient candidates for the regulation of duplex stability with light.

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Section: Introductionmentioning

confidence: 99%

Azobenzene C‐Nucleosides for Photocontrolled Hybridization of DNA at Room Temperature

Goldau

Murayama

Brieke

et al. 2015

Chemistry A European J

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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%

“…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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“…Among the different stimuli, light is a practical trigger for enabling responsive materials, as exemplified by the incorporation of photoswitchable ligands into biomolecular systems in view of controlling their conformation and activity in a reversible manner . Several groups have already developed photoresponsive DNA molecules by covalently linking photoswitching molecules within the nucleic acid structure (e.g., azobenzenes between base pairs) . This covalent approach permits the formation and dissociation of DNA duplex by illuminating the azo‐modified oligonucleotide with UV light, which is valuable for the photoregulation of bioreactions .…”

Section: Introductionmentioning

confidence: 99%

Photomodulation of DNA‐Templated Supramolecular Assemblies

Rubio‐Magnieto

Phan

Fossépré

et al. 2017

Chemistry A European J

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A new type of DNA ligand that contains a phosphate-binding group and a photoresponsive azobenzene moiety is reported. When the azobenzene is in trans configuration, the ligand binds to the minor groove of a double-stranded DNA, whereas it partially desorbs upon trans-cis isomerisation with light. The ability to photoswitch the ligand upon interaction with DNA is evidenced by (chir)optical signatures, and deciphered by the differences of binding geometry, stability, and dynamics of the DNA/ligand complexes for the two isomers. We exploit these properties to photomodulate DNA-templated self-assembly, through the incorporation of another π-stacking DNA ligand, which together with the photoresponsive ligand form mixed supramolecular complexes along DNA. Our study demonstrates that well-designed photoresponsive DNA binders can be used to modulate multicomponent supramolecular DNA assemblies.

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Photoisomerization Quantum Yield of Azobenzene-Modified DNA Depends on Local Sequence

Cited by 49 publications

References 29 publications

Azobenzene C‐Nucleosides for Photocontrolled Hybridization of DNA at Room Temperature

Azobenzene C‐Nucleosides for Photocontrolled Hybridization of DNA at Room Temperature

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

Photomodulation of DNA‐Templated Supramolecular Assemblies

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