Dual door entry to exciplex emission in a chimeric DNA duplex containing non-nucleoside–nucleoside pair

Abstract

Dual door entry to exciplex formation was established in a chimeric DNA duplex wherein a fluorescent non-nucleosidic base surrogate () is paired against a fluorescent nucleosidic base surrogate (). Packing of the nucleobases via intercalative stacking interactions led to an exciplex emission either via FRET from the donor or direct excitation of the FRET acceptor .

Design of “Click” Fluorescent Labeled 2′-deoxyuridines via C5-[4-(2-Propynyl(methyl)amino)]phenyl Acetylene as a Universal Linker: Synthesis, Photophysical Properties, and Interaction with BSA

“…A Sonogashira coupling with trimethylsilylacetylene affording compound 3 underwent propargylation to yield TMS-protected linker unit 4 . The TMS-protected donor acetylene linker was then coupled with bis-TBDMS-protected 5-iodo-2′-deoxyuridine through its free propargyl end via a Sonogashira coupling to get compound 7 . The deprotection of TMS group ultimately afforded the bis-protected 2′-deoxyuridine containing donor-substituted phenylacetylene as universal linker 8 (Scheme ).…”

“…As a part of our continuous research efforts in the design of solvofluorochromic molecules/biomolecular building blocks, , we thought that it would be worthwhile to design dual-emissive modified nucleosides. Based on our experience, literature reports, and wider applicability, we considered design of C-5-labeled uridines as model nucleoside probes useable for DNA analysis in the future. ,, However, there is no report wherein C5-position of 2′-deoxyuridine is linked by an electron-donor unit as a postsynthetically modifiable functional group which effectively can generate a modulated fluorescence property of a fluorophore if attached at the terminus or the terminal alkyne can be reacted with a fluorophoric azide functionality.…”

“…Inspired by our previous result and motivated by the importance of a dual-emitting probe for DNA analysis, we thought that it would be worthwhile to generate a set of fluorescent 2′-deoxyuridine nucleosides which could show interesting intramolecular charge-transfer property or dual emission. We further thought that attaching an electron-donor phenylacetylene unit as a postsynthetically modifiable functional group at the C5-position of 2′-deoxyuridine would be beneficial to generate a set of fluorescent 2′-deoxyuridines with modulated fluorescence property of a fluorophore via azide–alkyne cycloaddition reaction. , Furthermore, the same nucleoside if incorporated into DNA can offer the opportunity of generating fluorescent oligonucleotide probes via post synthetic click reaction with modulated fluorescence properties. Following the aforementioned design logic, herein we report the synthesis of 5-(3-((4-ethynylphenyl)­(methyl)­amino)­propynyl)-2′-deoxyuridine as a possible postsynthetically modifiable nucleoside and its application to generate a set of triazolyl fluorescent 2′-deoxyuridines.…”

Design and Synthesis of Triazolyl‐Donor/Acceptor Unnatural Nucleosides and Oligonucleotide Probes Containing Triazolyl‐Phenanthrene Nucleoside

“…More interestingly, in this chimeric duplex, we have shown that the packing of the nucleobases via intercalative stacking interaction lead to an exciplex emission either via FRET from donor TPhen B Do or direct excitation of FRET acceptor OxoPy S. Therefore, the newly designed chimeric DNA duplex represents a very interesting dual-door entry system for exciplex emission (Fig. 1.32.9; Bag et al, 2014). To the best of our knowledge, this is a highly unique discovery that would open a new dimension for constructing DNA systems useful in devising optoelectronics, and might find application in chemistry, biology, material sciences, and diagnostic technology.…”

“…Therefore, the newly designed chimeric DNA duplex represents a very interesting dual‐door entry system for exciplex emission (Fig. ; Bag et al, ). To the best of our knowledge, this is a highly unique discovery that would open a new dimension for constructing DNA systems useful in devising optoelectronics, and might find application in chemistry, biology, material sciences, and diagnostic technology.…”