Next Article in Journal
Hydrogels and Their Applications in Targeted Drug Delivery
Next Article in Special Issue
Differentiation between Enamines and Tautomerizable Imines Oxidation Reaction Mechanism using Electron-Vibration-Vibration Two Dimensional Infrared Spectroscopy
Previous Article in Journal
One-Pot Synthesis of Triazolobenzodiazepines Through Decarboxylative [3 + 2] Cycloaddition of Nonstabilized Azomethine Ylides and Cu-Free Click Reactions
Previous Article in Special Issue
Probing Coherent Vibrations of Organic Phosphonate Radical Cations with Femtosecond Time-Resolved Mass Spectrometry
Article Menu
Issue 3 (February-1) cover image

Export Article

Open AccessArticle
Molecules 2019, 24(3), 602; https://doi.org/10.3390/molecules24030602

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
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)
Full-Text   |   PDF [2864 KB, uploaded 10 February 2019]   |  

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 infrared; fluorescence; site-specific spectroscopic probe; 4-cyanoindole; unnatural nucleosides; DNA
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 (CC BY 4.0).
SciFeed

Share & Cite This Article

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.

Show more citation formats Show less citations formats

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

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Molecules EISSN 1420-3049 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top