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

Željka Ban,Carsten Schmuck,Ivo Piantanida,Biserka Žinić,Robert Vianello

doi:10.3390/molecules22122213

Željka Ban, Carsten Schmuck + Show 3 more

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https://doi.org/10.3390/molecules22122213

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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.

Highlights

Molecular visualization and recognition of DNA and RNA are an important area of ongoing research in medicine and molecular biology, in which small molecules can be useful dyes and effective anticancer, antibiotic and antiviral therapeutic agents [1]
GCP, both well known for their capability to strongly interact with nucleic fragments pyrrolocytosine nucleobase (Pyrr-C) and GCP, both well known for their capability to strongly interact with nucleic acids
Compounds 2 and 3 contain a fluorescent analogue of cytosine, we studied their interactions with ss-polynucleotides

Summary

Introduction

Molecular visualization and recognition of DNA and RNA are an important area of ongoing research in medicine and molecular biology, in which small molecules can be useful dyes and effective anticancer, antibiotic and antiviral therapeutic agents [1]. That was mostly due to a lack of interest since small molecules generally bind more strongly to multi-stranded nucleic acid structures than to single-stranded (ss) polymers. Single-stranded nucleic acids such as poly(A) have critical roles in cell biology [3,4,5], while single stranded G-rich structures can fold in a variety of G-quadruplexes. Some RNA in the genomes of various cardioviruses and encephalomyocarditis viruses contain stretches composed of more than 75% cytosine, and single stranded C-polymers can adopt a non-B form structure called i-motif under slightly acidic or neutral pH [6,7]. Very few small molecules reveal selective binding to single stranded DNA or RNA structures

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