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

Ban, Željka; Matić, Josipa; Žinić, Biserka; Foller Füchtbauer, Anders; Wilhelmsson, L. Marcus; Piantanida, Ivo (2020) Flexibility and Preorganization of Fluorescent Nucleobase-Pyrene Conjugates Control DNA and RNA Recognition. Molecules, 25 (9). ISSN 1420-3049

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Abstract

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 acidfluorescent 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 nucleobasefluorophore pre-organization.

Item Type: Article
Uncontrolled Keywords: DNA/RNA recognition ; hydrogen bonding ; fluorescent nucleobase ; pyrene ; intramolecular pre-organization
Subjects: NATURAL SCIENCES > Chemistry
Divisions: Division of Organic Chemistry and Biochemistry
Projects:
Project titleProject leaderProject codeProject type
Višekromoforne probe za prepoznavanje pojedinih struktura DNA, RNA i proteinaPiantanida, IvoIP-2018-01-5475HRZZ
Depositing User: Željka Ban
Date Deposited: 07 Jan 2021 13:08
Last Modified: 07 Jan 2021 13:08
URI: http://fulir.irb.hr/id/eprint/6155
DOI: 10.3390/molecules25092188

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