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Nucleobase–Guanidiniocarbonyl-Pyrrole Conjugates as Novel Fluorimetric Sensors for Single Stranded RNA

Ban, Željka; Žinić, Biserka; Vianello, Robert; Schmuck, Carsten; Piantanida, Ivo (2017) Nucleobase–Guanidiniocarbonyl-Pyrrole Conjugates as Novel Fluorimetric Sensors for Single Stranded RNA. Molecules, 22 (12). ISSN 1420-3049

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Abstract

We demonstrate here for the first time that a guanidiniocarbonyl-pyrrole (GCP) unit can be applied for the fine recognition of single stranded RNA sequences—an intuitively unexpected result since so far binding of the GCP unit to ds-DNA or ds-RNA relied strongly on minor or major groove interactions, as shown in previous work. Two novel nucleobase–GCP isosteric conjugates differing in the flexibility of GCP unit revealed a fluorimetric recognition of various single stranded RNA, which could be additionally regulated by pH. The more rigid conjugate showed a specific fluorescence increase for poly A only at pH 7, whereby this response could be reversibly switched-off at pH 5. The more flexible derivative revealed selective fluorescence quenching by poly G at pH 7 but no change for poly A, whereas its recognition of poly AH+ can be switched-on at pH 5. The computational analysis confirmed the important role of the GCP fragment and its protonation states in the sensing of polynucleotides and revealed that it is affected by the intrinsic dynamical features of conjugates themselves. Both conjugates showed a negligible response to uracil and cytosine ss-RNA as well as ds-RNA at pH 7, and only weak interactions with ds-DNA. Thus, nucleobase–GCP conjugates can be considered as novel lead compounds for the design of ss-RNA or ss-DNA selective fluorimetric probes.

Item Type: Article
Uncontrolled Keywords: pyrrolocytosine ; guanidiniocarbonyl-pyrrole ; DNA/RNA binding ; fluorimetric recognition
Subjects: NATURAL SCIENCES > Chemistry
Divisions: Division of Organic Chemistry and Biochemistry
Projects:
Project titleProject leaderProject codeProject type
Višenamjensko očitavanje DNA / RNA sekundarne strukture molekularnim kemijskim senzorima-DNA/RNA-MolSenseIvo PiantanidaIP-2013-11-1477HRZZ
Depositing User: Ivo Piantanida
Date Deposited: 19 Jan 2018 08:43
Last Modified: 19 Jan 2018 08:43
URI: http://fulir.irb.hr/id/eprint/3840
DOI: 10.3390/molecules22122213

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