Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response

Crnolatac, Ivo; Rogan, Iva; Majić, Boris; Tomić, Sanja; Deligeorgiev, Todor; Horvat, Gordan; Makuc, Damjan; Plavec, Janez; Piantanida, Ivo

doi:10.1016/j.aca.2016.08.021

Cited by 16 publications

(17 citation statements)

References 17 publications

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“…Furthermore, 1 binds to ds‐DNA/RNA as a groove binder but, in contrast with most groove binders, it also interacts strongly with ss‐RNA, by acting as a spindle around which ss‐RNAs are wrapped due to a combination of electrostatic, H‐bonding and hydrophobic interactions. As most small molecule interactions with ss‐RNA are based on an intercalative binding mode, often combined with additional H‐bonding, whereby helicity of ss‐RNA is preserved or even enhanced, the binding mode of 1 presented herein is unique. Such ss‐RNA condensation due to complexation (extended strand to globular transformation) could protect its backbone against RNAase degradation and also facilitate its cellular uptake and distribution, opening new possibilities for RNA‐based applications.…”

Section: Resultsmentioning

confidence: 99%

A Quadrupolar Bis‐Triarylborane Chromophore as a Fluorimetric and Chirooptic Probe for Simultaneous and Selective Sensing of DNA, RNA and Proteins

Ban

Griesbeck

Tomić

et al. 2020

Chemistry A European J

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A water‐soluble tetracationic quadrupolar bis‐triarylborane chromophore showed strong binding to ds‐DNA, ds‐RNA, ss‐RNA, as well as to the naturally most abundant protein, BSA. The novel dye can distinguish between DNA/RNA and BSA by fluorescence emission separated by Δtrueν˜ =3600 cm−1, allowing for the simultaneous quantification of DNA/RNA and protein (BSA) in a mixture. The applicability of such fluorimetric differentiation in vitro was demonstrated, strongly supporting a protein‐like target as a dominant binding site of 1 in cells. Moreover, our dye also bound strongly to ss‐RNA, with the unusual rod‐like structure of the dye, decorated by four positive charges at its termini and having a hydrophobic core, acting as a spindle for wrapping A, C and U ss‐RNAs, but not poly G, the latter preserving its secondary structure. To the best of our knowledge, such unmatched, multifaceted binding activity of a small molecule toward DNA, RNA, and proteins and the selectivity of its fluorimetric and chirooptic response makes the quadrupolar bis‐triarylborane a novel chromophore/fluorophore moiety for biochemical applications.

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Section: Resultsmentioning

confidence: 99%

A Quadrupolar Bis‐Triarylborane Chromophore as a Fluorimetric and Chirooptic Probe for Simultaneous and Selective Sensing of DNA, RNA and Proteins

Ban

Griesbeck

Tomić

et al. 2020

Chemistry A European J

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“…However, for another polynucleotide, the same ligand can give only one binding mode based on the uniform aggregation at excess of ligand over polynucleotide bases at r > 0.4 ( Fig. 8 , right) [ 30 ].…”

Section: Reviewmentioning

confidence: 99%

“… CD titration of poly rA-poly rU (left) and poly rU (right) ( c (polynucleotide) = 2.0 × 10 −5 mol dm −3 ) with ligand L at molar ratios r = [L]/[polynucleotide] (pH 7.0, sodium cacodylate buffer, I = 0.05 mol dm −3 ). Adapted from [ 30 ]. …”

Section: Reviewmentioning

confidence: 99%

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Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

Šmidlehner

Piantanida

Pescitelli

2018

Beilstein J. Org. Chem.

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115

136

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The structural characterization of non-covalent complexes between nucleic acids and small molecules (ligands) is of a paramount significance to bioorganic research. Highly informative methods about nucleic acid/ligand complexes such as single crystal X-ray diffraction or NMR spectroscopy cannot be performed under biologically compatible conditions and are extensively time consuming. Therefore, in search for faster methods which can be applied to conditions that are at least similar to the naturally occurring ones, a set of polarization spectroscopy methods has shown highly promising results. Electronic circular dichroism (ECD) is the most commonly used method for the characterization of the helical structure of DNA and RNA and their complexes with ligands. Less common but complementary to ECD, is flow-oriented linear dichroism (LD). Other methods such as vibrational CD (VCD) and emission-based methods (FDCD, CPL), can also be used for suitable samples. Despite the popularity of polarization spectroscopy in biophysics, aside several highly focused reviews on the application of these methods to DNA/RNA research, there is no systematic tutorial covering all mentioned methods as a tool for the characterization of adducts between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably. 84

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“…The UV/Vis spectra of new dyes revealed strong hypochromic and moderate bathochromic effect upon titration with ds-DNA and ds-RNA. Detailed analysis of titration data was hampered by aggregation of 4b, since it was not possible to distinguish the effects of the aggregation-disaggregation equilibrium from the dye monomer binding to DNA and eventually formation of dye aggregate within the DNA/RNA (often reported for cyanine dyes (Crnolatac et al 2016); (Crnolatac et al 2013); (Tumir et al 2012)). Fortuitously, intrinsically non-fluorescent 4a, 4b upon titration with polynucleotides revealed strong emission (Fig.…”

Section: Resultsmentioning

confidence: 99%

Novel DNA/RNA-targeting amino acid beacon for the versatile incorporation at any position within the peptide backbone

Šmidlehner

Piantanida

2017

Amino Acids

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One-pot tandem synthesis was for the first time applied to attach fluorophore to the amino acid side chain, yielding amino acid ready for peptide coupling at the N-terminus, and also upon activation at the C-terminus. Two new compounds differing only in fluorophore-linker length showed exceptional fluorimetric and CD recognition between DS-RNA and DS-DNA, thus being promising beacons for versatile peptide incorporation.

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Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response

Cited by 16 publications

References 17 publications

A Quadrupolar Bis‐Triarylborane Chromophore as a Fluorimetric and Chirooptic Probe for Simultaneous and Selective Sensing of DNA, RNA and Proteins

A Quadrupolar Bis‐Triarylborane Chromophore as a Fluorimetric and Chirooptic Probe for Simultaneous and Selective Sensing of DNA, RNA and Proteins

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

Novel DNA/RNA-targeting amino acid beacon for the versatile incorporation at any position within the peptide backbone

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