A 2′,4′-Bridged Nucleic Acid Containing 2-Pyridone as a Nucleobase: Efficient Recognition of a C⋅G Interruption by Triplex Formation with a Pyrimidine Motif

Obika, Satoshi; Hari, Yoshiyuki; Sekiguchi, Mitsuaki; Imanishi, Takeshi

doi:10.1002/1521-3773(20010601)40:11<2079::aid-anie2079>3.0.co;2-z

Cited by 65 publications

(17 citation statements)

References 14 publications

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“…We designed a simple 2-pyridone (PD) as a nucleobase without the functional groups either of T or of C to recognize an AT or a GC base pair, respectively. [49] The presence of the 5-methyl congener ( Me P B , Figure 16) in a TFO gave a triplex formation result similar to that seen with P B . Moreover, a 2-pyridone moiety attached to a 2Ј,4Ј-BNA/LNA (P B , Figure 16) led to an increased T m value of 9°C without loss in CG selectivity (ΔT m Ն 9°C).…”

Section: Approaches Based On a Parallel Motifmentioning

confidence: 61%

“…[48] Of these, 2APm formed the most stable triplet with a CG base pair at pH 7.0. [49][50][51] In UV melting experiments at physiological pH, the affinity and selectivity of PD towards a CG base pair appeared to be comparable with those of 4H T, although the CG recognition scheme for PD (Figure 15) was different from the 4H T-CG triplet as shown in Figure 13. We designed a simple 2-pyridone (PD) as a nucleobase without the functional groups either of T or of C to recognize an AT or a GC base pair, respectively.…”

Section: Approaches Based On a Parallel Motifmentioning

confidence: 99%

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Towards the Sequence‐Selective Recognition of Double‐Stranded DNA Containing Pyrimidine‐Purine Interruptions by Triplex‐Forming Oligonucleotides

2012

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Triplex formation with double‐stranded DNA (dsDNA) by oligonucleotides has potential for applications in attractive technologies such as gene therapy and genetic diagnosis. However, triplex‐forming oligonucleotides (TFOs) can only recognize homopurine strands in homopurine‐homopyrimidine regions in dsDNA, either through Hoogsteen or through reverse‐Hoogsteen hydrogen bonds. A straightforward and powerful approach to overcoming this sequence limitation is the development of artificial nucleic acids capable of recognizing specific pyrimidine‐purine interruptions (i.e., a CG or TA base pair) in triplex formation. This review describes artificial nucleic acids, especially those containing non‐natural nucleobases, developed to recognize CG or TA base pairs in dsDNA targets.

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Section: Approaches Based On a Parallel Motifmentioning

confidence: 61%

Section: Approaches Based On a Parallel Motifmentioning

confidence: 99%

Towards the Sequence‐Selective Recognition of Double‐Stranded DNA Containing Pyrimidine‐Purine Interruptions by Triplex‐Forming Oligonucleotides

2012

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“…One promising approach reported was to connect the 2′‐ and 4′‐positions of the sugar structure by a 2′ O ,4′ C ‐methylene bridge, which could fix the sugar moiety in a locked N‐type conformation. The resulting oligonucleotide analogs bearing 2,5‐anhydro furanose structures were called 2′,4′‐BNA/LNA (Scheme ) and showed high binding affinity toward dsDNA targets in a sequence‐specific manner. In the reported literature, the 2′ O ,4′ C ‐methylene bridge was established in good yield by nucleophilic attack from the C2′‐hydroxyl to the sulfonated C5′‐position under alkaline conditions as shown in Scheme .…”

Section: 5‐anhydro Furanosementioning

confidence: 99%

The Construction of Anhydro Monosaccharides

Xie

Lin

et al. 2016

Asian J Org Chem

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Anhydro monosaccharide is as pecific and distinctive category of carbohydrates, which is found in many naturally deriveda nd artificial bioactive substrates. In the field of organic chemistry,s ome anhydro sugars can be used as common synthons to construct different carbohydrate structures. The development of efficient methodologies for the constructiono fv ariousa nhydro sugar fragments is very important in carbohydrate chemistry,w hich has attracted considerable attention in the past few years. This reviewm ainly covers the development of new synthetic methods since 2000 and gives an overview of the development in the formation of anhydro monosaccharide structures. It systematically summarizes all methodst oe stablish an intramolecular ether bridge in furanose and pyranose structures, which are the mostc ommonly used monosaccharide fragments in carbohydrate chemistry.

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“…Recently, interesting nucleoside analogs have been reported from Leumann's [19,20] and Imanishi's groups [21,22], which stabilize parallel-triplexes by forming one hydrogen bond to the cytosine base at a C-G interrupting site. The bicyclic sugar structure of Imanishi's nucleoside analogs (BNA or LNA) is thought to bring additional stabilizing effect (see Chapter written by T. Imanishi).…”

Section: Molecular Design Of Nucleoside Analogs To Expand Recognitionmentioning

confidence: 99%

Molecular Design for Specific Recognition and Reaction in Genome-Targeting Chemistry

Sasaki¹,

Nagatsugi²

2005

Frontiers in Organic Chemistry

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Molecules that can target DNA or RNA with high efficiency and specificity are of great interest because of potential applications to modulation of gene expression at a specific site. Our approach in genome-targeting chemistry has been focused on development of reactive molecules with high base-as well as sequence selectivity. This paper summarizes our contributions in this field. At first, a general concept of reactive molecules in genome-targeting chemistry is introduced. In the following section, molecular design to achieve specific and efficient reactions in the living system is described. Two new reactive molecules, 2-amino-6-vinylpurine derivative as an efficient cross-linking agent, and the Snitroso-6-thioguanosine as a selective S to N nitoroso group transfer agent are summarized. These two molecules demonstrate successful examples of reactive agents that are activated only in the complementary hybrids. In the third section, new nucleoside analogs to expand recognition codes of triplex formation are discussed. We have recently developed non-natural nucleoside analogs (W-shaped nucleoside analog: WNA) having a heterocyclic ring as a recognition unit and an aromatic ring as a stacking part on the bicyclo[3.3.0]octane skeleton. It has been shown that the two analogs, WNA-T with a thymine and WNA-C with a cytosine, exhibit stable formation of non-natural triplexes containing a TA and a CG interrupting site with high stability, respectively. These new genome-targeting molecules will be applied to artificial modulation of gene expression in vitro as well as in vivo.

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A 2′,4′-Bridged Nucleic Acid Containing 2-Pyridone as a Nucleobase: Efficient Recognition of a C⋅G Interruption by Triplex Formation with a Pyrimidine Motif

Cited by 65 publications

References 14 publications

Towards the Sequence‐Selective Recognition of Double‐Stranded DNA Containing Pyrimidine‐Purine Interruptions by Triplex‐Forming Oligonucleotides

Towards the Sequence‐Selective Recognition of Double‐Stranded DNA Containing Pyrimidine‐Purine Interruptions by Triplex‐Forming Oligonucleotides

The Construction of Anhydro Monosaccharides

Molecular Design for Specific Recognition and Reaction in Genome-Targeting Chemistry

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