Mass transfer process and separation mechanism of four 5'-ribonucleotides on a strong acid cation exchange resin.

5'-ribonucleotides including adenosine 5'-monophosphate (AMP), cytidine 5'-monophsphate (CMP), guanosine 5'-monophosphate (GMP) and uridine 5'-monophosphate (UMP) have been widely used in the food and pharmaceutical industries. This work focused on the assessment of mass transfer process and separation mechanism of four 5'-ribonucleotides and counter-ion Na+ on the strong cation exchange resin NH-1. The intraparticle diffusion was determined as the rate-limiting step for the mass transfer of AMP, CMP, GMP, and Na+ on the resin NH-1 through the Boyd model. Meanwhile, a homogeneous surface diffusion model (HSDM) combing ion exchange and physical adsorption was proposed and tested against adsorption kinetic data in the batch adsorption systems. The fixed-bed film-surface diffusion model based on the HSDM was then developed and successfully predicted the concentration profiles of 5'-ribonucleotides and the change of pH at the outlet of the fixed-bed in the dynamic adsorption and separation process. Finally, the separation mechanism of 5'-ribonucleotides was presented combining model prediction and experimental results. The separation of UMP, GMP and CMP were mainly based on their differences in isoelectric points, while that of AMP and CMP were lied with the discrepancy of their physical adsorption binding capacity with the resin NH-1.

Adsorption mechanisms of RNA mononucleotides on silver nanoparticles.

Surface-enhanced Raman scattering (SERS) of four RNA mononucleotides (AMP, GMP, CMP and UMP) has been studied on the citrate-reduced silver colloid aggregated with sodium sulfate. Concentration dependent spectra in the range of 1×10(-7)-1×10(-4) mol dm(-3) were obtained, assigned and interpreted according to the surface selection rules. For purine mononucleotides, AMP and GMP, adsorption onto the silver nanoparticles through the six-membered ring of the nitrogenous base was suggested. Concentration dependent splitting of the ring breathing band in the spectra of AMP indicated coexistence of two species on the silver surface, which differed in contribution of the adenine N1 atom and the exocyclic NH2 group in binding. Unlike the AMP spectra, the spectra of GMP implied only one mode of adsorption of the molecules onto the silver nanoparticles, taking place through the guanine N1H and C=O group. Weak SERS spectra of pyrimidine mononucleotides, CMP and UMP, pointed to involvement of carbonyl oxygen in adsorption process, whereby the molecules adopted the position on the nanoparticles with ribose close to the metal surface. Intense bands in the low wavenumber region, associated with stretching of the formed Ag-N and/or Ag-O bonds, supported chemical binding of the RNA mononucleotides with the silver surface.

Gas-phase isolation of diethyl guanosine 5'-monophosphate and its conformational assignment.

We show that intact neutral molecules of guanosine 5'-monophosphate can be vaporized by laser desorption when its phosphate group is esterified. The UV and IR spectroscopic measurements of this nucleotide reveal the existence of a novel internal hydrogen-bonding conformation of the phosphate group and guanine moiety.

NaDDBS as a dispersion agent for multiwalled carbon nanotubes in capillary EKC separation of nucleotides.

A novel pseudostationary phase (PSP) of multiwalled carbon nanotubes (MWCNTs) dispersed with sodium dodecylbenzenesulfonate (NaDDBS) was used for the EKC separation of nucleotides. NaDDBS has a long hydrophobic chain and a benzylsulfonate group. It suspends more MWCNTs (about 100-fold) than SDS, and the π-π interaction between the benzene ring of NaDDBS and MWCNTs prolongs the slurry suspension time. Using NaDDBS as a surfactant can reduce the required amount of MWCNTs and decrease the baseline noise. To produce a stable suspension, the optimum ratio (w/w) of MWCNTs to NaDDBS was investigated with turbidimetry. In this context, several parameters affecting EKC separation were studied, including buffer pH, composition, concentration, and the organic modifier. Use of NaDDBS (8 mg/L)/MWCNTs (0.8 mg/L) as the PSP in a phosphate buffer (30 mM, pH 8) yielded complete resolution of seven geometric isomers of a nucleoside monophosphate. In stacking mode, with 10% MeOH in the sample plug, the mixture of nucleoside mono-, di-, and tri-phosphates was satisfactorily separated in phosphate buffer (50 mM, pH 9). The results indicate that nucleotides with bases containing more electron-withdrawing groups interact more strongly with MWCNTs. The system has been used to separate oligonucleotides, and to analyze nucleotides in a complex matrix sample.

Liquid-core waveguide technology for coupling column liquid chromatography and Raman spectroscopy.

The on-line coupling of liquid chromatography (LC) and Raman spectroscopy (RS) via an entirely plastic liquid-core waveguide (LCW) was optimized in terms of excitation wavelength of the laser, especially in relation to the fluorescence background, and the length of the LCW. Excitation at 632.8 nm (He-Ne laser) was found to be a good compromise between a wavelength long enough to strongly reduce the fluorescence background and, on the other hand, short enough to avoid (re)-absorption of laser light and Raman signals by H2O in LCWs of considerable length. This conclusion is supported by a theoretical discussion on the optimization of LCW lengths as function of the excitation wavelength for H2O and 2H2O. When using the He-Ne laser the optimum length is approximately 50 cm for H2O; this corresponds to a detection cell volume of 19 microl for an LCW of 220 microm I.D., which is fully compatible with conventional-size LC. The influence of an organic modifier, usually necessary for reversed-phase LC, on the free spectral window was evaluated. The potential applicability of LC-LCW-RS was shown for a mixture of adenosine 5'-monophosphate (AMP), guanosine 5'-monophosphate (GMP) and uridine 5'-monophosphate (UMP), utilizing an aqueous eluent without the addition of a modifier. Improved detectability was achieved by using the stopped-flow mode and applying a large-volume-injection procedure (injection volume: 200 microl). Under these conditions, the limit of identification for AMP, GMP and UMP was in the 0.1-0.5-mg/ml range.

In vitro selection of a novel catalytic RNA: characterization of a sulfur alkylation reaction and interaction with a small peptide.

An in vitro RNA selection for catalytic activity was used to co-select for binding activity to a small peptide. 5'-phosphorothioate-modified RNA (GMPS-RNA) sequences were selected from a randomized pool of oligoribonucleotides for their ability to accelerate a halide substitution reaction with N-bromoacetyl-bradykinin (BrBK). One RNA selected shows a 2,420-fold increase in rate of reaction with BrBK relative to the starting pool. This reaction is specifically inhibited by free bradykinin (Ki 230 microM), indicating that interactions with bradykinin contribute to the rate enhancement. Inhibition of the reaction by the peptide requires both the amino- and carboxy-terminal arginine residues of the peptide for optimal inhibition activity. Reaction with N-bromoacetamide is not enhanced, indicating that the intrinsic reactivity of the 5' phosphorothioate is not increased in the selected RNA. Through 3'-end boundary analysis, much of the catalytic activity of the selected GMPS-RNA is shown to reside in a hairpin structure in the selected region of the molecule. This hairpin structure is also implicated in the recognition of the peptide substrate.

Direct assay method for guanosine 5'-monophosphate reductase activity.

A sensitive and simple micromethod for the accurate measurement of GMP reductase (EC 1.6.6.8) activity in crude extracts is described. The reaction product of [8-14C]IMP was separated from the substrate [8-14C]GMP by descending chromatography on Whatman DE81 ion-exchange paper. This separation method provides an analysis of the possible interfering reactions, such as the metabolic conversion of the substrate GMP to GDP, GTP, and/or guanosine, and guanine and the loss of the product IMP to inosine, hypoxanthine, and other metabolites. Low blank values (70-90 cpm) were obtained consistently with this assay because the IMP spot moves faster than the GMP spot. The major advantages of this method are direct measurement of GMP reductase activity in crude extracts, high sensitivity (with a limit of detection of < 10 pmol of IMP production), high reproducibility (< +/- 5%), and capability to measure activity in small samples (9 micrograms protein).

O-ribosyl-phosphate purine as a constant modified nucleotide located at position 64 in cytoplasmic initiator tRNAs(Met) of yeasts.

The unknown modified nucleotide G*, isolated from both Schizosaccharomyces pombe and Torulopsis utilis initiator tRNAs(Met), has been identified as an O-ribosyl-(1"----2')-guanosine-5"-phosphate, called Gr(p), by means of HPLC, UV-absorption, mass spectrometry and periodate oxidation procedures. By comparison with the previously published structure of Ar(p) isolated from Saccharomyces cerevisiae initiator tRNA(Met), the (1"----2')-glycosidic bond in Gr(p) has been postulated to have a beta-spatial conformation. The modified nucleotide Gr(p) is located at position 64 in the tRNA(Met) molecules, i.e. at the same position as Ar(p). Since we have also characterized Gr(p) in Candida albicans initiator tRNA(Met), the phosphoribosylation of purine 64 can be considered as a constant nucleotide modification in the cytoplasmic initiator tRNAs(Met) of all yeast species so far sequenced. Precise evidence for the presence of Gr(p) in initiator tRNAs(Met) of several plants is also reported.

Purinergic stimulation of astroblast proliferation: guanosine and its nucleotides stimulate cell division in chick astroblasts.

A highly active fraction that was mitogenic for astroblasts but which contained no amino acids was identified during the purification of peptides from chick embryo brains. This material was purified by ultracentrifugation, ultrafiltration through Diaflo PM-30 and YM-2 membranes and retention on Diaflo YC-05, followed by ion exchange chromatography and reversed phase high performance liquid chromatography (HPLC) on a C18 Deltapak column. On thin layer chromatography and HPLC the material co-chromatographed with authentic commercially-obtained GMP. Its ultraviolet absorption spectrum was also identical with that of GMP. 1H and 31P nuclear magnetic resonance spectra of the isolated material were identical with those of GMP. The close match between the fast atom bombardment (FAB) mass spectra of the unknown material and authentic GMP indicated that the unknown material was GMP of molecular weight 363 Da. Authentic, commercial GMP stimulated the growth of cultured chick astroblasts in the same dose-dependent manner as the material from chick embryo brains; maximal stimulation was at 50 microM. Guanosine, GDP, and GTP also stimulated cell proliferation. The nucleotides were equally as effective as guanosine. 5'-Guanylyl imidodiphosphate, guanosine 5'-O-(2-thiodiphosphate), and guanosine 5'-N-(3-thiotriphosphate), guanine nucleotides which are relatively resistant to enzymatic hydrolysis, were also mitogenic, indicating that the nucleotides do not need to be degraded to nucleosides to be active and that they probably act extracellularly. Guanine nucleosides and nucleotides promoted astroblast growth when other growth factors were removed from the culture medium. The mitogenic effects of guanosine and its nucleotides were inhibited in a dose-dependent fashion by micromolar concentrations of theophylline, a characteristic of phenomena mediated by purinergic receptors. Guanosine and its nucleotides are released in micromolar concentrations by hypoxic or dying cells. Under these circumstances these compounds may stimulate division of adjacent cells in vivo.

The preparation and spectroscopic characterization of a weakly self-associating salt of guanylyl-(3'-5')-guanosine.

The tetramethylammonium salt of guanylyl-(3'-5')-guanosine has been prepared by a cation-exchange technique and it has been found that the tetramethylammonium ion drastically reduces the self-association of GpG in solution. This has allowed the characterization of GpG by FTIR and 1-D and 2-D NMR spectroscopy. A complete, well-resolved 1H NMR spectrum in D2O has been obtained and all resonances have been assigned. A weak, essentially non-cooperative intermolecular association is observed in solution (15-20 mM) below 40 degrees C. The association occurs via base stacking and base-base hydrogen bonding.

Factor 390 chromophores: phosphodiester between AMP or GMP and methanogen factor 420.

Two chromophores with absorbance maxima at 390 nm (factors 390) have been isolated from oxidized cells of Methanobacterium thermoautotrophicum delta H. The isolation procedure included anion-exchange chromatography of the soluble cofactor pool followed by reverse-phase chromatography. The factor 390 species are novel derivatives of methanogen coenzyme factor 420 in which the 5-deazaflavin 8-hydroxy group is in a phosphodiester linkage to adenosine 5'-phosphate or guanosine 5'-phosphate. The structural assignments were based, in part, on the UV-visible and 1H NMR spectra. In addition, the results from amino acid analysis, phosphate determination, 31P NMR spectroscopy, and fast atom bombardment mass spectrometry were consistent with the proposed structures. Confirmation of the factor 390 structures was made following phosphodiesterase release of the nucleotide monophosphates from factor 420. The nucleotide monophosphates were identified as AMP and GMP by UV-visible spectra and based on elution position by using reverse-phase and anion-exchange high-performance liquid chromatography. The presence of AMP was further demonstrated by using adenylate-5'-phosphate kinase which induced a spectral shift during conversion of the sample to IMP. In addition, the presence of GMP was established by a specific enzymatic assay.

Synthesis of compositionally unique DNA by terminal deoxynucleotidyl transferase.

Studies on the composition and characterization of DNA product(s) synthesized by calf thymus terminal deoxynucleotidyl transferase were performed using homopolymeric single-stranded, calf thymus double-stranded, and native DNA resident in calf thymus chromatin preparations as priming DNA species. Synthesis was carried out using equimolar concentrations of all four deoxynucleoside triphosphates as substrates and Mg2+ or Mn2+ as an effective divalent cation. Irrespective of the nature of the priming DNA or the divalent cation, the DNA product contained 60-70% dGMP residues, 10-15% each of the two pyrimidine residues, and 5-10% dAMP residues. The product synthesized using chromatin DNA as initiator was predominantly single-stranded and its synthesis was resistant to actinomycin D. The predilection of terminal deoxynucleotidyl transferase to synthesize dGMP-rich products on natural or homopolymeric DNA primers suggests that such products may represent biologically important recognition signal sequences.

Mechanism of the mRNA guanylyltransferase reaction: isolation of N epsilon-phospholysine and GMP (5' leads to N epsilon) lysine from the guanylyl-enzyme intermediate.

The mRNA capping reaction catalyzed by rat liver mRNA guanylyltransferase proceeds through an enzyme-GMP intermediate in which GMP is linked to the enzyme by a phosphoamide linkage. The studies described here show that GMP is bound to the epsilon-amino group of lysine of rat liver guanylyltransferase. The enzyme-[32P]GMP intermediate was digested with pronase to a [32P]GMP-peptide which was then converted to [32P]phosphoryl-peptide through periodate oxidation followed by beta-elimination. After alkaline hydrolysis of the [32P]phosphoryl-peptide, the major radioactive product co-electrophoresed with the authentic N epsilon-phospholysine on DEAE-cellulose paper. Neither [32P]Nimid-phosphohistidine nor Nguanido-phosphoarginine was detected in the hydrolysates. Furthermore, formation of N epsilon-guanylyl-lysine linkage on the enzyme was more directly shown by isolation of [32P]GMP(5' leads to N epsilon)lysine when the steps of periodate oxidation and beta-elimination were omitted. The results indicate that the nucleophile in the guanylyltransferase to which the guanylyl residue is linked is the epsilon-amino group of a lysine residue. [32P]Phosphoryl-lysine was also isolated from the vaccinia virus capping enzyme-[32P]GMP intermediate. Guanylyltransferase from HeLa cells, wheat germ, Artemia salina and yeast also formed the enzyme-GMP complex and, from the stability of the complex, the linkage between the enzyme and GMP was suggested to be a phosphoamide.

New syntheses of N-(guanosin-8-yl)-4-aminobiphenyl and its 5'-monophosphate.

N-Acetoxy-4-trifluoroacetylaminobiphenyl (N-acetoxy-TFAABP) reacted readily with Guo and GMP at neutrality in a one-step fashion to yield N-(guanosin-8-yl)4-aminobiphenyl (Guo-ABP) (I) and N(guanosin-8-yl)-4-aminobiphenyl-5'-monophosphate (GMP-ABP) (II), respectively. GMP-ABP could also be formed in much lower yield from the reaction of N-acetoxy-4-formylaminobiphenyl (N-acetoxy-FABP) with GMP (pH 7.0) under more rigorous conditions. Enzymatic hydrolysis of GMP-ABP with alkaline phosphatase in Tris buffer (pH 8.0) at 37 degrees C yielded Guo-ABP. Guo-ABP showed a brilliant blue fluorescence on exposure to 366 nm UV light and its UV absorption spectrum was identical to that of Guo-ABP prepared by Kriek via a different route. Elemental analysis and nuclear magnetic resonance (NMR) data further confirmed the identity of this compound.