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Issue 31, 2015
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Photophysical and structural investigation of a PyA-modified adenine cluster: its potential use for fluorescent DNA probes exhibiting distinct emission color changes

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Abstract

In this study, we found a PyA-modified adenine cluster (A-cluster), a minimum fluorescent unit for significant emission wavelength changes, and investigated its photophysical and structural properties. The basic A-cluster unit was an adenine-pentad duplex containing stacked PyA pairs in the center aligned in an antiparallel manner. Spectral analysis of the A-cluster revealed remarkable reddish fluorescence with a large Stokes shift (∼195 nm) and a long life-time constant (31 ns), originated from exciton states formed by PyA pairs and neighboring adenines. Structurally, the exciton state of the A-cluster exhibited unusually high stability, relative to that of other five-mismatched duplexes, as a result of stabilization through strong stacking interactions (zipper-like structure) of the mismatched A–A and PyA pairs, rather than through traditional Watson–Crick base pairing. These spectral and structural properties of the A-clusters were specific to the adenine bases and highly disturbed by introducing other bases (T, G, and especially C) or an abasic site into the A-cluster, whereas they were enhanced through synergistic effects in systems containing multiple A-clusters. As a minimum unit for these unique properties, finally, the A-cluster was exploited as a fluorescent probing system for specific nucleic acid sequences, such as miR-21, accompanying distinct fluorescence color changes from blue to red. These findings indicated the potential utility of the A-cluster as a part of fluorescent probes exhibiting clear signaling upon micro-environmental changes.

Graphical abstract: Photophysical and structural investigation of a PyA-modified adenine cluster: its potential use for fluorescent DNA probes exhibiting distinct emission color changes

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Publication details

The article was received on 09 Jun 2015, accepted on 29 Jun 2015 and first published on 29 Jun 2015


Article type: Paper
DOI: 10.1039/C5OB01159K
Author version available: Download Author version (PDF)
Citation: Org. Biomol. Chem., 2015,13, 8470-8478
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    Photophysical and structural investigation of a PyA-modified adenine cluster: its potential use for fluorescent DNA probes exhibiting distinct emission color changes

    K. T. Kim, W. Heo, T. Joo and B. H. Kim, Org. Biomol. Chem., 2015, 13, 8470
    DOI: 10.1039/C5OB01159K

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