Accurate molecular weight measurements of nucleoside phosphoramidites: a suitable matrix of mass spectrometry

Nucleoside phosphoramidites (PAs) are the most widely used building blocks in contemporary solid-phase synthesis of oligonucleotides. The accurate molecular weight (MW) measurements of such molecules, which contain acid-labile moieties, may be easily determined by mass spectrometry using a matrix system, triethanolamine (TEOA)-NaCl, on liquid secondary ion mass spectrometry (LSIMS) equipped with a double-focusing mass spectrometer. The present method measures rapidly and easily the accurate MWs of various PAs as adduct ions [M+Na]⁺ with average mass error smaller than 0.4 ppm, allowing the formulas of various PAs in place of elemental analysis. Further, it was found that intensities of molecular-related ions could be enhanced to the highest degree by adjustment of the mole ratio of PA and NaCl fixing the amount of TEOA on LSIMS, making the present method powerful tool for the MS identification of PAs.     

Laser Spectroscopy of the CCO Radical in the 0.77-μm Region: Analysis of theÃ(020)κΠ andÃΠi(001) States

TheÃ(020)κ³Π–X³Σ⁻(000) andóΠ_i(001)–X³Σ⁻(000) bands of the CCO radical have been investigated by laser spectroscopy with two types of tunable laser system. An analysis was made simultaneously for both the bands to establish line assignments and determine molecular constants for both theÃ(020) andÃ(001) states. A coupling constant between these two states was also determined by assuming the interaction to be of Fermi type.     

Near-infrared diode laser spectroscopy of free radicals

Spectroscopic results on the radicals HCSi, CCO, and FeC obtained by studying in detail energy level structures using 0.8 microm diode laser system are reported. Of these radicals, the CCO radical was investigated mainly using Fabry-Perot type diode lasers with inconvenient mode gaps in the early stage of our near-infrared diode laser spectroscopic study of free radicals, and on the other hand, the FeC and HCSi radicals were studied using an external cavity diode laser. For the FeC radical, which is an interesting radical composed of an iron atom having 3d electrons, information on spin-orbit interaction between the triplet electronic ground state and a low-lying singlet electronic excited state is reported somewhat in detail. For the HCSi and CCO radicals, spectral particularities produced by a Renner-Teller interaction and a spin-orbit interaction are described for their high-resolution spectroscopic interest.     

Association of Am with humic substances isolated from river waters with different water quality

The association properties of Am with aquatic humic substances in a 0.01M NaClO₄ solution at pH 6-8 were studied on the basis of molecular size distribution. Ten humic substances isolated from river water with different water quality (pH 3.9-8.0 and dissolved organic carbon (DOC) concentration of 2-40 mg/l) were used for comparing their effects on the association of Am. The molecular size distribution of Am in the presence of humic substances from an uncolored river water (DOC 2 mg/l) was different from that at the experimental systems using humic substances from brownish and high DOC (14-40 mg/l) river waters.     

Comparability of composition of carbon functional groups in humic acids between inverse-gated decoupling and cross polarization/magic angle spinning 13C nuclear magnetic resonance techniques

To find a certain relation between the composition of carbon functional groups of humic acids derived from liquid state ¹³C nuclear magnetic resonance (NMR) spectra acquired with inverse-gated decoupling (IGD), known as a quantitative pulse sequence, and that by solid-state ¹³C NMR with cross polarization/magic angle spinning (CPMAS) techniques, fifteen soil humic acid samples with a wide range of aromaticity were analyzed. Relationships between the proportions of humic acid carbon as alkyl, O-alkyl, and aromatic carbon assessed by the two methods could be regressed to y = ax (r = 0.932-0.956; P < 0.005), respectively. The contents of alkyl, O-alkyl, and aromatic carbon assessed by CPMAS method were larger than those found by IGD method. However, the differences between the two methods were small and exclusive regression to y = x was also significant (r = 0.775-0.941; P < 0.005). Aromaticity calculated from ¹³C CPMAS NMR data also did not differ significantly from those computed from ¹³C NMR spectra with IGD. These observations indicated the comparability of the relative content of carbon functional groups in humic acids except for carboxyl and carbonyl carbon.     

Synthesis of novel tetrazole C5-linked C0- and C2-ribonucleoside phosphoramidites using MePOM and POM groups for probing RNA catalysis

Novel C5-linked C₀- and C₂-tetrazole ribonucleoside phosphoramidites were designed and synthesized via tetrazole C-nucleosides. Pivaloyloxymethyl (POM) and methyl-substituted POM (MePOM) groups were introduced as N-protecting groups in the tetrazole ring that can be readily removed under mild basic conditions. The phosphoramidites were successfully incorporated into the VS ribozyme substrate and hence providing a chemogenetic approach to determine which nucleobases of ribozymes function as the acid or base, in the studies of ribozyme general acid and base catalysis.     

Optimization of conditions for high-performance size-exclusion chromatography of different soil humic acids.

A method of high-performance size-exclusion chromatography (HPSEC) for a wide variety of soil humic acids (HAs) was developed. Two types of soil HAs (Cambisol and Andosol HAs), which have substantially different chemical properties, showed different effects of salt and organic solvent concentrations in the eluent on chromatograms. A Shodex OHpak SB-805 HQ column with 10 mM sodium phosphate buffer (pH 7.0) containing 25% of acetonitrile (v/v) was found to be applicable for different HAs, and showed high reproducibility and recovery (87.0 - 94.5%). The Cambisol HA was fractionated into five fractions using an ultrafiltration with different molecular-weight cut-offs. The order of the molecular weights of the five fractions calculated from the HPSEC analysis corresponded to that defined by ultrafiltration. This supported the reliability of the method.     

Laser Spectroscopy of the CCO Radical in the 0.77-μm Region: Analysis of theÃ(020)κΠ andÃΠi(001) States

TheÃ(020)κ³Π–X³Σ⁻(000) andóΠ_i(001)–X³Σ⁻(000) bands of the CCO radical have been investigated by laser spectroscopy with two types of tunable laser system. An analysis was made simultaneously for both the bands to establish line assignments and determine molecular constants for both theÃ(020) andÃ(001) states. A coupling constant between these two states was also determined by assuming the interaction to be of Fermi type.     

Molecular size fractionation of soil humic acids using preparative high performance size-exclusion chromatography

High performance size-exclusion chromatography (HPSEC) is useful for the molecular size separation of soil humic acids (HAs), but there is no method available for various HAs with different chemical properties. In this paper the authors propose a new preparative HPSEC method for various soil HAs. Three soil HAs with different chemical properties were fractionated by a Shodex OHpak SB-2004 HQ column with 10mM sodium phosphate buffer (pH 7.0)/acetonitrile (3:1, v/v) as an eluent. The HAs eluted within a reasonable column range time (12-25 min) without peak tailing. Preparative HPSEC chromatograms of these HAs indicated that non-size-exclusion effects were suppressed. The separated fractions were analyzed by HPSEC to determine their apparent molecular weights. These decreased sequentially from fraction 1 to fraction 10, suggesting that the HAs had been separated by their molecular size. The size-separated fractions of the soil HA were mixed to compare them with unfractionated HA. The analytical HPSEC chromatogram of the mixed HA was almost identical to that of the unfractionated HA. It appears that the HAs do not adsorb specifically to the column during preparative HPSEC. Our preparative HPSEC method allows for rapid and reproducible separation of various soil HAs by molecular size.