Telomeric i-motifs and C-strands inhibit parallel G-quadruplex extension by telomerase.

Telomeric C-rich repeated DNA sequences fold into tetrahelical i-motif structures in vitro at acidic pH. While studies have suggested that i-motifs may form in cells, little is known about their potential role in human telomere biology. In this study, we explore the effect of telomeric C-strands and i-motifs on the ability of human telomerase to extend G-rich substrates. To promote i-motif formation at neutral pH, we use telomeric sequences where the cytidines have been substituted with 2'-fluoroarabinocytidine. Using FRET-based studies, we show that the stabilized i-motifs resist hybridization to concomitant parallel G-quadruplexes, implying that both structures could exist simultaneously at telomeric termini. Moreover, through telomerase activity assays, we show that both unstructured telomeric C-strands and telomeric i-motifs can inhibit the activity and processivity of telomerase extension of parallel G-quadruplexes and linear telomeric DNA. The data suggest at least three modes of inhibition by C-strands and i-motifs: direct hybridization to the substrate DNA, hybridization to nascent product DNA resulting in early telomerase dissociation, and interference with the unique mechanism of telomerase unwinding and extension of a G-quadruplex. Overall, this study highlights a potential inhibitory role for the telomeric C-strand in telomere maintenance.

Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting.

Thermodynamic preferences to form non-native conformations are crucial for understanding how nucleic acids fold and function. However, they are difficult to measure experimentally because this requires accurately determining the population of minor low-abundance (<10%) conformations in a sea of other conformations. Here, we show that melting experiments enable facile measurements of thermodynamic preferences to adopt nonnative conformations in DNA and RNA. The key to this "delta-melt" approach is to use chemical modifications to render specific minor non-native conformations the major state. The validity and robustness of delta-melt is established for four different non-native conformations under various physiological conditions and sequence contexts through independent measurements of thermodynamic preferences using NMR. Delta-melt is faster relative to NMR, simple, and cost-effective and enables thermodynamic preferences to be measured for exceptionally low-populated conformations. Using delta-melt, we obtained rare insights into conformational cooperativity, obtaining evidence for significant cooperativity (1.0 to 2.5 kcal/mol) when simultaneously forming two adjacent Hoogsteen base pairs. We also measured the thermodynamic preferences to form G-C+ and A-T Hoogsteen and A-T base open states for nearly all 16 trinucleotide sequence contexts and found distinct sequence-specific variations on the order of 2 to 3 kcal/mol. This rich landscape of sequence-specific non-native minor conformations in the DNA double helix may help shape the sequence specificity of DNA biochemistry. Thus, melting experiments can now be used to access thermodynamic information regarding regions of the free energy landscape of biomolecules beyond the native folded and unfolded conformations.

Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.

Biomolecules form dynamic ensembles of many inter-converting conformations which are key for understanding how they fold and function. However, determining ensembles is challenging because the information required to specify atomic structures for thousands of conformations far exceeds that of experimental measurements. We addressed this data gap and dramatically simplified and accelerated RNA ensemble determination by using structure prediction tools that leverage the growing database of RNA structures to generate a conformation library. Refinement of this library with NMR residual dipolar couplings provided an atomistic ensemble model for HIV-1 TAR, and the model accuracy was independently supported by comparisons to quantum-mechanical calculations of NMR chemical shifts, comparison to a crystal structure of a substate, and through designed ensemble redistribution via atomic mutagenesis. Applications to TAR bulge variants and more complex tertiary RNAs support the generality of this approach and the potential to make the determination of atomic-resolution RNA ensembles routine.

2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states.

2'-O-Methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribose sugar pucker equilibrium toward the C3'-endo conformation formed in canonical duplexes. However, little is known about how Nm might more broadly alter the dynamic ensembles of flexible RNAs containing bulges and internal loops. Here, using NMR and the HIV-1 transactivation response (TAR) element as a model system, we show that Nm preferentially stabilizes alternative secondary structures in which the Nm-modified nucleotides are paired, increasing both the abundance and lifetime of low-populated short-lived excited states by up to 10-fold. The extent of stabilization increased with number of Nm modifications and was also dependent on Mg2+. Through phi-value analysis, the Nm modification also provided rare insights into the structure of the transition state for conformational exchange. Our results suggest that Nm could alter the biological activities of Nm-modified RNAs by modulating their secondary structural ensembles as well as establish the utility of Nm as a tool for the discovery and characterization of RNA excited state conformations.

A mechanism for the extension and unfolding of parallel telomeric G-quadruplexes by human telomerase at single-molecule resolution.

Telomeric G-quadruplexes (G4) were long believed to form a protective structure at telomeres, preventing their extension by the ribonucleoprotein telomerase. Contrary to this belief, we have previously demonstrated that parallel-stranded conformations of telomeric G4 can be extended by human and ciliate telomerase. However, a mechanistic understanding of the interaction of telomerase with structured DNA remained elusive. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) microscopy and bulk-phase enzymology to propose a mechanism for the resolution and extension of parallel G4 by telomerase. Binding is initiated by the RNA template of telomerase interacting with the G-quadruplex; nucleotide addition then proceeds to the end of the RNA template. It is only through the large conformational change of translocation following synthesis that the G-quadruplex structure is completely unfolded to a linear product. Surprisingly, parallel G4 stabilization with either small molecule ligands or by chemical modification does not always inhibit G4 unfolding and extension by telomerase. These data reveal that telomerase is a parallel G-quadruplex resolvase.

Modification of messenger RNA by 2'-O-methylation regulates gene expression in vivo.

Epitranscriptomic modifications of mRNA are important regulators of gene expression. While internal 2'-O-methylation (Nm) has been discovered on mRNA, questions remain about its origin and function in cells and organisms. Here, we show that internal Nm modification can be guided by small nucleolar RNAs (snoRNAs), and that these Nm sites can regulate mRNA and protein expression. Specifically, two box C/D snoRNAs (SNORDs) and the 2'-O-methyltransferase fibrillarin lead to Nm modification in the protein-coding region of peroxidasin (Pxdn). The presence of Nm modification increases Pxdn mRNA expression but inhibits its translation, regulating PXDN protein expression and enzyme activity both in vitro and in vivo. Our findings support a model in which snoRNA-guided Nm modifications of mRNA can regulate physiologic gene expression by altering mRNA levels and tuning protein translation.

i-Motif DNA: structural features and significance to cell biology.

The i-motif represents a paradigmatic example of the wide structural versatility of nucleic acids. In remarkable contrast to duplex DNA, i-motifs are four-stranded DNA structures held together by hemi- protonated and intercalated cytosine base pairs (C:C+). First observed 25 years ago, and considered by many as a mere structural oddity, interest in and discussion on the biological role of i-motifs have grown dramatically in recent years. In this review we focus on structural aspects of i-motif formation, the factors leading to its stabilization and recent studies describing the possible role of i-motifs in fundamental biological processes.

Controlled Growth and Grafting of High-Density Au Nanoparticles on Zinc Oxide Thin Films by Photo-Deposition.

The integration of high-purity nano-objects on substrates remains a great challenge for addressing scaling-up issues in nanotechnology. For instance, grafting gold nanoparticles (NPs) on zinc oxide films, a major step process for catalysis or photovoltaic applications, still remains difficult to master. We report a modified photodeposition (P-D) approach that achieves tight control of the NPs size (7.5 ± 3 nm), shape (spherical), purity, and high areal density (3500 ± 10 NPs/µm2) on ZnO films. This deposition method is also compatible with large ZnO surface areas. Combining electronic microscopy and X-ray photoelectron spectroscopy measurements, we demonstrate that growth occurs primarily in confined spaces (between the grains of the ZnO film), resulting in gold NPs embedded within the ZnO surface grains thus establishing a unique NPs/surface arrangement. This modified P-D process offers a powerful method to control nanoparticle morphology and areal density and to achieve strong Au interaction with the metal oxide substrate. This work also highlights the key role of ZnO surface morphology to control the NPs density and their size distribution. Furthermore, we experimentally demonstrate an increase of the ZnO photocatalytic activity due to high densities of Au NPs, opening applications for the decontamination of water or the photoreduction of water for hydrogen production.

Probing Synergistic Effects of DNA Methylation and 2'-ß-Fluorination on i-Motif Stability.

The possible role of DNA i-motif structures in telomere biology and in the transcriptional regulation of oncogene promoter regions is supported by several recent studies. Herein we investigate the effect of four cytidine nucleosides (and combinations thereof) on i-motif structure and stability, namely 2'-deoxycytidine (dC), 2'-deoxy-5-methyl-cytidine (5-Me-dC), 2'-deoxy-2'-fluoro-arabinocytidine (2'F-araC), and 2'-deoxy-2'-fluoro-5-methyl-arabinocytidine (5-Me-2'F-araC). The base pair 5-Me-2'F-araC:2'F-araC produced i-motifs with a pH1/2 ("pKa ") value that closely matches physiological pH (7.34±0.3). NMR analysis of the most stable telomeric sequence (HJ-2) at pH 7.0 indicated that the structure is stabilized by hybrid 5-Me-dC:2'F-araC hemiprotonated base pairs and therefore highlights the significance of the interplay between base and sugar modifications on the stability of i-motif structures.

2'-Fluoroarabinonucleic acid modification traps G-quadruplex and i-motif structures in human telomeric DNA.

Human telomeres and promoter regions of genes fulfill a significant role in cellular aging and cancer. These regions comprise of guanine and cytosine-rich repeats, which under certain conditions can fold into G-quadruplex (G4) and i-motif structures, respectively. Herein, we use UV, circular dichroism and NMR spectroscopy to study several human telomeric sequences and demonstrate that G4/i-motif-duplex interconversion kinetics are slowed down dramatically by 2'-ß-fluorination and the presence of G4/i-motif-duplex junctions. NMR-monitored kinetic experiments on 1:1 mixtures of native and modified C- and G-rich human telomeric sequences reveal that strand hybridization kinetics are controlled by G4 or i-motif unfolding. Furthermore, we provide NMR evidence for the formation of a hybrid complex containing G4 and i-motif structures proximal to a duplex DNA segment at neutral pH. While the presence of i-motif and G4 folds may be mutually exclusive in promoter genome sequences, our results suggest that they may co-exist transiently as intermediates in telomeric sequences.

Titanium coordination compounds: from discrete metal complexes to metal-organic frameworks.

Owing to their promise in photocatalysis and optoelectronics, titanium based metal-organic frameworks (MOFs) are one of the most appealing classes of MOFs reported to date. Nevertheless, Ti-MOFs are still very scarce because of their challenging synthesis associated with a poor degree of control of their chemistry and crystallization. This review aims at giving an overview of the recent progress in this field focusing on the most relevant existing titanium coordination compounds as well as their promising photoredox properties. Not only Ti-MOFs but also Ti-oxo-clusters will be discussed and particular interest will be dedicated to highlight the different successful synthetic strategies allowing to overcome the still "unpredictable" reactivity of titanium ions, particularly to afford crystalline porous coordination polymers.

Mapping the affinity landscape of Thrombin-binding aptamers on 2΄F-ANA/DNA chimeric G-Quadruplex microarrays.

In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2΄-Fluoroarabinonucleic acid (2΄F-ANA) is a prime candidate for such use in microarrays. Indeed, 2΄F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered. We thus synthesized the first microarrays containing 2΄F-ANA and 2΄F-ANA/DNA chimeric sequences to fully map the binding affinity landscape of the TBA1 thrombin-binding G-quadruplex aptamer containing all 32 768 possible DNA-to-2΄F-ANA mutations. The resulting microarray was screened against thrombin to identify a series of promising 2΄F-ANA-modified aptamer candidates with Kds significantly lower than that of the unmodified control and which were found to adopt highly stable, antiparallel-folded G-quadruplex structures. The solution structure of the TBA1 aptamer modified with 2΄F-ANA at position T3 shows that fluorine substitution preorganizes the dinucleotide loop into the proper conformation for interaction with thrombin. Overall, our work strengthens the potential of 2΄F-ANA in aptamer research and further expands non-genomic applications of nucleic acids microarrays.

Investigating the Case of Titanium(IV) Carboxyphenolate Photoactive Coordination Polymers.

The reactivity of 2,5-dihydroxyterephthalic acid (H4DOBDC) with titanium(IV) precursors was thoroughly investigated for the synthesis of metal-organic frameworks under solvothermal conditions. Four crystalline phases were isolated whose structures were studied by a combination of single-crystal or powder X-ray diffraction and solid-state NMR. The strong coordination ability of the phenolate moieties was found to favor the formation of isolated TiO6 octahedra bearing solely organic ligands in the resulting structures, unless hydrothermal conditions and precondensed inorganic precursors are used. It is worth noting that these solids strongly absorb visible light, as a consequence of the ligand-to-metal charge transfer (LMCT) arising from Ti-phenolate bonds. Preliminary photocatalytic tests suggest that one compound, namely, MIL-167, presents a higher activity for hydrogen evolution than the titanium carboxylate MIL-125-NH2 but that such an effect cannot be directly correlated with its improved light absorption feature.

Stabilization of i-motif structures by 2'-ß-fluorination of DNA.

i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH(+)). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2'-endo conformation, instead of the C3'-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology.

Aqueous removal of diclofenac by plated elemental iron: bimetallic systems.

The aqueous removal of diclofenac (DF) by micrometric iron particles (Fe(0)) and amended Fe(0) (Me(0)(Fe(0))) under oxic and anoxic conditions was investigated. Bimetallic systems were obtained by plating the surface of Fe with Co, Cu, Ir, Ni, Pd and Sn. Experimental results confirmed the superiority of (Me(0)(Fe(0))) for DF removal except for IrFe (oxic) and SnFe (anoxic). Under anoxic conditions, Pd was by far the most efficient plating element followed by Ir, Ni, Cu, Co and Sn. However, under oxic conditions, Pd and Cu showed almost the same efficiency in removing DF followed by Ni, Co, Sn and Ir. Oxidative and reductive DF transformation products were identified under oxic and anoxic conditions respectively. In some systems (e.g. CoFe and SnFe oxic/anoxic; PdFe oxic; NiFe anoxic), no transformation products could be detected. This was ascribed to the nature of the plating element and its impact on the process of the formation of metal corrosion products (MCPs). MCPs are known for their high potential to strongly adsorb, bond, sequestrate and enmesh both the original contaminant and its reaction products. Obtained results corroborate the universal validity of the view, that aqueous contaminants are basically removed by adsorption and co-precipitation.

Investigating the mechanism of clofibric acid removal in Fe(0)/H2O systems.

Since the introduction of iron wall technology, the inherent relationship between contaminant removal and iron corrosion has been mostly attributed to electron transfer from the metal body (direct reduction). This thermodynamically founded premise has failed to explain several experimental facts. Recently, a new concept considering adsorption and co-precipitation as fundamental contaminant removal mechanisms was introduced. This consistent concept has faced very skeptic views and necessarily needs experimental validation. The present work was the first independent attempt to validate the new concept using clofibric acid (CLO) as model compound. For this purpose, a powdered Fe(0) material (Fe(0)) was used in CLO removal experiments under various experimental conditions. Additional experiments were performed with plated Fe(0) (mFe(0): Fe(0)/Pd(0), Fe(0)/Ni(0)) to support the discussion of removal mechanism. Main investigated experimental variables included: abundance of O(2), abundance of iron corrosion products (ICPs) and shaking operations. Results corroborated the concept that quantitative contaminant removal in Fe(0)/H(2)O systems occurs within the oxide-film in the vicinity of Fe(0). Additionally, mixing type and shaking intensity significantly influenced the extent of CLO removal. More importantly, HPLC/MS revealed that the identity of reaction products depends on the extent of iron corrosion or the abundance of ICPs. The investigation of the CLO/Fe(0)/H(2)O system disproved the popular view that direct reduction mediates contaminant removal in the presence of Fe(0).

Antibiotic removal from water: elimination of amoxicillin and ampicillin by microscale and nanoscale iron particles.

Zerovalent iron powder (ZVI or Fe(0)) and nanoparticulate ZVI (nZVI or nFe(0)) are proposed as cost-effective materials for the removal of aqueous antibiotics. Results showed complete removal of Amoxicillin (AMX) and Ampicillin (AMP) upon contact with Fe(0) and nFe(0). Antibiotics removal was attributed to three different mechanisms: (i) a rapid rupture of the beta-lactam ring (reduction), (ii) an adsorption of AMX and AMP onto iron corrosion products and (iii) sequestration of AMX and AMP in the matrix of precipitating iron hydroxides (co-precipitation with iron corrosion products). Kinetic studies demonstrated that AMP and AMX (20 mg L(-1)) undergo first-order decay with half-lives of about 60.3+/-3.1 and 43.5+/-2.1 min respectively after contact with ZVI under oxic conditions. In contrast, reactions under anoxic conditions demonstrated better degradation with t(1/2) of about 11.5+/-0.6 and 11.2+/-0.6 min for AMP and AMX respectively. NaCl additions accelerated Fe(0) consumption, shortening the service life of Fe(0) treatment systems.