4-Cyanoindole-2'-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics

Unnatural nucleosides possessing unique spectroscopic properties that mimic natural nucleobases in both size and chemical structure are ideally suited for spectroscopic measurements of DNA/RNA structure and dynamics in a site-specific manner. However, such unnatural nucleosides are scarce, which pro...

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Bibliographic Details
Published in:Molecules (Basel, Switzerland) Switzerland), 2019-02, Vol.24 (3), p.602
Main Authors: Ahmed, Ismail A, Acharyya, Arusha, Eng, Christina M, Rodgers, Jeffrey M, DeGrado, William F, Jo, Hyunil, Gai, Feng
Format: Article
Language:English
Subjects:
4-cyanoindole
Amino acids
Bases (nucleic acids)
Binding
Deoxyribonucleic acid
DNA
DNA structure
Fluorescence
Fluorescence spectroscopy
Guanine
High-throughput screening
infrared
Nucleosides
Protein interaction
Proteins
Single-stranded DNA
site-specific spectroscopic probe
Solvents
Spectrum analysis
unnatural nucleosides
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Summary:Unnatural nucleosides possessing unique spectroscopic properties that mimic natural nucleobases in both size and chemical structure are ideally suited for spectroscopic measurements of DNA/RNA structure and dynamics in a site-specific manner. However, such unnatural nucleosides are scarce, which prompts us to explore the utility of a recently found unnatural nucleoside, 4-cyanoindole-2'-deoxyribonucleoside (4CNI-NS), as a site-specific spectroscopic probe of DNA. A recent study revealed that 4CNI-NS is a universal nucleobase that maintains the high fluorescence quantum yield of 4-cyanoindole and that among the four natural nucleobases, only guanine can significantly quench its fluorescence. Herein, we further show that the C≡N stretching frequency of 4CNI-NS is sensitive to the local environment, making it a useful site-specific infrared probe of oligonucleotides. In addition, we demonstrate that the fluorescence-quencher pair formed by 4CNI-NS and guanine can be used to quantitatively assess the binding affinity of a single-stranded DNA to the protein system of interest via fluorescence spectroscopy, among other applications. We believe that this fluorescence binding assay is especially useful as its potentiality allows high-throughput screening of DNA⁻protein interactions.
ISSN:1420-3049
1420-3049
DOI:10.3390/molecules24030602