Exploring the energy landscape of a small RNA hairpin

The energy landscape of a small RNA tetraloop hairpin is explored by temperature jump kinetics and base-substitution. The folding kinetics are single-exponential near the folding transition midpoint T(m). An additional fast phase appears below the midpoint, and an additional slow phase appears above the midpoint. Stem mutation affects the high-temperature phase, while loop mutation affects the low-temperature phase. An adjusted 2-D lattice model reproduces the temperature-dependent phases, although it oversimplifies the structural interpretation. A four-state free energy landscape model is generated based on the lattice model. This model explains the thermodynamics and multiphase kinetics over the full temperature range of the experiments. An analysis of three variants shows that one of the intermediate RNA structures is a stacking-related trap affected by stem but not loop modification, while the other is an early intermediate that forms some stem and loop structure. Even a very fast-folding 8-mer RNA with an ideal tetraloop sequence has a rugged energy landscape, ideal for testing analytical and computational models.     

Michael and ring expansion reactions of 6-carboethoxy-3,5-diaryl-2-cyclohexen-1-ones

When -keto-ester1 a was reacted with dimethyl acetylenedicarboxylate ring expansion occurred to give substituted cyclooctadienones.Michael reactions of the title compounds1 with unsaturated ketones gave adducts, some of which underwent further cyclization reactions. A new route to -tetralone ring system10 via cyclization of the intermediateMichael adduct9 is described.

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Michael- und Ringerweiterungsreaktionen von 6-Carboethoxy-3,5-diaryl-2-cyclohexen-1-onen

Zusammenfassung Bei der Reaktion von -Keto-ester1 a mit Dimethyl-acetylendicarboxylat wurden unter Ringerweiterung substituierte Cyclooctadienone erhalten. DieMichael-Reaktion der Titelverbindung1 mit ungesättigten Ketonen ergab Addukte, von denen einige weitere Cyclisierungsreaktionen eingingen. Es wird ein neuer Weg zum -Tetralonsystem10 über die Cyclisierung des intermediärenMichael-Addukts9 beschrieben.

     

High pressure Raman spectroscopy of single-walled carbon nanotubes: Effect of chemical environment on individual nanotubes and the nanotube bundle

The pressure-induced tangential mode Raman peak shifts for single-walled carbon nanotubes (SWNTs) have been studied using a variety of different solvents as hydrostatic pressure-transmitting media. The variation in the nanotube response to hydrostatic pressure with different pressure transmitting media is evidence that the common solvents used are able to penetrate the interstitial spaces in the nanotube bundle. With hexane, we find the surprising result that the individual nanotubes appear unaffected by hydrostatic pressures (i.e. a flat Raman response) up to 0.7 GPa. Qualitatively similar results have been obtained with butanol. Following the approach of Amer et al. [J. Chem. Phys. 121 (2004) 2752], we speculate that this is due to the inability of SWNTs to adsorb some solvents onto their surface at lower pressures. We also find that the role of cohesive energy density in the solvent-nanotube interaction is more complex than previously thought.     

New ideas in neutrino detection

What is new in the field of neutrino detection? In addition to new projects probing both the low and high ends of the neutrino energy scale, an inexpensive, effective technique is being developed to allow tagging of antineutrinos in water Cherenkov (WC) detectors via the addition to water of a solute with a large neutron cross-section and energetic γ daughters. Gadolinium is an excellent candidate since in recent years it has become very inexpensive, now less than $8 per kilogram in the form of commercially available gadolinium trichloride. This non-toxic, non-reactive substance is highly soluble in water. Neutron capture on gadolinium yields an 8.0 MeV gamma cascade easily seen in detectors like Super-Kamiokande. The uses of GdCl₃ as a possible upgrade for the Super-Kamiokande detector — with a view toward improving its performance as an antineutrino detector for supernova neutrinos and reactor neutrinos — are discussed, as are the ongoing R&;D efforts which aim to make this dream a reality within the next two years.     

Yeast deoxyribodipyrimidine photolyase (photoreactivating enzyme): optimum conditions for activity and competitive inhibition

Abstract— Using flash photolytic techniques and direct chemical measurements of the conversion of the substrate (conversion of thymine dimers in DNA to monomeric thymine), we have determined photolyase concentrations in partially purified preparations of soluble proteins from yeast and have determined under continuous intense light the forward rate constant k₁ for binding of the enzyme and its substrate under a variety of conditions. The ionic requirements and the sharp peak of ionic strength dependence are independent of the species of uni-univalent salts used in the assay. At infinite dilution, the k₁ for denatured DNA, and its ionic strength dependence, both appear identical to the values for native DNA. Both unirradiated denatured and unirradiated native DNA inhibit binding, denatured DNA being 10- to 20-fold more effective. These combined factors have been taken into account to devise a sensitive assay for photoreactivable lesions in unlabeled DNA by competition in a flash photoreactivation reaction. The assay is used to measure dark repair in Micrococcus luteus in complete medium. After a dose of 100 J/m² the wild type of this organism removes photoreactivable lesions (pyrimidine dimers) from its DNA with a half-time of 7 min at 35°C.     

Selection of internal standards for quantitative analysis by matrix-assisted laser desorption-ionization (MALDI) time-of-flight mass spectrometry

The selection of an appropriate internal standard (IS) for quantification by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is critical for the successful application of quantitative MALDI. Selection of the IS depends on the chemical similarity of the analyte and IS and the mass separation of the analyte and IS as a function of instrumental peak resolution. For the quantification of bovine insulin, a series of internal standards including horse heart cytochrome C, bovine insulin chain B, des-pentapeptide human insulin, and des-octapeptide porcine insulin was investigated. Des-pentapeptide human insulin was found to be the most appropriate internal standard (relative standard deviation of the standard curve slope = 2.99%, correlation coefficient = 0.988 in the range of 0.5-0.4 μmol/L). Two methods for measuring of the MALDI signal intensity were evaluated, direct peak integration following subtraction of a linear background and non-linear least squares curve fitting. The results obtained with these methods were equivalent.     

Studies of consecutive reactions of quinones in a reversed geometry mass spectrometer

Consecutive reactions involving the ejection of molecules of carbon monoxide from quinone systems have been studied. Using a reversed geometry double focusing mass spectrometer, the individual steps of a consecutive reaction may be separated into different field free regions. The structure of ions formed in the ion source may be compared with those formed from the fragmentation of metastable ions in a field free region by studying differences in the pattern of translational energies released when they break. In the case of anthraquinone it is found that two structures exist for the [M? CO]^+˙ ion. Critical energy measurements strengthen this argument. Furthermore, ¹⁸O labelling has been used to distinguish between the loss of carbon monoxide from different positions on the molecular ion of 1-hydroxyanthraquinone.