Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs
Alrun N. Koller
Joachim W. Engels
- The thermodynamics of base pairing is of fundamental importance. Fluorinated base analogs are valuable tools for investigating pairing interactions. To understand the influence of direct base–base interactions in relation to the role of water, pairing free energies between natural nucleobases and fluorinated analogs are estimated by potential of mean force calculations. Compared to pairing of AU and GC, pairing involving fluorinated analogs is unfavorable by 0.5–1.0 kcal mol -1. Decomposing the pairing free energies into enthalpic and entropic contributions reveals fundamental differences for Watson–Crick pairs compared to pairs involving fluorinated analogs. These differences originate from direct base–base interactions and contributions of water. Pairing free energies of fluorinated base analogs with natural bases are less unfavorable by 0.5–1.0 kcal mol -1 compared to non-fluorinated analogs. This is attributed to stabilizing C–F…H–N dipolar interactions and stronger N…H–C hydrogen bonds, demonstrating direct and indirect influences of fluorine. 7-methyl-7H-purine and its 9-deaza analog (Z) have been suggested as members of a new class of non-fluorinated base analogs. Z is found to be the least destabilizing universal base in the context of RNA known to date. This is the first experimental evidence for nitrogen-containing heterocylces as bioisosteres of aromatic rings bearing fluorine atoms.
A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects
Jesper B. Bramsen
Malgorzata M. Pakula
Thomas B. Hansen
Suzy L. Wengel
Joachim W. Engels
- Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2–8 of either siRNA strand counting from the 5'-end) and complementary sequences in the 3'UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA–target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low.
The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions
- G-quadruplex topologies of telomeric repeat sequences from vertebrates were investigated in the presence of molecular crowding (MC) mimetics, namely polyethylene glycol 200 (PEG), Ficoll 70 as well as Xenopus laevis egg extract by CD and NMR spectroscopy and native PAGE. Here, we show that the conformational behavior of the telomeric repeats in X. laevis egg extract or in Ficoll is notably different from that observed in the presence of PEG. While the behavior of the telomeric repeat in X. laevis egg extract or in Ficoll resembles results obtained under dilute conditions, PEG promotes the formation of high-order parallel topologies. Our data suggest that PEG should not be used as a MC mimetic.
Age-related cellular copper dynamics in the fungal ageing model Podospora anserina and in ageing human fibroblasts
Christian Quintus Scheckhuber
Bernd O. Kolbesen
Heinz D. Osiewacz
- In previous investigations an impact of cellular copper homeostasis on ageing of the ascomycete Podospora anserina has been demonstrated. Here we provide new data indicating that mitochondria play a major role in this process. Determination of copper in the cytosolic fraction using total reflection X-ray fluorescence spectroscopy analysis and eGfp reporter gene studies indicate an age-related increase of cytosolic copper levels. We show that components of the mitochondrial matrix (i.e. eGFP targeted to mitochondria) become released from the organelle during ageing. Decreasing the accessibility of mitochondrial copper in P. anserina via targeting a copper metallothionein to the mitochondrial matrix was found to result in a switch from a copper-dependent cytochrome-c oxidase to a copper-independent alternative oxidase type of respiration and results in lifespan extension. In addition, we demonstrate that increased copper concentrations in the culture medium lead to the appearance of senescence biomarkers in human diploid fibroblasts (HDFs). Significantly, expression of copper-regulated genes is induced during in vitro ageing in medium devoid of excess copper suggesting that cytosolic copper levels also increase during senescence of HDFs. These data suggest that the identified molecular pathway of age-dependent copper dynamics may not be restricted to P. anserina but may be conserved from lower eukaryotes to humans.
5-Lipoxygenase: underappreciated role of a pro-inflammatory enzyme in tumorigenesis
Astrid Stefanie Fischer
Svenja Dorothea Steinbrink
Thorsten Jürgen Maier
- Leukotrienes constitute a group of bioactive lipids generated by the 5-lipoxygenase (5-LO) pathway. An increasing body of evidence supports an acute role for 5-LO products already during the earliest stages of pancreatic, prostate, and colorectal carcinogenesis. Several pieces of experimental data form the basis for this hypothesis and suggest a correlation between 5-LO expression and tumor cell viability. First, several independent studies documented an overexpression of 5-LO in primary tumor cells as well as in established cancer cell lines. Second, addition of 5-LO products to cultured tumor cells also led to increased cell proliferation and activation of anti-apoptotic signaling pathways. 5-LO antisense technology approaches demonstrated impaired tumor cell growth due to reduction of 5-LO expression. Lastly, pharmacological inhibition of 5-LO potently suppressed tumor cell growth by inducing cell cycle arrest and triggering cell death via the intrinsic apoptotic pathway. However, the documented strong cytotoxic off-target effects of 5-LO inhibitors, in combination with the relatively high concentrations of 5-LO products needed to achieve mitogenic effects in cell culture assays, raise concern over the assignment of the cause, and question the relationship between 5-LO products and tumorigenesis. Keywords: leukotriene, apoptosis, cell proliferation, mitogenic effects, cytotoxicity
Molekulare Gymnastik : Rotationen, Schwingungen und chemische Reaktionen
- Bei jeder chemischen Reaktion werden Bindungen gebrochen und andere neu geknüpft. Dabei ändert sich die Anordnung und eventuell Anzahl der Atome im Molekül. Voraussetzung hierfür sind Bewegungen der beteiligten Atome und Moleküle. Um chemische Umwandlungen in "Echtzeit" zu studieren, müssen Untersuchungen im Zeitbereich der Schwingungs- und Rotationsdynamik durchgeführt werden. Dazu nutzen Wissenschaftler des Instituts für Physikalische und Theoretische Chemie die Möglichkeiten der modernen Ultrakurzzeit-Lasertechnik.
Ton Quoc Cuong
- The title compound, C15H25N5, is an aminalization product between 2,6-diacetylpyridine and 1,3-diaminopropane. It crystallizes with two independent molecules in the asymmetric unit with different conformations. In the first molecule, the methyl groups are cis oriented with respect to the pyridine ring [N—C—C—C torsion angles = 72.5 (1) and 80.3 (1)°], while they are trans oriented in the second molecule [N—C—C—C torsion angles = 82.6 (1) and -90.8 (1)°]. Each of the two molecules forms centrosymmetric dimers held together by N—H[cdots, three dots, centered]N hydrogen bonds, thus forming R 2 2(16) rings. The two dimers are interlinked by additional N—H[cdots, three dots, centered]N bonds into R 4 4(14) rings, building chains along the a axis. These patterns influence the orientation (either equatorial or axial) of the N—H bonds.
A monoclinic modification of propane-1,3-diyl bis(pyridine-3-carboxylate)
- In the title compound, C15H14N2O4, (I), the molecule lies on a twofold rotation axis which passes through the central C atom of the aliphatic chain, giving one half-molecule per asymmetric unit. The structure is a monoclinic polymorph of the triclinic structure previously reported [Brito, Vallejos, Bolte & López-Rodríguez (2010). Acta Cryst. E66, o792], (II). The most obvious difference between them is the O/C/C/C—O/C/C/C torsion angle [58.2 (7)° in (I) and 173.4 (3)/70.2 (3)° in (II) for GG and TG conformations, respectively]. Another important difference is observed in the dihedral angle between the planes of the aromatic rings [86.49 (7)° for (I) and 76.4 (3)° for (II)]. The crystal structure features a weak pi–pi interaction [centroid–centroid distance = 4.1397 (10)Å]; this latter kind of interaction is not evident in the triclinic polymorph.
- In the crystal of the title compound, C8H8ClN3S, molecules are connected by N—H[cdots, three dots, centered]S hydrogen bonds into strips parallel to the (112) planes and running along . One of the amino H atoms is not involved in a classical hydrogen bond. In addition, there is a rather short intermolecular Cl ... S distance of 3.3814 (5) Å.
- The title compound, [Tl4(C4H9O)4], featuring a (Tl—O)4 cube, crystallizes with a quarter-molecule (located on a special position of site symmetry An external file that holds a picture, illustration, etc. Object name is e-66-m1621-efi1.jpg..) and a half-molecule (located on a special position of site symmetry 23.) in the asymmetric unit. The Tl—O bond distances range from 2.463 (12) to 2.506 (12) Å. All O—Tl—O bond angles are smaller than 90° whereas the Tl—O—Tl angles are wider than a rectangular angle.