ArticleNucleic acids research2005
Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Hybridization Probes Featuring a Pyrenylpyridine C-Nucleoside or Its Palladacycle as a Fluorescent Sensor Moiety.Chembiochem : a European journal of chemical biology · 2025Article
- Significant Broad-Spectrum Antiviral Activity of Bi121 against Different Variants of SARS-CoV-2.Viruses · 2023Article
- Article
- Covalently attached intercalators restore duplex stability and splice-switching activity to triazole-modified oligonucleotides.RSC chemical biology · 2022Article
- Strong π-stacking causes unusually large anisotropic thermal expansion and thermochromism.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry.Nucleic acids research · 2021Article
- 5-Aza-7-deazaguanine-Isoguanine and Guanine-Isoguanine Base Pairs in Watson-Crick DNA: The Impact of Purine Tracts, Clickable Dendritic Side Chains, and Pyrene Adducts.Chemistry (Weinheim an der Bergstrasse, Germany) · 2021Article
- Reductive Charge Transfer through an RNA Aptamer.Angewandte Chemie (International ed. in English) · 2020Article
- Synthesis and biophysical characterization of oligonucleotides modified with O2'-alkylated RNA monomers featuring substituted pyrene moieties.Organic & biomolecular chemistry · 2019Article
- A fluorescent methylation-switchable probe for highly sensitive analysis of FTOChemical science · 2018Article
- Detection of cofilin mRNA by hybridization-sensitive double-stranded fluorescent probes.RSC advances · 2018Article
- Fluorogenic PNA probes.Beilstein journal of organic chemistry · 2018Review
- Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides.Molecules (Basel, Switzerland) · 2017Review
- 25 years and still going strong: 2'-O-(pyren-1-yl)methylribonucleotides - versatile building blocks for applications in molecular biology, diagnostics and materials science.Organic & biomolecular chemistry · 2017Review
- Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2'-triphenylene- and coronene-functionalized RNA monomers.Organic & biomolecular chemistry · 2017Article
- Merging Two Strategies for Mixed-Sequence Recognition of Double-Stranded DNA: Pseudocomplementary Invader Probes.The Journal of organic chemistry · 2016Article
- Synthesis and characterization of oligodeoxyribonucleotides modified with 2'-thio-2'-deoxy-2'-S-(pyren-1-yl)methyluridine.Bioorganic & medicinal chemistry letters · 2015Article
- Mixed-Sequence Recognition of Double-Stranded DNA Using Enzymatically Stable Phosphorothioate Invader Probes.Molecules (Basel, Switzerland) · 2015Article
- Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2'-alkylated RNA monomers.Organic & biomolecular chemistry · 2014Article
- DFT and MD study of the divalent-cation-mediated interaction of ochratoxin A with DNA nucleosides.Journal of molecular modeling · 2014Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Through binding and fluorescence studies of oligonucleotides covalently attached to a pyrene group via one carbon linker at the sugar residue, we previously found that pyrene-modified RNA oligonucleotides do not emit well in the single-stranded form, yet the attached pyrene emits with a significantly high quantum yield upon binding to a complementary RNA strand. In sharp contrast, similarly modified pyrene-DNA probes exhibit very weak fluorescence both in the double-stranded and single-stranded forms. The pyrene-modified RNA oligonucleotides therefore provide a useful tool for monitoring RNA hybridization. The purpose of this paper is to present the structural basis for the different fluorescence properties of pyrene-modified RNA/RNA and pyrene-modified DNA/DNA duplexes. The results of absorption, fluorescence anisotropy and circular dichroism studies all consistently indicated that the pyrene attached to the RNA duplex is located outside of the duplex, whereas the pyrene incorporated into the DNA duplex intercalates into the double helix. (1)H NMR measurements unambiguously confirmed that the pyrene attached to the DNA duplex indeed intercalates between the base pairs of the duplex. Molecular dynamics simulations support these differences in the local structural elements around the pyrene between the pyrene-RNA/RNA and the pyrene-DNA/DNA duplexes.
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