Acid–base properties of functionalised tripodal polyamines and their interaction with nucleotides and nucleic acids

Sornosa-Ten, Alejandra; Albelda, M. Teresa; Frías, Juan C.; Garcı́a-España, Enrique; Llinares, José M.; Budimir, Ana; Piantanida, Ivo

doi:10.1039/c000124d

Cited by 14 publications

(8 citation statements)

References 56 publications

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“…Bookmark not defined. In this frame, our groups launched a program to develop synthetic open-chain polyamine ligands able to bind selectively RNA over DNA 15 However, the first family of ligands exhibited negligible in vitro activity in cancer cell cultures due to a poor cellular uptake caused by their high charge at physiological conditions. In order to improve cell uptake, we prepared aryl-linked (pyridine and phenanthroline) bis-polyaza pyridinophane ligands (L2 and L5 in Scheme 1) with the same charge as the previous family but possessing a much higher hydrophobicity due to their bulky conformation induced by an internal hydrogen bond network 16 The selectivity achieved by these polyazapyridinophane ligands for ds-RNA (poly A-poly U) over ds-DNA (poly dA-poly dT) was explained by the differences in the steric properties of the binding sites of these polynucleotides.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives

Stojković

González‐García

Šupljika

et al. 2018

International Journal of Biological Macromolecules

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Two bis-polyaza pyridinophane derivatives and their monomeric reference compounds revealed strong interactions with ds-DNA and RNA. The bis-derivatives show a specific condensation of GC- and IC-DNA, which is almost two orders of magnitude more efficient than the well-known condensation agent spermine. The type of condensed DNA was identified as ψ-DNA, characterized by the exceptionally strong CD signals. At variance to the almost silent AT(U) polynucleotides, these strong CD signals allow the determination of GC-condensates at nanomolar nucleobase concentrations. Detailed thermodynamic characterisation by ITC reveals significant differences between the DNA binding of the bis-derivative compounds (enthalpy driven) and that of spermine and of their monomeric counterparts (entropy driven). Atomic force microscopy confirmed GC-DNA compaction by the bis-derivatives and the formation of toroid- and rod-like structures responsible for the ψ-type pattern in the CD spectra.

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Section: Accepted Manuscriptmentioning

confidence: 99%

Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives

Stojković

González‐García

Šupljika

et al. 2018

International Journal of Biological Macromolecules

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“…The new bands were assigned to the structural parts of polynucleotides, which due to involvement in interaction with the small molecules, came close to the metal surface, enabling enhancement of scattered radiation. Apart from electrostatic interactions between the positively charged polyamine molecules and negatively charged phosphate backbone, hydrogen bonds between the flexible polyamine chains and nucleobases were recognized as the main driving forces in groove binding . Given that the structure of small molecules affected not only the binding mode with nucleic acids but also the cell permeability, structurally related polyamine molecules consisting of two polyaza pyridinophanes linked by a pyridine or phenanthroline unit have been synthesized and their interactions with DNA/RNA polynucleotides studied …”

Section: Introductionmentioning

confidence: 99%

Revealing interactions between polyaza pyridinophane compounds and DNA/RNA polynucleotides by SERS spectroscopy

Dijanošić

Miljanić

Piantanida

et al. 2014

J Raman Spectroscopy

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Surface‐enhanced Raman scattering spectroscopy (SERS) in the near‐infrared region had been applied to study interactions of polyaza pyridinophanes with single stranded RNA and double stranded DNA and RNA polynucleotides. Studied compounds, PYPOD and PHENPOD, differed in the central aromatic moiety, pyridine and phenanthroline, respectively, which linked two cyclic amines. An intense scattering was obtained from molecules adsorbed onto the silver nanoparticles, showing nonlinear concentration dependence in the 6.5 × 10−8−6.5 × 10−5 M range. New bands in spectra of PYPOD/polynucleotide and PHENPOD/polynucleotide mixtures were assigned to vibrational modes of polynucleotide moieties involved in interactions. SERS spectra of both polyaza pyridinophanes with single stranded RNA polynucleotides indicated hydrogen bonding between the small molecules and the nucleic bases of poly A, poly C and poly U, whereas an interaction of only PYPOD with poly G was suggested. SERS spectra implied that both compounds bound into the minor groove of the helical poly dAdT–poly dAdT polynucleotide, while none of polyaza pyridinophanes interacted with the grooves of the poly dGdC–poly dGdC polynucleotide. Nevertheless, intensity ratios suggested intercalation of the phenanthroline moiety of the PHENPOD molecules into the double helix of the guanine‐cytosine polynucleotide. Spectral features also indicated binding of the PYPOD molecules within the major groove of the double stranded RNA analog. Copyright © 2014 John Wiley & Sons, Ltd.

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“…The studied compounds strongly stabilize DNA against thermal denaturation. 22 Such DNA binding most likely involves DNA groove binding by interactions of protonated amino groups as well as hydrogen bonding and aromatic stacking interactions of aromatic moieties (Im and Py) with DNA base-pairs. Interactions of the polyamine molecules with single-stranded RNA polynucleotides (poly A, poly G, poly C, poly U), doublestranded DNA polynucleotides (poly dAdT-poly dAdT, poly dGdC-poly dGdC) and calf thymus DNA (ct-DNA) were studied by surface-enhanced Raman spectroscopy in the silver citrate colloid at neutral pH.…”

Section: Introductionmentioning

confidence: 99%

Surface-enhanced Raman study of the interactions between tripodal cationic polyamines and polynucleotides

Miljanić

Dijanošić

Piantanida

et al. 2011

Analyst

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Raman and surface-enhanced Raman spectra of new DNA/RNA-binding compounds consisting of three imidazole (Im) and three pyridine (Py) rings connected by tripodal polyaminomethylene linkages were obtained by the near-infrared excitation at 1064 nm. Study of interactions of Im and Py polyamines with single-stranded RNA polynucleotides (poly A, poly G, poly C, poly U), double-stranded DNA polynucleotides (poly dAdT-poly dAdT, poly dGdC-poly dGdC) and calf thymus DNA (ct-DNA) by surface-enhanced Raman spectroscopy (SERS) reveals unambiguous enhancement of the Raman scattering from the small molecules as well as appearance of new bands in spectra associated mainly with nucleobases. The SERS experiments point toward comparable interactions of Im and Py polyamines with single-stranded purine and pyrimidine polynucleotides. Furthermore, SERS experiments with double stranded polynucleotides reveal the base-pair dependent selectivity of Im and Py, whereby interactions within both, major and minor groove are indicated for poly dAdT-poly dAdT, at variance to preferred binding of Im and Py to only major groove of poly dGdC-poly dGdC. SERS spectra of Im and Py with ct-DNA imply that protonated amino groups of these compounds preferentially interact with N7 atoms (adenine, guanine) while nitrogen in aromatic rings of polyamines might be attracted to C6-NH(2) (adenine), all sites being located at the major groove of the DNA helix. Wavenumber downshift of the imidazole (Im) and pyridine (Py) ring vibrations supports aromatic stacking interactions of imidazole and pyridine aromatic moieties with DNA base-pairs.

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Acid–base properties of functionalised tripodal polyamines and their interaction with nucleotides and nucleic acids

Cited by 14 publications

References 56 publications

Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives

Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives

Revealing interactions between polyaza pyridinophane compounds and DNA/RNA polynucleotides by SERS spectroscopy

Surface-enhanced Raman study of the interactions between tripodal cationic polyamines and polynucleotides

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