Insulator Base Pairs for Lighting‐up Perylenediimide in a DNA Duplex

Kashida, Hiromu; Sekiguchi, Koji; Asanuma, Hiroyuki

doi:10.1002/chem.201001638

Cited by 28 publications

(24 citation statements)

References 25 publications

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“…Inspired by this interaction we decided to study the possible formation of glucosenucleobase pairs.S ince monosaccharides can stack on DNA bases and possess OH groups capable of making hydrogen bonds at the edge of their coinlike structure,like natural bases (Figure 2a), we placed ap otential glucose-nucleobase pair inside aD NA double helix to investigate its properties ( Figure 2b). [6] Glucose (glc) was linked to the phosphodiester backbone of DNAt hrough af lexible glycerol linker through its anomeric position. [6] Glucose (glc) was linked to the phosphodiester backbone of DNAt hrough af lexible glycerol linker through its anomeric position.…”

supporting

confidence: 88%

“…[4] Stacking of sugars on top of the guanine tetrad of aD NA G-quadruplex was also characterized. [6] Figure 1. a) Structure of paromomycin. [3] Tw oh ydrogen bonds are formed between ring Iofparomomycin and A1408.…”

mentioning

confidence: 99%

“…[3] Tw oh ydrogen bonds are formed between ring Iofparomomycin and A1408. [6] Figure 1. a) Structure of paromomycin. This model system also allows us to study possible sugar-sugar pairs.T he only non-aromatic nucleobases reported previously are Leumanns phenyl cyclohexyl interstrand base [5] and Kashidas isopropylcyclohexane and methylcyclohexane DNAb ase insulators.…”

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confidence: 99%

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Glucose–Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA

et al. 2016

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Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside-RNA recognition, glucose-nucleobase pairs have been examined. Deoxyoligonucleotides with a 6-deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6-Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6-deoxyglucose-guanine pair closely resembles a purine-pyrimidine geometry. Quantum chemical calculations indicate that glucose-purine pairs are as stable as a natural T-A pair.

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confidence: 88%

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confidence: 99%

mentioning

confidence: 99%

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Glucose–Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA

et al. 2016

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“…However another polyaromatic molecule, perylene, is currently an object of increasing interest as a highly sensitive dye to measure local microenvironment changes within nucleic acids, e.g. those caused by hybridization [20][21][22] . Fluorescence of perylene is typically observed at 450-500 nm and its excited lifetime is relatively short (4-5 ns) while the fluorescence quantum yield is very high (0.5-1.0) 23 .…”

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confidence: 99%

Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

Astakhova

Kumar

Wengel

2011

Collect. Czech. Chem. Commun.

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Dedicated to Professor Antonín Holý on the occasion of his 75th birthday in recognition of his outstanding contributions to the area of nucleic acid chemistry.Herein, a novel fluorescent nucleotide analogue, perylene-2′-amino-α-L-LNA, has been prepared and studied within synthetic oligonucleotides of different sequences. The phosphoramidite reagent was synthesized in 85% overall yield starting from 2′-amino-α-L-LNA nucleoside. Incorporation efficiency of the resulting perylene-2′-amino-α-L-LNA monomer (T*) into synthetic oligonucleotides was significantly improved by replacement of the typically used 1H-tetrazole activator with pyridine hydrochloride. Generally, oligonucleotides containing monomer T* showed high binding affinity towards complementary DNA and RNA targets, batochromically shifted excitation/emission wavelengths with respect to the often applied polyaromatic hydrocarbon pyrene, high fluorescent quantum yields and very low target detection limits (5-10 nM). Fluorescence of single stranded LNA/DNA mixmer oligonucleotide having two incorporations of monomers T* was quenched (quantum yield Φ F = 0.21) relative to duplexes of this probe with complementary DNA and RNA (Φ F = 0.42 and 0.35, respectively). On the contrary, a strong fluorescence quenching upon target binding was demonstrated by two short oligonucleotides of analogues sequences containing monomers T* at 5′-and 3′-terminal positions. We explain the hybridization-induced light-up effect observed for double-labeled probe by a reduction of fluorescence quenching due to precise positioning of the fluorophores within the double-stranded complexes. Furthermore, we propose that a covalent link between two T* monomers in the double-labeled probe provides a remarkable degree of rigidity in the double helix which enforces positioning of the bulky perylene moieties in the nonpolar groove resulting in reduced fluorescence quenching.

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“…Wesentlich für diese Anwendung dürfte die Tatsache sein, dass die Molekülgrçße eines PBI in etwa derjenigen eines Basenpaares entspricht, und dass es somit auch eine ähnlich starke p-p-Wechselwirkung zu benachbarten Basenpaaren in DNA aufweisen dürfte. [87] Ein zweiter Ansatz basiert auf der Einführung elektronenschiebender Substituenten in die PBI-Buchtpositionen. Damit dies auch in einer internen Position mçglich ist, muss an entsprechender Stelle im Gegenstrang ein basenfreies 2'-Desoxyribofuranosid-Derivat eingebaut sein.…”

Section: Chemieunclassified

Molekülverbände von Perylenbisimid‐Farbstoffen in Wasser

2012

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Perylenbisimide zählen zu den bedeutendsten funktionellen Farbstoffen mit vielfältigen Anwendungsmöglichkeiten. Aufgrund ihrer chemischen Robustheit, Photostabilität und herausragenden optischen und elektronischen Eigenschaften wurden sie als Pigmentfarbstoffe, Fluoreszenzsonden sowie n‐Halbleiter in der organischen Elektronik und Photovoltaik eingesetzt. Das ausgedehnte quadrupolare π‐System dieser Farbstoffklasse ermöglichte außerdem die Herstellung zahlreicher supramolekularer Architekturen mit faszinierenden photophysikalischen Eigenschaften. Jedoch blieb der supramolekulare Ansatz zur Bildung von Perylenbisimid‐Molekülverbänden größtenteils organischen Medien vorbehalten. Erfreulicherweise gab es in den letzten Jahren beachtliche Bemühungen zur Entwicklung von wasserlöslichen Perylenbisimiden und deren Anwendungen in wässrigen Medien. Dieser Aufsatz gibt einen aktuellen Überblick über die Selbstorganisation von Perylenbisimiden durch π‐π‐Wechselwirkung im wässrigen Medium. Synthetische Strategien zur Herstellung von wasserlöslichen Perylenbisimiden und der Einfluss des Wassers auf die π‐π‐Stapelung von Perylenbisimiden, sowie daraus resultierende Anwendungen werden eingehend diskutiert.

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Insulator Base Pairs for Lighting‐up Perylenediimide in a DNA Duplex

Cited by 28 publications

References 25 publications

Glucose–Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA

Glucose–Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA

Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

Molekülverbände von Perylenbisimid‐Farbstoffen in Wasser

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