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Open AccessArticle

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

1
Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
2
Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
3
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Chong Fang
Molecules 2019, 24(3), 602; https://doi.org/10.3390/molecules24030602
Received: 20 December 2018 / Revised: 26 January 2019 / Accepted: 5 February 2019 / Published: 8 February 2019
(This article belongs to the Special Issue Vibrational Probes of Biomolecular 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 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. View Full-Text
Keywords: infrared; fluorescence; site-specific spectroscopic probe; 4-cyanoindole; unnatural nucleosides; DNA infrared; fluorescence; site-specific spectroscopic probe; 4-cyanoindole; unnatural nucleosides; DNA
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Ahmed, I.A.; Acharyya, A.; Eng, C.M.; Rodgers, J.M.; DeGrado, W.F.; Jo, H.; Gai, F. 4-Cyanoindole-2′-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics. Molecules 2019, 24, 602.

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