Synthesis of carboxamide linked dimers, αT*αT and αUCl*αT. — duplex and triplex stabilities of the corresponding α oligodeoxynucleotides

Aleem, Abdel Aleem H. Abdel; Larsen, Erik; Pedersen, Erik B.

doi:10.1016/0040-4020(95)00404-v

Cited by 4 publications

(1 citation statement)

References 18 publications

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“…The internal acridine leads to a better stabilization of complexes (Δ T m = +13 °C) than an acridine covalently linked to the 5‘-end of the oligonucleotide (Δ T m = +8 °C), suggesting the existence of a preferential site of interaction/intercalation for the acridine ring at the three-way junction. The binding of oligonucleotides to hairpin-containing nucleic acids could also be stabilized by insertion of modified bases such as a 5-methyl- N 4 -(1-pyrenylmethyl)cytidine or a 2‘-deoxy-5-methyl- N 4 -(4-phenoxyphenyl)cytidine instead of an acridine ring ( − ).…”

Section: Discussionmentioning

confidence: 99%

Recognition of Hairpin-Containing Single-Stranded DNA by Oligonucleotides Containing Internal Acridine Derivatives

François

Hélène

1999

Bioconjugate Chem.

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Oligodeoxynucleotides with an internal intercalating agent have been targeted to single-stranded sequences containing hairpin structures. The oligonucleotide binds to nonadjacent single-stranded sequences on both sides of the hairpin structure in such a way as to form a three-way junction. The acridine derivative is inserted at a position that allows it to interact with the three-way junction. The melting temperature (Tm) of complexes formed between the hairpin-containing target and oligonucleotides containing one internal acridine derivative was higher than that obtained with the same target and an unmodified oligonucleotide (DeltaTm = +13 degrees C). The internal acridine provided the oligonucleotide with a higher affinity than covalent attachment to the 5' end. Oligonucleotides could also be designed to recognize a hairpin-containing single-stranded nucleic acid by formation of Watson-Crick hydrogen bonds with a single-stranded part and Hoogsteen hydrogen bonds with the stem of the hairpin. An internal acridine derivative was introduced at the junction between the two domains, the double helix domain with Watson-Crick base pairs and the triple helix domain involving Hoogsteen base triplets in the major groove of the hairpin stem. Oligonucleotides with an internal acridine or an acridine at their 5' end have similar binding affinities for the stem-loop-containing target. The bis-modified oligonucleotide containing two acridines, one at the 5' end and one at an internal site, did not exhibit a higher affinity than the oligonucleotides with only one intercalating agent. The design of oligonucleotides with an internal intercalating agent might be of interest to control gene expression through recognition of secondary structures in single-stranded targets.

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Section: Discussionmentioning

confidence: 99%

Recognition of Hairpin-Containing Single-Stranded DNA by Oligonucleotides Containing Internal Acridine Derivatives

François

Hélène

1999

Bioconjugate Chem.

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From Anionic to Cationic α‐Anomeric Oligodeoxynucleotides

Morvan

Debart

2010

Chemistry & Biodiversity

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Donor/acceptor chromophores-decorated triazolyl unnatural nucleosides: synthesis, photophysical properties and study of interaction with BSA

et al. 2016

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Much effort has been put forth to develop unnatural, stable, hydrophobic base pairs with orthogonal recognition properties and study their effect on DNA duplex stabilisation. Our continuous efforts on the design of fluorescent unnatural biomolecular building blocks lead us to the synthesis of some triazolyl donor/acceptor unnatural nucleosides via an azide-alkyne 1,3-dipolar cycloaddition reaction as a key step, which we want to report herein. We have studied their photophysical properties and found interesting solvatochromic fluorescence for two of the nucleosides. Photophysical interactions among two donor-acceptor β-nucleosides as well as a pair of α/β-nucleosides have also been evaluated. Furthermore, we have exploited one of the fluorescent nucleosides in studying its interaction with BSA with the help of UV-visible and steady state fluorescence techniques. Our design concept is based on the hypothesis that a pair of such donor/acceptor nucleosides might be involved in π-stacking as well as in photophysical interactions, leading to stabilization of the DNA duplex if such nucleosides can be incorporated into short oligonucleotide sequences. Therefore, the designed bases may find application in biophysical studies in the context of DNA.

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Synthesis of carboxamide linked dimers, αTαT and αUClαT. — duplex and triplex stabilities of the corresponding α oligodeoxynucleotides

Cited by 4 publications

References 18 publications

Recognition of Hairpin-Containing Single-Stranded DNA by Oligonucleotides Containing Internal Acridine Derivatives

Recognition of Hairpin-Containing Single-Stranded DNA by Oligonucleotides Containing Internal Acridine Derivatives

From Anionic to Cationic α‐Anomeric Oligodeoxynucleotides

Donor/acceptor chromophores-decorated triazolyl unnatural nucleosides: synthesis, photophysical properties and study of interaction with BSA

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