Thermal difference spectra: a specific signature for nucleic acid structures

We show that nucleic acid structures may be conveniently and inexpensively characterized by their UV thermal difference spectra. A thermal difference spectrum (TDS) is obtained for a nucleic acid by simply recording the ultraviolet absorbance spectra of the unfolded and folded states at temperatures above and below its melting temperature (T(m)). The difference between these two spectra is the TDS. The TDS has a specific shape that is unique for each type of nucleic acid structure, a conclusion that is based on a comparison of >900 spectra from 200 different sequences. The shape of the TDS reflects the subtleties of base stacking interactions that occur uniquely within each type of nucleic acid structure. TDS provides a simple, inexpensive and rapid method to obtain structural insight into nucleic acid structures, which is applicable to both DNA and RNA from short oligomers to polynucleotides. TDS complements circular dichroism as a tool for the structural characterization of nucleic acids in solution

Kinetics of double-chain reversals bridging contiguous quartets in tetramolecular quadruplexes

Repetitive 5′GGXGG DNA segments abound in, or near, regulatory regions of the genome and may form unusual structures called G-quadruplexes. Using NMR spectroscopy, we demonstrate that a family of 5′GCGGXGGY sequences adopts a folding topology containing double-chain reversals. The topology is composed of two bistranded quadruplex monomeric units linked by formation of G:C:G:C tetrads. We provide a complete thermodynamic and kinetic analysis of 13 different sequences using absorbance spectroscopy and DSC, and compare their kinetics with a canonical tetrameric parallel-stranded quadruplex formed by TG(4)T. We demonstrate large differences (up to 10(5)-fold) in the association constants of these quadruplexes depending on primary sequence; the fastest samples exhibiting association rate equal or higher than the canonical TG(4)T quadruplex. In contrast, all sequences studied here unfold at a lower temperature than this quadruplex. Some sequences have thermodynamic stability comparable to the canonical TG(4)T tetramolecular quadruplex, but with faster association and dissociation. Sequence effects on the dissociation processes are discussed in light of structural data

The exception that confirms the rule: a higher-order telomeric G-quadruplex structure more stable in sodium than in potassium

International audienceDNA and RNA guanine-quadruplexes (G4s) are stabilized by several cations, in particular by potassium and sodium ions. Generally, potassium stabilizes guanine-quartet assemblies to a larger extent than sodium; in this article we report about a higherorder G4 structure more stable in sodium than in potassium. Repeats of the DNA GGGTTA telomeric motif fold into contiguous G4 units. Using three independent approaches (thermal denaturation experiments, isothermal molecular-beacon and proteinbinding assays), we show that the (GGGTTA) 7 GGG sequence, folding into two contiguous G4 units, exhibits an unusual feature among G4 motifs: despite a lower thermal stability, its sodium conformation is more stable than its potassium counterpart at physiological temperature. Using differential scanning calorimetry and mutated sequences, we show that this switch in the relative stability of the sodium and potassium conformations (occurring around 45 • C in 100 mM cation concentration) is the result of a more favorable enthalpy change upon folding in sodium, generated by stabilizing interactions between the two G4 units in the sodium conformation. Our work demonstrates that interactions between G4 structural domains can make a higherorder structure more stable in sodium than in potassium, even though its G4 structural domains are individually more stable in potassium than in sodium

Biochimie

During clinical trials, a number of fully characterized molecules are dropped along the way because they do not provide enough benefit for the patient. Some of them show limited side effects and might be of great use for other applications. AS1411 is a nucleolin-targeting aptamer that underwent phase II clinical trials as anticancer agent. Here, we show that AS1411 exhibits extremely potent antiviral activity and is therefore an attractive new lead as anti-HIV agent

Bioaugmentation: Possible solution in the treatment of Bio-Refractory Organic Compounds (Bio-ROCs)

International audienceWater quality is questionable when looking at the emerging pollutants that accumulate in hydrosphere day after day. In terms of water treatments to eliminate organic compounds, biological treatments are the most used technique, especially the conventional activated sludge (CAS) process. Unfortunately, several of these compounds such as petroleum and industrial wastes, some pesticides, pharmaceuticals, and hormonal substances appear to be refractory to such treatments and can join the different water surfaces from other natural environments especially contaminated soils. Physical and chemical treatments, in particularly the advanced oxidation processes (AOPs) are able to degrade some of these pollutants, but the nature and the possible effects of oxidation by-products remain controversial when complete mineralization does not occur. The aim of this article is to shed light on new and renewed biotechnological techniques recently introduced to resolve recalcitrance problem. Amending activated sludge with additional microorganisms able to produce versatile enzymes to enhance biodegradability or "bioaugmentation", is gradually considered as a possible solution for the recalcitrance of Bio-Refractory Organic Compounds (Bio-ROCs). The use of this technique, traditionally in soil remediation field, and recently in water and sediments treatment is reviewed in this paper

INFLUENCE OF STIRRING SPEED AND GAS-TO-LIQUID RATIO ON ACTIVATED SLUDGE PERFORMANCE IN CARBAMAZEPINE ELIMINATION USING RESPONSE SURFACE METHODOLOGY AND PRINCIPAL COMPONENT ANALYSIS

International audienc

Quadruplex Turncoats: Cation-Dependent Folding and Stability of Quadruplex-DNA Double Switches

International audienceQuadruplex (G4) nucleic acids, a family of secondary structures formed by guanine-rich sequences, exhibit an important structural polymorphism. We demonstrate here that G-rich DNA sequences may function as a double switch based on different triggers provided that their quadruplex structures and stability display a high dependence on cation nature and concentration. A first switch is based on a remarkable antiparallel to parallel conversion, taking place in a few seconds at room temperature by addition of low KCl amounts to a sodium-rich sample. The second switch involves the conversion of alternative antiparallel quadruplex structures binding only one cation, formed in the presence of submillimolar potassium or strontium concentrations, to parallel structures by increasing the cation concentration. Incidentally, extremely low K+ or Sr2+ concentrations (≤ 5 equivalents) are sufficient to induce G4 formation in a buffer devoid of other G4-promoting cations, and we suggest that the alternative structures observed contain only two tetrads. Such DNA systems are biological relevant targets, can be used in nanotechnology applications, and are valuable methodological tool for the understanding of DNA quadruplex folding, notably at low cation concentrations. We demonstrate that this behavior is not restricted to a narrow set of sequences but can also be found for other G-quadruplex forming motifs, arguing for widespread applications

Enhancement of ethanol production from synthetic medium model of hydrolysate of macroalgae

International audienceAmong biomass materials available, macroalgae is a promising alternative to traditional energy crops. The absence of lignin, a high growth rate and a richness of fermentable sugars and nitrogen, are real gains for a competitive ethanol production. But the presence of salts can be an obstacle to obtain relevant performances. Experiments were carried out with a synthetic medium adjusted on algal hydrolysate composition in order to reduce resource limitations and variations of composition. The behavior of four yeast strains for ethanol production was investigated Candida guilliermondii, Scheffersomyces stipitis, Kluyveromyces marxianus and Saccharomyces cerevisiae. Glucose, which is the most abundant sugar in the targeted algal hydrolysate (Ulva spp), was completely assimilated by all of the considered strains, even in the presence of salts at levels found in macroalgal hydrolysates (0.25 M of sodium chloride and 0.21 M of sulfate). The use of peptone as nitrogen source enhanced kinetics of consumption and production. For instance, the rate of ethanol production by S. cerevisiae in the presence of peptone was six times higher than that obtained using ammonium, 0.6 and 0.1 g L−1 h−1 respectively. In the presence of salts, the rates of glucose consumption and ethanol production were lowered for the considered strains, except for K. marxianus. Nevertheless, S. cerevisiae could be the most promising strain to valorize Ulva spp hydrolysate in bioethanol, in terms of ethanol produced (7.5–7.9 g L−1) whether in the presence or in absence of salts