Threading polyintercalators with extremely slow dissociation rates and extended DNA binding sites

Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators

GC-rich sequences are recurring motifs in oncogenes and retroviruses and could be targeted by noncovalent major-groove therapeutic ligands. We considered the palindromic sequence d(G₁G₂C₃G₄C₅C₆)₂, and designed several oligopeptide derivatives of the anticancer intercalator mitoxantrone. The stability of their complexes with an 18-mer oligonucleotide encompassing this sequence in its center was validated using polarizable molecular dynamics. We report the most salient structural features of two novel compounds, having a dialkylammonium group as a side chain on both arms. The anthraquinone ring is intercalated in the central d(CpG)₂ sequence with its long axis perpendicular to that of the two base pairs. On each strand, this enables each ammonium group to bind in-register to O₆/N₇ of the two facing G bases upstream. We subsequently designed tris-intercalating derivatives, each dialkylammonium substituted with a connector to an N₉-aminoacridine intercalator extending our target range from a six- to a ten-base-pair palindromic sequence, d(C₁G₂G₃G₄C₅G₆C₇C₈C₉G₁₀)₂. The structural features of the complex of the most promising derivative are reported. The present design strategy paves the way for designing intercalator-oligopeptide derivatives with even higher selectivity, targeting an increased number of DNA bases, going beyond ten.

Low molecular weight self-assembling peptide-based materials for cell culture, antimicrobial, anti-inflammatory, wound healing, anticancer, drug delivery, bioimaging and 3D bioprinting applications

In this review, we have focused on the design and development of low molecular weight self-assembling peptide-based materials for various applications including cell proliferation, tissue engineering, antibacterial, antifungal, anti-inflammatory, anticancer, wound healing, drug delivery, bioimaging and 3D bioprinting. The first part of the review describes about stimuli and various noncovalent interactions, which are the key components of various self-assembly processes for the construction of organized structures. Subsequently, the chemical functionalization of the peptides has been discussed, which is required for the designing of self-assembling peptide-based soft materials. Various low molecular weight self-assembling peptides have been discussed to explain the important structural features for the construction of defined functional nanostructures. Finally, we have discussed various examples of low molecular weight self-assembling peptide-based materials for cell culture, antimicrobial, anti-inflammatory, anticancer, wound healing, drug delivery, bioimaging and 3D bioprinting applications.

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

A novel naphthalene diimde analogue (NDI) equipped at the imide positions with two guanidinio-carbonyl-pyrrole (GCP) pendant arms interacted significantly stronger with ds-DNA at pH 5 than at pH 7, due to reversible protonation of the GCP arms. This was consequence of a pH-switchable threading intercalation into ds-DNAs only at pH 5, while at neutral conditions (pH 7) NDI-GCP₂ switched to the DNA minor groove binding. Intriguingly, NDI-GCP₂ was at both pH values studied bound to the ds-RNA major groove, still showing a higher affinity and thermal denaturation effect at pH 5 due to GCP protonation. At excess over the DNA/RNA conjugate NDI-GCP₂ showed also aggregation along the ds-polynucleotide and AFM and DLS demonstrated that NDI-GCP₂ has pronounced ds-DNA condensation ability.

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

Two novel unnatural amino acids, prepared by linking a dicationic purple-coloured and fluorescent naphthalene diimide (NDI) at core position to amino acid side chains of variable length, strongly interacted with ds-DNA/RNA by threading intercalation. Different from a reference NDI dye with identical visible range absorbance (520–540 nm) and Stokes shifts in emission (+60 nm, quantum yield > 0.2), only these amino acid–NDI conjugates showed selective fluorimetric response for GC-DNA in respect to AT(U)-polynucleotides. The DNA/RNA binding-induced circular dichroism (ICD) response of NDI at 450–550 nm strongly depended on the length and rigidity of the linker to the amino acid unit, which controls the orientation of the NDI unit inside within the intercalative binding site. The ICD selectivity also depends on the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA.

Conjugates of Classical DNA/RNA Binder with Nucleobase: Chemical, Biochemical and Biomedical Applications

Among the most intensively studied classes of small molecules (molecular weight < 650) in biomedical research are small molecules that non-covalently bind to DNA/RNA, and another intensively studied class is nucleobase derivatives. Both classes have been intensively elaborated in many books and reviews. However, conjugates consisting of DNA/RNA binder covalently linked to nucleobase are much less studied and have not been reviewed in the last two decades. Therefore, this review summarized reports on the design of classical DNA/RNA binder - nucleobase conjugates, as well as data about their interactions with various DNA or RNA targets, and even in some cases protein targets are involved. According to these data, the most important structural aspects of selective or even specific recognition between small molecule and target are proposed, and where possible related biochemical and biomedical aspects were discussed. The general conclusion is that this, rather new class of molecules showed an amazing set of recognition tools for numerous DNA or RNA targets in the last two decades, as well as few intriguing in vitro and in vivo selectivities. Several lead research lines show promising advancements toward either novel, highly selective markers or bioactive, potentially druggable molecules.

Exploiting the interactions of aromatic units for folding and assembly in aqueous environments

A variety of non-covalent interactions (including hydrogen bonding, ionic interactions, metal coordination and desolvation/solvation) have been utilized to organize oligomers into well-defined structures. Herein is described a survey of aromatic foldamers that capitalize on electrostatic complementarity of substituted aromatic units to drive folding and assembly in aqueous environments. A brief description of recent advances in the understanding of aromatic interactions is provided, followed by examples of foldamers that exploit interactions between aromatic units to drive their assembly in predictable fashion. The history of our aromatic foldamers is traced from the first structure designed to fold into a pleated structure in an aqueous environment to a heteroduplex system more related to nucleic acids. Taken together, the results demonstrate that electrostatic complementarity of aromatic units provides a versatile framework for driving predictable folding and assembly in aqueous environments.

Kinetic evidence for interaction of TMPyP4 with two different G-quadruplex conformations of human telomeric DNA

BACKGROUND

Stabilization of G-quadruplex helices by small ligands has attracted growing attention because they inhibit the activity of the enzyme telomerase, which is overexpressed in >80% cancer cells. TMPyP4, one of the most studied G-quadruplex ligands, is used as a model to show that the ligands can exhibit different binding features with different conformations of a human telomeric specific sequence.

METHODS

UV-Vis, FRET melting Assay, Isothermal Titration Calorimetry, Time-resolved Fluorescence lifetime, T-Jump and Molecular Dynamics.

RESULTS

TMPyP4 yields two different complexes with two Tel22 telomeric conformations in the presence of Na⁺ or K⁺. T-Jump kinetic experiments show that the rates of formation and dissociation of these complexes in the ms time scale differ by one order of magnitude. MD simulations reveal that, in K⁺ buffer, "hybrid 1" conformation yields kinetic constants on interaction with TMPyP4 one order lower than "hybrid 2". The binding involves π-π stacking with external loop bases.

CONCLUSIONS

For the first time we show that for a particular buffer TMPyP4 interacts in a kinetically different way with the two Tel22 conformations even if the complexes formed are thermodynamically indistinguishable.

GENERAL SIGNIFICANCE

G-quadruplexes, endowed with technological applications and potential impact on regulation mechanisms, define a new research field. The possibility of building different conformations from same sequence is a complex issue that confers G-quadruplexes very interesting features. The obtaining of reliable kinetic data constitutes an efficient tool to determine reaction mechanisms between conformations and small molecules.

Glycoluril-Derived Molecular Clips are Potent and Selective Receptors for Cationic Dyes in Water

Molecular clip 1 remains monomeric in water and engages in host-guest recognition processes with suitable guests. We report the K_a values for 32 1⋅guest complexes measured by ¹ H NMR, UV/Vis, and fluorescence titrations. The cavity of 1 is shaped by aromatic surfaces of negative electrostatic potential and therefore displays high affinity and selectivity for planar and cationic aromatic guests that distinguishes it from CB[n] receptors that prefer aliphatic over aromatic guests. Electrostatic effects play a dominant role in the recognition process whereby ion-dipole interactions may occur between ammonium ions and the C=O groups of 1, between the SO₃^- groups of 1 and pendant cationic groups on the guest, and within the cavity of 1 by cation-π interactions. Host 1 displays a high affinity toward dicationic guests with large planar aromatic surfaces (e.g. naphthalene diimide NDI+ and perylene diimide PDI+) and cationic dyes derived from acridine (e.g. methylene blue and azure A). The critical importance of cation-π interactions was ascertained by a comparison of analogous neutral and cationic guests (e.g. methylene violet vs. methylene blue; quinoline vs. N-methylquinolinium; acridine vs. N-methylacridinium; neutral red vs. neutral red H⁺ ) the affinities of which differ by up to 380-fold. We demonstrate that the high affinity of 1 toward methylene blue (K_a =3.92×10⁷  m^-1 ; K_d =25 nm) allows for the selective sequestration and destaining of U87 cells stained with methylene blue.

Thermodynamics and kinetic studies in the binding interaction of cyclic naphthalene diimide derivatives with double stranded DNAs

Previously, we reported our investigations of the interaction between a cyclic naphthalene diimide derivative (cNDI 1) and double stranded DNA (dsDNA) (Bioorg. Med. Chem.2014, 22, 2593). Here, we report the synthesis of the novel cNDI 2, which has shorter linker chains than cNDI 1. We performed comparative investigations of the interactions of both cNDI 1 and cNDI 2 with different types of dsDNA, including analysis of their thermodynamics and kinetics. Interactions between the cNDIs and calf thymus DNA (CT-DNA), poly[d(A-T)]2, or poly[d(G-C)]2 were explored by physicochemical and biochemical methods, including UV-Vis spectroscopy, circular dichroism (CD) spectroscopy, stopped-flow kinetics, and a topoisomerase I assay. Upon addition of cNDIs to CT-DNA, the existence of an induced CD signal at approximately the wavelength of the naphthalene diimide chromophore and unwinding of the DNA duplex, as detected by the topoisomerase I assay, revealed that cNDIs bound to the DNA duplex. As indicated by the steric constraint in the formation of the complex, bis-threading intercalation was the more favorable binding mode. UV-Vis spectroscopic titration of the cNDIs with DNA duplexes showed affinities on the order of 10(5)-10(6)M(-1), with a stoichiometry of one cNDI molecule per four DNA base pairs. Thermodynamic parameters (ΔG, ΔH, and ΔS) based on the van't Hoff equation indicated that exothermic and entropy-dependent hydrophobic interactions played a major role in the reaction. Stopped-flow association and dissociation analysis showed that cNDI interactions with poly[d(G-C)]2 were more stable and had a slower dissociation rate than their interactions with poly[d(A-T)]2 and CT-DNA. Measurement of ionic strength indicated that electrostatic attraction is also an important component of the interaction between cNDIs and CT-DNA. Because of its longer linker chain, cNDI 1 showed higher binding selectivity, a more entropically favorable interaction, and much slower dissociation from dsDNA than cNDI 2.

Assorted morphosynthesis: access to multi-faceted nano-architectures from a super-responsive dual π-functional amphiphilic construct

An electronically segmented amphiphile was created by conjugating two π-functional units (HQ/NDI) for the first time.

Interactions of cyclic and non-cyclic naphthalene diimide derivatives with different nucleic acids

Recently, strategy based on stabilization of G-quadruplex telomeric DNA by small organic molecule has been realized by naphthalene diimide derivatives (NDIs). At the same time NDIs bind to DNA duplex as threading intercalators. Here we present cyclic derivative of naphthalene diimide (ligand 1) as DNA-binding ligand with ability to recognition of different structures of telomeric G-quadruplexes and ability to bis-intercalate to double-stranded helixes. The results have been compared to non-cyclic derivative (ligand 2) and revealed that preferential binding of ligands to nucleic acids strongly depends on their topology and structural features of ligands.

Gated electron sharing within dynamic naphthalene diimide-based oligorotaxanes

The controlled self-assembly of well-defined and spatially ordered π-systems has attracted considerable interest because of their potential applications in organic electronics. An important contemporary pursuit relates to the investigation of charge transport across noncovalently coupled components in a stepwise fashion. Dynamic oligorotaxanes, prepared by template-directed methods, provide a scaffold for directing the construction of monodisperse one-dimensional assemblies in which the functional units communicate electronically through-space by way of π-orbital interactions. Reported herein is a series of oligorotaxanes containing one, two, three and four naphthalene diimide (NDI) redox-active units, which have been shown by cyclic voltammetry, and by EPR and ENDOR spectroscopies, to share electrons across the NDI stacks. Thermally driven motions between the neighboring NDI units in the oligorotaxanes influence the passage of electrons through the NDI stacks in a manner reminiscent of the conformationally gated charge transfer observed in DNA.

NDI and DAN DNA: nucleic acid-directed assembly of NDI and DAN

Two novel DNA base surrogate phosphoramidites 1 and 2, based upon relatively electron-rich 1,5-dialkoxynaphthalene (DAN) and relatively electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI), respectively, were designed, synthesized, and incorporated into DNA oligonucleotide strands. The DAN and NDI artificial DNA bases were inserted within a three-base-pair region within the interior of a 12-mer oligonucleotide duplex in various sequential arrangements and investigated with CD spectroscopy and UV melting curve analysis. The CD spectra of the modified duplexes indicated B-form DNA topology. Melting curve analyses revealed trends in DNA duplex stability that correlate with the known association of DAN and NDI moieties in aqueous solution as well as the known favorable interactions between NDI and natural DNA base pairs. This demonstrates that DNA duplex stability and specificity can be driven by the electrostatic complementarity between DAN and NDI. In the most favorable case, an NDI-DAN-NDI arrangement in the middle of the DNA duplex was found to be approximately as stabilizing as three A-T base pairs.

Direct core functionalisation of naphthalenediimides by iridium catalysed C–H borylation

We report the first boron-substituted naphthalenediimides (NDIs), prepared by iridium catalysed C–H activation. Both mono- and diborylated products are available, which have been further elaborated by Suzuki–Miyaura coupling.

Developing bivalent ligands to target CUG triplet repeats, the causative agent of myotonic dystrophy type 1

An expanded CUG repeat transcript (CUG(exp)) is the causative agent of myotonic dystrophy type 1 (DM1) by sequestering muscleblind-like 1 protein (MBNL1), a regulator of alternative splicing. On the basis of a ligand (1) that was previously reported to be active in an in vitro assay, we present the synthesis of a small library containing 10 dimeric ligands (4-13) that differ in length, composition, and attachment point of the linking chain. The oligoamino linkers gave a greater gain in affinity for CUG RNA and were more effective when compared to oligoether linkers. The most potent in vitro ligand (9) was shown to be aqueous-soluble and both cell- and nucleus-permeable, displaying almost complete dispersion of MBNL1 ribonuclear foci in a DM1 cell model. Direct evidence for the bioactivity of 9 was observed in its ability to disperse ribonuclear foci in individual live DM1 model cells using time-lapse confocal fluorescence microscopy.