Site-Selective RNA Cleavage by DNA Bearing a Base Pair-Mimic Nucleoside

Nakano, Shu‐ichi; Uotani, Yuuki; Uenishi, Kazuya; Fujii, Masayuki; Sugimoto, Naoki

doi:10.1021/ja045445s

Cited by 29 publications

(27 citation statements)

References 16 publications

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“…The sugar-phosphate backbone of RNA perturbed due to the unstacking conformation can be preferentially hydrolyzed as a consequence of specific base catalysis at the site adopting the in-line attack arrangement [52, 53]. Indeed, we found highly site-selective cleavage at any ribonucleotide base opposite A X in an RNA/DNA duplex [54]. The RNA-hydrolyzing activity agrees with the base flipping model in which A X forces the opposite base to flip out in an unstacked position (Figure 6(c)).…”

Section: The Base Pair Analogs Of a Base Pair-mimic Structurementioning

confidence: 99%

Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

Nakano

Fujii

Sugimoto

2011

Journal of Nucleic Acids

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Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

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Section: The Base Pair Analogs Of a Base Pair-mimic Structurementioning

confidence: 99%

Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

Nakano

Fujii

Sugimoto

2011

Journal of Nucleic Acids

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“…The T m (melting temperature) values among the natural duplexes containing A/A, A/G, A/C, and A/U pairs differed by 12.9°C. 31 The large difference was due to the formation of A/U WatsonÍCrick base pairs and single mismatch pairs of A/A, A/G, and A/C in the middle of the RNA/DNA duplex. In contrast, the T m values of duplexes containing A phe in place of A to form A phe /A, A phe /G, A phe /C, and A phe /U pairs were almost the same (only 0.8°C differences in their T m values).…”

Section: õ3mentioning

confidence: 99%

“…We observed that the RNA strand was efficiently hydrolyzed on the 3¤-side of the ribonucleotide opposite A phe . 31 Importantly, the RNA cleavage was highly site-selective, and any RNA sequence was cleaved when hybridizing with DNA containing A phe . The RNA-hydrolyzing activity suggests that A phe stacks into the duplex stably and rigidly and that the ribonucleotide opposite A phe flips into an unstacked position regardless of the nucleotide species (Figure 6c).…”

Section: õ3mentioning

confidence: 99%

Designable DNA Functions toward New Nanobiotechnology

Sugimoto¹

2009

Bulletin of the Chemical Society of Japan

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DNA has many properties that cannot be attained with other molecules. The ability of DNA to form base pairing and its structural polymorphism allow the formation of distinct secondary and tertiary structures and may have further catalytic or aptamer function. It is also of great advantage that the base pairing of a short oligonucleotide sequence can be well predicted and designed with the thermodynamic parameters of WatsonÍCrick base pairs, mismatch pairs, and noncanonical base pairs based on the nearest-neighbor model. We have investigated the thermodynamics of various types of oligonucleotide structures, and obtained the nearest-neighbor parameters for WatsonÍCrick base pair formations and fundamental information regarding the nucleotide interactions. The data of the DNA interaction energy were also applied for molecular design of a DNA logic gate and DNA nanowire. I will further discuss the importance of quantitative data of DNA interaction energy toward the rational design of artificial DNAs carried out by our laboratory, such as base pairmimic nucleosides and DNA containing bipyridine units, useful as nanobiodevices and nanobiomaterial.1. Extraction of "Quantity" from the Quality of DNA 1.1 DNA toward the Nanobio-Research Field. DNA has excellent properties applied to technology uses, such as the recognition of target sequences, self-assembly into defined structures, and catalytic or aptamer functions. Oligonucleotides have been examined for constructing functional molecules, because they can be synthesized by an automated synthesizer and are available commercially at a relatively low cost. Association of oligonucleotides further constructs large-sized complexes and their noncovalent interaction has an advantage of reversible assembly. Moreover, conjugation of a DNA strand with other functional materials including other biomolecules, fluorescent dyes, and metal plate surfaces or nanoparticles allows an expansion of the DNA function. Therefore, DNA is one of the most promising nanobiomaterials suitable as nanoscale materials, nano-sized devices, and medicinal and therapeutic uses. In fact, development of nanobiomaterials that apply the properties of DNA to nanotechnology have become of broader interest over the past several years. 1Í4The most important property of DNA is the ability to form base pairing mediated by interbase hydrogen bonds. The major structure of DNA is the double helical structure of WatsonÍ Crick base pairs. Figure 1 shows the famous WatsonÍCrick base pairs, of which the purine (A or G) and pyrimidine (C, T, or U) nucleotides associate with each other in accordance to the geometry of hydrogen donors and acceptors on the bases. All the nucleotide bases adopt an anti configuration at the glycosidic bond in a right-handed antiparallel-stranded duplex, and the structural isomorphism among A/T, A/U, and G/C base pairs ensures the distance between glycosidic bonds of approximately 1 nm. The base stacking interaction is important for the integrity of the duplex. The stacking interaction does not ...

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“…Bulky non-natural nucleobase (A-T base-pair mimic) was introduced to sequence-recognizing DNA. The phosphodiester linkage of RNA substrate, which is adjacent to the nucleobase opposite to the mimic, was cleaved by Mg(II) [54]. It would be also possible that, in some of previously reported artificial ribonucleases, the target phosphodiester linkages were in fact activated by non-covalent interactions of substrate RNA with the additives and this "pinpoint activation" exerted notable effects on the site-selective RNA scission.…”

Section: Other Non-covalent Systems Employing "Pinpoint Activator"mentioning

confidence: 99%

Site-Selective Artificial Ribonucleases and their Applications

Kuzuya¹,

Komiyama

2007

COC

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Recent developments in artificial enzymes for site-selective scission of RNA have been reviewed, and their advantages over ribozymes are discussed. Most of previous reports involve covalent fixation of molecular scissors to sequence-recognizing moieties. However, non-covalent strategy, in which these two components are never covalently bound each other, has made remarkable progresses. When oligonucleotide bearing an acridine (site-selective activator) forms duplex with RNA substrate, the phosphodiester linkage of the RNA in front of the acridine is selectively activated and hydrolyzed by various metal ions (e.g., Lu(III). These non-covalent artificial ribonucleases are simple enough to be used for various more complicated systems. For example, tandem activator for clipping of desired fragment from long RNA substrate is obtained by attaching two acridines to an oligonucleotide. By analyzing the resultant RNA fragment with MALDI-TOFMS, the RNA substrate is accurately genotyped in terms of both single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (Indels).

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Site-Selective RNA Cleavage by DNA Bearing a Base Pair-Mimic Nucleoside

Cited by 29 publications

References 16 publications

Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

Designable DNA Functions toward New Nanobiotechnology

Site-Selective Artificial Ribonucleases and their Applications

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