Sensing of Different Human Telomeric G-Quadruplex DNA Topologies by Natural Alkaloid Allocryptopine Using Spectroscopic Techniques

The mechanism of UP1 binding and unfolding of human telomeric DNA G-quadruplex

The human telomere contains multiple copies of the DNA sequence d(TTAGGG) which can fold into higher order intramolecular G-quadruplexes and regulate the maintenance of telomere length and chromosomal integrity. The nucleic acid binding protein heteronuclear ribonucleoprotein A1 (hnRNP A1) and its N-terminus proteolytic product UP1 have been shown to efficiently bind and unfold telomeric DNA G-quadruplex. However, the understanding of the molecular mechanism of the UP1 binding and unfolding telomeric G-quadruplexes is still limited. Here, we performed biochemical and biophysical characterizations of UP1 binding and unfolding of human telomeric DNA G-quadruplex d[AGGG(TTAGGG)3], and in combination of systematic site-direct mutagenesis of two tandem RNA recognition motifs (RRMs) in UP1, revealed that RRM1 is responsible for initial binding and unfolding, whereas RRM2 assists RRM1 to complete the unfolding of G-quadruplex. Isothermal titration calorimetry (ITC) and circular dichroism (CD) studies of the interactions between UP1 and DNA G-quadruplex variants indicate that the "TAG" binding motif in Loop2 of telomeric G-quadruplex is critical for UP1 recognition and G-quadruplex unfolding initiation. Together we depict a model for molecular mechanism of hnRNP A1 (UP1) binding and unfolding of the human telomeric DNA G-quadruplex.

Safety and efficacy of a feed additive consisting of Macleaya cordata (Willd.) R. Br. extract and leaves (Sangrovit® extra) for all poultry species (excluding laying and breeding birds) (Phytobiotics Futterzusatzstoffe GmbH)

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the safety and efficacy of Macleaya cordata (Willd.) R. Br. extract and leaves (Sangrovit® Extra) when used as a zootechnical feed additive (functional group: other zootechnical additives) for all poultry species (excluding laying and breeding birds). The additive is standardised to contain a concentration of the sum of the four alkaloids sanguinarine, chelerythrine, protopine and allocryptopine of 1.25%, with 0.5% sanguinarine. Owing to the presence of the DNA intercalators sanguinarine and chelerythrine, a concern for genotoxicity was identified. The EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) had no safety concerns when the additive is used at the recommended level of 150 mg/kg complete feed (corresponding to 0.750 mg sanguinarine/kg complete feed) for chickens for fattening and other poultry species for fattening. No conclusion can be drawn for poultry reared for laying/breeding. The use of Sangrovit® Extra in poultry species for fattening at the maximum recommended level was considered of low concern for consumers. The additive was shown to be irritant to the eyes but not irritant to skin or a skin sensitiser. The FEEDAP Panel could not exclude the potential of the additive to be a respiratory sensitiser. When handling the additive, exposure of unprotected users to sanguinarine and chelerythrine may occur. Therefore, to reduce the risk, the exposure of users should be reduced. The use of Sangrovit® Extra as a feed additive under the proposed conditions of use was considered safe for the environment. The additive Sangrovit® Extra had the potential to be efficacious in improving performance of chickens for fattening at 45 mg/kg complete feed. This conclusion was extended to chickens reared for laying/breeding and extrapolated to all poultry species for fattening or reared for laying/breeding.

Discriminating between Parallel, Anti-Parallel and Hybrid G-Quadruplexes: Mechanistic Details on Their Binding to Small Molecules

G-quadruplexes (G4) are now extensively recognised as a peculiar non-canonical DNA geometry that plays a prime importance role in processes of biological relevance whose number is increasing continuously. The same is true for the less-studied RNA G4 counterpart. G4s are stable structures; however, their geometrical parameters may be finely tuned not only by the presence of particular sequences of nucleotides but also by the salt content of the medium or by a small molecule that may act as a peculiar topology inducer. As far as the interest in G4s increases and our knowledge of these species deepens, researchers do not only verify the G4s binding by small molecules and the subsequent G4 stabilisation. The most innovative studies now aim to elucidate the mechanistic details of the interaction and the ability of a target species (drug) to bind only to a peculiar G4 geometry. In this focused review, we survey the advances in the studies of the binding of small molecules of medical interest to G4s, with particular attention to the ability of these species to bind differently (intercalation, lateral binding or sitting atop) to different G4 topologies (parallel, anti-parallel or hybrid structures). Some species, given the very high affinity with some peculiar G4 topology, can first bind to a less favourable geometry and then induce its conversion. This aspect is also considered.

Synthesis and Spectroscopic Investigation of a Hexaaza Lanthanum(III) Macrocycle with a Hybrid-Type G4 DNA Stabilizing Effect

Herein we present a mononuclear lanthanum(III) complex obtained in a template cyclocondensation reaction of lanthanum(III) nitrate salt, 1,2-propanediamine, and 2,6-diacetylpyridine (LaPA complex). A preliminary investigation of the biological potential of this compound was conducted using a biomedically relevant target Tel26. We found that, different from parallel G4, antiparallel G4, and duplex DNA, only a hybrid-type G4 structure of Tel26 in a K⁺ solution was significantly stabilized by ≥7 °C, which emerged in our UV melting studies. Moreover, LaPA induced structural changes in the Tel26 structure in a K⁺-deprived solution, suggesting that it may also lead to conformational changes in "non-G4" telomeric DNA.

Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes

DNA and RNA sequences rich in guanine can fold into noncanonical structures called G-quadruplexes (GQs), which exhibit a common stem structure of Hoogsteen hydrogen-bonded guanine tetrads and diverse loop structures. GQ sequence motifs are overrepresented in promoters, origins of replication, telomeres, and untranslated regions in mRNA, suggesting roles in modulating gene expression and preserving genomic integrity. Given these roles and unique aspects of different structures, GQs are attractive targets for drug design, but greater insight into GQ folding pathways and the interactions stabilizing them is required. Here, we performed molecular dynamics simulations to study two bimolecular GQs, a telomeric DNA GQ and the analogous telomeric repeat-containing RNA (TERRA) GQ. We applied the Drude polarizable force field, which we show outperforms the additive CHARMM36 force field in both ion retention and maintenance of the GQ folds. The polarizable simulations reveal that the GQs bind bulk K+ ions differently, and that the TERRA GQ accumulates more K+ ions, suggesting different ion interactions stabilize these structures. Nucleobase dipole moments vary as a function of position and also contribute to ion binding. Finally, we show that the TERRA GQ is more sensitive than the telomeric DNA GQ to water-mediated modulation of ion-induced dipole-dipole interactions.