Incorporation of cyclic azobenzene into oligodeoxynucleotides for the photo-regulation of DNA hybridization

Eljabu, Fatma Mohamed; Dhruval, Joshi; Yan, Hongbin

doi:10.1016/j.bmcl.2015.10.043

Cited by 21 publications

(23 citation statements)

References 15 publications

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“…Since this contribution, tetra‐ ortho ‐fluoroazobenzenes have been mainly used in materials science, and their applications in a biological context are scarce . Along these lines, there have been only a few cAzo derivatives used to modulate DNA hybridization and to control the helical conformation of peptides …”

Section: Introductionmentioning

confidence: 99%

Modulating Protein–Protein Interactions with Visible‐Light‐Responsive Peptide Backbone Photoswitches

et al. 2019

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Life relies on a myriad of carefully orchestrated processes, in which proteins and their direct interplay ultimately determine cellular function and disease. Modulation of this complex crosstalk has recently attracted attention, even as a novel therapeutic strategy. Herein, we describe the synthesis and characterization of two visible‐light‐responsive peptide backbone photoswitches based on azobenzene derivatives, to exert optical control over protein–protein interactions (PPI). The novel peptidomimetics undergo fast and reversible isomerization with low photochemical fatigue under alternatively blue‐/green‐light irradiation cycles. Both bind in the nanomolar range to the protein of interest. Importantly, the best peptidomimetic displays a clear difference between isomers in its protein‐binding capacity and, in turn, in its potential to inhibit enzymatic activity through PPI disruption. In addition, crystal structure determination, docking and molecular dynamics calculations allow a molecular interpretation and open up new avenues in the design and synthesis of future photoswitchable PPI modulators.

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Section: Introductionmentioning

confidence: 99%

Modulating Protein–Protein Interactions with Visible‐Light‐Responsive Peptide Backbone Photoswitches

et al. 2019

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“…With the confirmation of trans ‐cAb structure, and our previous demonstration of the application of cAb as a photoregulation tool in DNA hybridization, our lab is currently exploring the utility of cAb in the regulation of processes such as transcription, aptamer binding and potentially optogenetics.…”

Section: Resultsmentioning

confidence: 99%

“…It was recently reported by us that cAb and analogs can be synthesized from 2,2’‐dinitrodibenzyl 3 , and transformed into the corresponding D‐threoninol conjugate phosphoramidite 4 (Scheme ) for incorporation into oligonucleotides through solid phase synthesis. We further demonstrated that photoisomerization of cAb can indeed be used to regulate DNA hybridization . While work is currently in progress in our lab to demonstrate the ability of cAb to regulate processes such as DNA transcription and aptamer binding, an understanding of the influence of functional groups of cAb on its photoisomerization properties is necessary in order to design a cAb system for its desired application.…”

Section: Figurementioning

confidence: 99%

“…The photoisomerization properties of a few cAb analogs, non‐substituted, Br‐, CN‐, carboxyl‐ and amino‐cAb, were investigated. The non‐substituted, Br‐, CN‐, carboxyl‐cAb were accessed through the chemistry that we demonstrated previously (Scheme ) ,. Thus, starting from 2,2’‐dinitrodibenzyl 3 , 11,12‐dihydrodibenzo[ c , g ][1, 2]diazocine‐5‐oxide 5 was obtained (Scheme ), which was subsequently subjected to bromination to yield 2‐bromo‐11,12‐dihydrodibenzo[ c , g ][1, 2] diazocine‐6‐oxide 6 .…”

Section: Figurementioning

confidence: 99%

“…Thus, starting from 2,2’‐dinitrodibenzyl 3 , 11,12‐dihydrodibenzo[ c , g ][1, 2]diazocine‐5‐oxide 5 was obtained (Scheme ), which was subsequently subjected to bromination to yield 2‐bromo‐11,12‐dihydrodibenzo[ c , g ][1, 2] diazocine‐6‐oxide 6 . In our previous publications,, bromine was used in this reaction, which proceeded very slowly, especially when the reaction was carried out on gram scales. An alternative procedure, where oxide 5 was treated with potassium bromate in the presence of concentrated sulfuric acid, led to complete conversion in 30 minutes, giving bromo oxide 6 in a moderate yield (44%) on gram scales.…”

Section: Figurementioning

confidence: 99%

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Confirmation of the Structure of Trans‐Cyclic Azobenzene by X‐Ray Crystallography and Spectroscopic Characterization of Cyclic Azobenzene Analogs

et al. 2018

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The photoisomerization properties of a series of cyclic azobenzene (cAb) analogs, including non-substituted, Br-, CN-, carboxyl-, and amino cAb, were compared. While the transform of these analogs show different degrees of thermal stability, no spectral changes in the absorption wavelengths were observed for amino cAb upon exposure to purple light. The 15 N NMR chemical shifts of cAb in both cis-and trans-forms were found to show a large difference from those of aromatic azobenzene; however, the trend of difference in chemical shift is in agreement with that obtained from quantum chemical calculations. More importantly, the structure of the photoisomerization product from cis-cAb was confirmed to be, indeed, the trans-cAb by X-ray diffraction experiments. The 15 NMR data of the cAb isomers and confirmation of trans-cAb through crystal structure will be of importance for future studies in the design and applications of cAb as a photoswitch.In recent years, spatiotemporal control has been recognized as a useful approach in modulating the structures and functions of biological systems due to the possibility of introducing two regulatory domains, time and location. [1][2][3] While cyclic azobenzene (cAb, 2) was first synthesized in 1910, [4] it only attracted interest very recently with the demonstration of a color change upon exposure to purple light. [5] Compared with the linear aromatic azobenzene (Ab) system 1 (Figure 1), which has found utilities in regulating the structures and functions of peptides, proteins and nucleic acids, [1,[6][7][8][9][10][11] cAb is unique in that the yellow-red isomerization is driven by visible light, and the thermodynamically stable form is the non-planar cis-, as opposed to the co-planar trans-form in Ab, potentially offering spatiotemporal regulation complementary to that of Ab.It was recently reported by us [12] that cAb and analogs can be synthesized from 2,2'-dinitrodibenzyl 3, and transformed into the corresponding D-threoninol conjugate phosphoramidite 4 (Scheme 1) for incorporation into oligonucleotides through solid phase synthesis. We further demonstrated that photoisomerization of cAb can indeed be used to regulate DNA hybridization. [13] While work is currently in progress in our lab to demonstrate the ability of cAb to regulate processes such as DNA transcription and aptamer binding, an understanding of the influence of functional groups of cAb on its photoisomerization properties is necessary in order to design a cAb system for its desired application. More importantly, while it has been assumed in the literature that cis-cAb is transformed into the red trans-cAb upon exposure to purple light, [5] no experimental evidence has been provided to confirm the structure of the photoisomerization product. We report herein the photoisomerization and thermostability of a series of cAb analogs, and the confirmation of the trans-cAb structure by Xray crystallography.The photoisomerization properties of a few cAb analogs, non-substituted, Br-, CN-, carboxyl-and amino-cAb, were inv...

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Molecular Switches as Building Blocks for DNA and RNA

Wagenknecht¹

2022

Molecular Photoswitches

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Incorporation of cyclic azobenzene into oligodeoxynucleotides for the photo-regulation of DNA hybridization

Cited by 21 publications

References 15 publications

Modulating Protein–Protein Interactions with Visible‐Light‐Responsive Peptide Backbone Photoswitches

Modulating Protein–Protein Interactions with Visible‐Light‐Responsive Peptide Backbone Photoswitches

Confirmation of the Structure of Trans‐Cyclic Azobenzene by X‐Ray Crystallography and Spectroscopic Characterization of Cyclic Azobenzene Analogs

Molecular Switches as Building Blocks for DNA and RNA

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