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

Ahmed, Ismail A.; Acharyya, Arusha; Eng, Christina M.; Rodgers, Jeffrey M.; DeGrado, William F.; Jo, Hyunil; Gai, Feng

doi:10.3390/molecules24030602

Submit to this Journal Review for this Journal Edit a Special Issue

Article Menu

...

Open AccessArticle

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

^1,†,

^2,†,

²,

³,

^3,*

and

Feng Gai

^2,*

Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA

Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA

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)

View Full-Text Download PDF

Browse Figures

Citation Export

Abstract

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

▼ Show Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Share and Cite

MDPI and ACS Style

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. https://doi.org/10.3390/molecules24030602

AMA Style

Ahmed IA, Acharyya A, Eng CM, Rodgers JM, DeGrado WF, Jo H, Gai F. 4-Cyanoindole-2′-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics. Molecules. 2019; 24(3):602. https://doi.org/10.3390/molecules24030602

Chicago/Turabian Style

Ahmed, Ismail A., Arusha Acharyya, Christina M. Eng, Jeffrey M. Rodgers, William F. DeGrado, Hyunil Jo, and Feng Gai. 2019. "4-Cyanoindole-2′-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics" Molecules 24, no. 3: 602. https://doi.org/10.3390/molecules24030602

Find Other Styles

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Metrics

Abstract views Pdf views Html views

Article Menu

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

Abstract

Share and Cite

Article Metrics

Article Access Statistics

Article Access Map by Country/Region

Further Information

Guidelines

MDPI Initiatives

Follow MDPI