An interstrand-wedged duplex composed of alternating DNAbase pairs and covalently attached intercalators

Liang, Xingguo; Nishioka, H.; Mochizuki, Toshio; Asanuma, Hiroyuki

doi:10.1039/b915993b

Cited by 19 publications

(27 citation statements)

References 57 publications

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“…As shown in Figure 6 b, an artificial duplex can be built with the ratio of azobenzenes to base pairs being 1:1. [33] The symmetry is greatly improved, although the azobenzene also inserts like a wedge and the structure is locally asymmetric. Interestingly, this artificial duplex is much more stable than the native duplex of the same sequence.…”

Section: Modes Of Duplex Formation Using Model 2-modified Oligonucleomentioning

confidence: 99%

“…[36] The photoregulation efficiency was further improved by using the artificial duplex as shown in Figure 6 b and 6 c. Almost no duplex can form in the cis form, and complete ON-OFF photoregulation became possible. [32,33] When a large substituting group is present in the para position of the distal benzene ring, interestingly, cis-azoben- zene forms a much more stable duplex than the trans form. [11] For a 12 bp duplex, the T m value of the cis form was higher than the trans one by 6.7 8C when Ip-Azo was used ( Figure 8).…”

Section: Modes Of Duplex Formation Using Model 2-modified Oligonucleomentioning

confidence: 99%

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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: Modes Of Duplex Formation Using Model 2-modified Oligonucleomentioning

confidence: 99%

Section: Modes Of Duplex Formation Using Model 2-modified Oligonucleomentioning

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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“…In the I‐W motif, base surrogates are introduced into both strands of the duplex as in 5′‐(NNX) n ‐NN‐3′ and 3′‐(NXN) n +1 ‐5′, resulting in alternating natural base pairs and functional molecules. Unlike the wedge motif, the I‐W motif is symmetric and is remarkably stable due to the stacking interactions between natural bases and the intercalated functional molecules . NMR analysis proved that canonical Watson–Crick base pairs form, each separated by the surrogate in the I‐W motif …”

Section: D‐threoninol As a Scaffold Of A Functional Molecule To Desigmentioning

confidence: 99%

“…Unlike the wedge motif, the I‐W motif is symmetric and is remarkably stable due to the stacking interactions between natural bases and the intercalated functional molecules . NMR analysis proved that canonical Watson–Crick base pairs form, each separated by the surrogate in the I‐W motif …”

Section: D‐threoninol As a Scaffold Of A Functional Molecule To Desigmentioning

confidence: 99%

De NovoDesign of Functional Oligonucleotides with Acyclic Scaffolds

Asanuma

Kashida

2014

The Chemical Record

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In this account, we demonstrate a new methodology for the de novo design of functional oligonucleotides with the acyclic scaffolds threoninol and serinol. Four functional motifs-wedge, interstrand-wedge, dimer, and cluster-have been prepared from natural DNA or RNA and functional base surrogates prepared from d-threoninol. The following applications of these motifs are described: (1) photoregulation of formation and dissociation of a DNA duplex modified with azobenzene, (2) sequence-specific detection of DNA using a fluorescent probe, (3) formation of fluorophore assemblies that mimic quantum dots, (4) improved strand selectivity of siRNA modified with a base surrogate, and (5) in vivo tracing of the RNAi pathway. Finally, we introduce artificial nucleic acids (XNAs) prepared from d-threoninol and serinol functionalized with each of the four nucleobases, which have unique properties compared with other acyclic XNAs. Functional oligonucleotides designed from acyclic scaffolds will be powerful tools for both DNA nanotechnology and biotechnology.

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“…[4,5] No waste was produced because only light, the cleanest source of energy, was used to drive the nanomachine, and the operation could be repeated for many cycles without loss of efficiency.…”

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A Light‐Driven DNA Nanomachine for the Efficient Photoswitching of RNA Digestion

et al. 2010

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Recently, DNA has gained attention as one of the most promising molecules for use in bottom-up nanotechnology. [1] In the last two decades, numerous DNA nanostructures with mechanical functions such as DNA tweezers, DNA walkers, and DNA gears have been constructed. [2,3] However, the practical use of DNA nanotechnology remains a great challenge. One of the problems limiting the application of DNA nanomachines is that oligo-DNAs or other small molecules have to be added as the "fuel" during each operation cycle, and "waste" molecules detrimentally accumulate in the system after several cycles.[3] Previously, we have tried to solve this problem by constructing a model photon-fueled nanomachine involving azobenzene moieties as photoswitches, based on the photoregulation of DNA hybridization. [4,5] No waste was produced because only light, the cleanest source of energy, was used to drive the nanomachine, and the operation could be repeated for many cycles without loss of efficiency.[4a] Efforts should be made to construct nanomachines that work on the single-molecule level, which is highly favorable for nanotechnology applications.[4c] In the present study, we constructed a machinelike photoresponsive DNAzyme that can work at the singlemolecule level (intramolecular nanomachine). The change of its topological conformation can be regulated simply by light irradiation. For the first time, complete ON-OFF photoswitching of RNA digestion has been realized by regulating the higher order structure of a DNAzyme-RNA complex.The 10-23 DNAzyme, captured from a DNA pool of random sequences by in vitro selection, was used here as the model system for constructing an RNA-cleaving nanomachine driven by photons.[6] As shown in Scheme 1 a, a photoresponsive machinelike DNAzyme (Dz7X) was constructed by attaching complementary azobenzene-modified sequences to both ends of the 10-23 DNAzyme. As in our previous design, the two azobenzene-modified sequences were able to form an interstrand-wedged duplex after hybridization. [4c,d] When visible light is applied, the azobenzene residues (X) take the trans form, and a very stable duplex structure involving seven azobenzene units and nine base pairs is formed.[4c] The modified DNAzyme Dz7X can be regarded as a DNA hairpin structure with a big loop (Scheme 1 a). In this case, the RNA-cleavage activity is expected to be suppressed because the topologically constrained higher order structure of the catalytic loop cannot form the correct conformation for cleavage, even when the RNA substrate hybridizes with both arms. On the other hand, when UV light is applied and azobenzene residues take the cis Scheme 1. Design of the machinelike photoresponsive DNAzyme (a) and sequences of DNAzymes and RNA targets used in this study (b). The azobenzene-modified DNAzymes show high activity only when azobenzenes (in red; its structure (X) is also shown) take the cis form after irradiation with UV light. RNA substrate (in green) was labeled with the fluorophore FITC at the 5' end. The sequence of catalytic lo...

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An interstrand-wedged duplex composed of alternating DNAbase pairs and covalently attached intercalators

Cited by 19 publications

References 57 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

De NovoDesign of Functional Oligonucleotides with Acyclic Scaffolds

A Light‐Driven DNA Nanomachine for the Efficient Photoswitching of RNA Digestion

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