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Article

Flexibility and Preorganization of Fluorescent Nucleobase-Pyrene Conjugates Control DNA and RNA Recognition

1
Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, Zagreb 10000, Croatia
2
Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
*
Authors to whom correspondence should be addressed.
Molecules 2020, 25(9), 2188; https://doi.org/10.3390/molecules25092188
Received: 10 March 2020 / Revised: 23 April 2020 / Accepted: 3 May 2020 / Published: 7 May 2020
We synthesized a new amino acid-fluorescent nucleobase derivative (qAN1-AA) and from it two new fluorescent nucleobase–fluorophore (pyrene) conjugates, whereby only the analogue with the longer and more flexible linker (qAN1-pyr2) self-folded into intramolecularly stacked qAN1/pyrene conformation, yielding characteristic, 100 nm-red-shifted emission (λmax = 500 nm). On the contrary, the shorter and more rigid linker resulted in non-stacked conformation (qAN1-pyr1), characterized by the emission of free pyrene at λmax = 400 nm. Both fluorescent nucleobase–fluorophore (pyrene) conjugates strongly interacted with ds-DNA/RNA grooves with similar affinity but opposite fluorescence response (due to pre-organization), whereas the amino acid-fluorescent base derivative (qAN1-AA) was inactive. However, only intramolecularly self-folded qAN1-pyr2 showed strong fluorescence selectivity toward poly U (Watson–Crick complementary to qAN1 nucleobase) and poly A (reverse Hoogsteen complementary to qAN1 nucleobase), while an opposite emission change was observed for non-complementary poly G and poly C. Non-folded analogue (qAN1-pyr1) showed no ss-RNA selectivity, demonstrating the importance of nucleobase-fluorophore pre-organization. View Full-Text
Keywords: DNA/RNA recognition; hydrogen bonding; fluorescent nucleobase; pyrene; intramolecular pre-organization DNA/RNA recognition; hydrogen bonding; fluorescent nucleobase; pyrene; intramolecular pre-organization
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MDPI and ACS Style

Ban, Ž.; Matić, J.; Žinić, B.; Foller Füchtbauer, A.; Wilhelmsson, L.M.; Piantanida, I. Flexibility and Preorganization of Fluorescent Nucleobase-Pyrene Conjugates Control DNA and RNA Recognition. Molecules 2020, 25, 2188. https://doi.org/10.3390/molecules25092188

AMA Style

Ban Ž, Matić J, Žinić B, Foller Füchtbauer A, Wilhelmsson LM, Piantanida I. Flexibility and Preorganization of Fluorescent Nucleobase-Pyrene Conjugates Control DNA and RNA Recognition. Molecules. 2020; 25(9):2188. https://doi.org/10.3390/molecules25092188

Chicago/Turabian Style

Ban, Željka, Josipa Matić, Biserka Žinić, Anders Foller Füchtbauer, L. M. Wilhelmsson, and Ivo Piantanida. 2020. "Flexibility and Preorganization of Fluorescent Nucleobase-Pyrene Conjugates Control DNA and RNA Recognition" Molecules 25, no. 9: 2188. https://doi.org/10.3390/molecules25092188

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