Enantioselective Incorporation of Azobenzenes into Oligodeoxyribonucleotide for Effective Photoregulation of Duplex Formation

Asanuma, Hiroyuki; Takarada, Tohru; Yoshida, Takayuki; Tamaru, Daisuke; Liang, Xingguo; Komiyama, Makoto

doi:10.1002/1521-3773(20010716)40:14<2671::aid-anie2671>3.0.co;2-z

Cited by 131 publications

(96 citation statements)

References 17 publications

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“…[13][14][15] A synthetically simpler approach is to incorporate the sensor unit into the oligonucleotide backbone. 15,16 This has been successfully achieved with pyrene 17 for the purpose of sensing using excimer formation, azobenzenes for photoswitching 18,19 and acridine for site selective RNA activation 20 and electron transfer studies. 21 However, of the many modified oligonucleotides that have been reported for fluorescence sensing purposes, generally they are limited in their ability to differentiate between all of the possible base-pairing partners.…”

contrasting

confidence: 99%

Anthracene-modified oligonucleotides as fluorescent DNA mismatch sensors: discrimination between various base-pair mismatches

Duprey

Bassani

Hyde

et al. 2011

Supramolecular Chemistry

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contrasting

confidence: 99%

Anthracene-modified oligonucleotides as fluorescent DNA mismatch sensors: discrimination between various base-pair mismatches

Duprey

Bassani

Hyde

et al. 2011

Supramolecular Chemistry

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“…We also believe that it is a key component to the functionalization of probes engineered to target thrombin. This conclusion is based on the work that has been done on synthesizing azobenzene phosphoramidite monomers and the fact that the NMR structures of both cis-and trans-states have been described (26)(27). Most recently, a full thermodynamic description based on nearestneighbor models of DNA duplex formation has been presented and successfully used to predict melting temperatures of azobenzeneincorporated DNA duplexes (29).…”

mentioning

confidence: 99%

Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe

Kim

Phillips

Liu

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

145

116

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The ability to inhibit an enzyme in a specific tissue with high spatial resolution combined with a readily available antidote should find many biomedical applications. We have accomplished this by taking advantage of the cis-trans photoisomerization of azobenzene molecules. Specifically, we positioned azobenzene moieties within the DNA sequence complementary to a 15-base-long thrombin aptamer and then linked the azobenzene-modified cDNA to the aptamer by a polyethylene glycol (PEG) linker to make a unimolecular conjugate. During the photoisomerization of azobenzene by visible light, the inhibition of thrombin is disabled because the probe hybridizes with the cDNA in the trans-azobenzene conformation so that the aptamer cannot bind its target thrombin. However, when UV light is applied, melting of the hairpin structure (duplex) is induced via trans-to-cis conversion, thereby changing conformation of the aptamer and making the aptamer free to bind to and inhibit its target thrombin. By using standard clotting assays, we measured the IC 200 of various probe designs in both states and concluded the feasibility of using photon energy to temporally and spatially regulate these enzymatic reactions. Thus, we can report the development of DNA probes in the form of photon-controllable (thrombin) inhibitors, termed PCIs, and we expect that this approach will be highly beneficial in future biomedical and pharmaceutical applications.anticoagulation ͉ aptamer ͉ enzyme inhibitor ͉ photo controllable ͉ thrombine O ver the last decade, extensive research has been devoted to the study of phototransformable molecules based on photochromism chemistry. This science has been applied to photooptical technology and such photomodulated devices as eyeglasses called Transitions (1-4). A photochromic compound has 2 molecular states: stable and relatively unstable. The 2 states are interchangeable by the effect of irradiation using different wavelengths and differ from one another in terms of both physical and chemical properties. The photoconversion mechanism can largely be divided into 3 transformation types: photochromic tautomerism, cis-trans isomerization, and photocyclization. Briefly, photoisomerization is a process in which molecular structural change between isomers is caused by photoexcitation. Therefore, because isomerization causes a conformational change that can change the overall structure of a molecule, cis-trans isomerization is an intriguing mechanism that can be used to regulate mechanical devices and biological reactions (5-8).As one of the most popular phototransformable molecules in use today, azobenzene and its derivatives belong to the cis-trans isomerization category and are composed of 2 phenyl rings linked by a NAN double bond (Fig. 1) (9). The 2 isomers can be switched with particular wavelengths of light: UV light at 365 nm, corresponding to the trans-to-cis conversion, and visible light at 465 nm, corresponding to the cis-to-trans isomerization. There are reports that demonstrate the possible applications of su...

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“…Threoninol has been used to introduce several units of Methyl Red moieties [10], photoactive azobenzenes [11,12], acridine [13], pyrene and perylene [14], tetrathiofulvalene [15] and DNA-binding drugs [8,9] in oligonucleotides. This compound can be obtained enantiomerically pure from commercial sources and have two hydroxyl groups (one primary and one secondary) and one amino group.…”

Section: Oligonucleotide Synthesismentioning

confidence: 99%

Synthesis and structural properties of oligonucleotides covalently linked to acridine and quindoline derivatives through a threoninol linker

Aviñó

Mazzini

Ferreira

et al. 2010

Bioorganic & Medicinal Chemistry

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Oligonucleotide conjugates containing acridine and quindoline derivatives linked through a threoninol molecule were synthesized. We showed that these conjugates formed duplexes and quadruplexes with higher thermal stability than the corresponding unmodified oligonucleotides.When acridine is located in the middle of the sequence, DNA duplexes have a similar stability independently of the natural base present in front of acridine. Self-complementary oligonucleotides and thrombin binding aptamers (TBA) carrying the acridine and quindoline molecules are studied by NMR.

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Enantioselective Incorporation of Azobenzenes into Oligodeoxyribonucleotide for Effective Photoregulation of Duplex Formation

Cited by 131 publications

References 17 publications

Anthracene-modified oligonucleotides as fluorescent DNA mismatch sensors: discrimination between various base-pair mismatches

Anthracene-modified oligonucleotides as fluorescent DNA mismatch sensors: discrimination between various base-pair mismatches

Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe

Synthesis and structural properties of oligonucleotides covalently linked to acridine and quindoline derivatives through a threoninol linker

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