High-performance liquid chromatography–mass selective detection assay for adenine released from a synthetic RNA substrate by ricin A chain

High-performance liquid chromatography (HPLC) and selected ion monitoring mass spectrometry (MS) were used to develop a quantitative assay for adenine released from a synthetic RNA substrate by ricin A chain, which contains the toxin's N-glycosidase activity. Because ricin and ricin A chain have potential applications as biotherapeutics and bioweapons, assays are needed to evaluate potency and potential inhibitors of activity. The detection limit for adenine was 0.02 microM (2.4 ng/ml), and the standard curve was linear up to 27.3 microM. The lower limit of quantitation was 0.27 microM and was reproducible throughout this range. Reaction characterization showed that most adenine was released by 5h and that the reaction could not be fully stopped with formic acid concentrations up to 0.75 mM (the maximum typically used for HPLC-MS). Injections were made at 2-min intervals, 10 injections could be performed before the column was backflushed, and no ricin A chain was observed in the column effluent. This assay would also be useful for ricin since ricin A chain did not pass through the HPLC column. With minor modifications to this system, the assay should provide rapid, sensitive, selective, and quantitative assessment of the activity of most ribosome-inactivating proteins. In addition, further chromatographic and mass spectrometric improvements could reduce sample requirements and analysis times.

[Determination of adefovir dipivoxil and its degradation products by reversed-phase high performance liquid chromatography]

A rapid and simple reversed-phase high performance liquid chromatographic (HPLC) method has been developed and validated for the routine analysis of adefovir dipivoxil and its degradation products (adefovir and mono-POM PMEA). The influences of pH, concentrations of buffer and acetonitrile to the retention of adefovir dipivoxil and its related substances have been investigated. The separation between adefovir dipivoxil and its degradation products was performed on a CN-3 column and the quantitation was achieved with UV detection at 260 nm. A mixture of acetonitrile and 25 mmol/L phosphate buffer (to adjust the pH to 4.0 with phosphoric acid) (33:67, v/v) was used as the mobile phase for isocratic elution with a flow rate of 1.0 mL/min. This method demonstrated the baseline separation of the three analytes free of interference within 8 min. The calibration curves were linear (r = 0.9999 and 0.9998) in the concentration range of 1.861-181.7 mg/L and 2.018-197.2 mg/L of adefovir dipivoxil and adefovir respectively. The average recoveries of adefovir dipivoxil and adefovir were 99.5%-101.0% and 99.1%-99.6% respectively, and the relative standard deviation was less than 1.0%. The minimum detectable quantity of adefovir was 1 ng (S/N = 3). The method is simple, reproducible and can be applied to the determination of adefovir dipivoxil and its degradation products simultaneously.

GATC-specific restriction and modification systems in treponemes

AIMS

To investigate the presence of GATC-specific modification and restriction activities in rumen isolates of Treponema sp.

METHODS

The presence of N6-methyladenine within GATC (Dam) sequences was analysed using isoschizomeric restriction endonucleases having different sensitivities to the methylation of the target sequence. A fast screening method was used for testing of site-specific endonuclease activities directly in crude cell extracts. Three out of six rumen isolates of Treponema sp. showed restriction activities. Restriction endonucleases were further purified by Heparin-Sepharose chromatography. Using PCR and specific primers, no sequence homologous to the T. pallidum dam gene was found.

CONCLUSIONS

Three rumen treponemal strains were documented to possess MboI isoschizomeric restriction-modification systems.

SIGNIFICANCE

This is the first report on restriction activity in rumen treponemes.

Rearrangement process occurring in the fragmentation of adefovir derivatives

The fragmentation of the antiviral drug adefovir dipivoxil and its two active metabolites, adefovir and monopivoxil adefovir, was investigated using both ion trap and triple-quadrupole mass spectrometers. Fragment ions due to loss of 30 Da were observed and attributed to an unanticipated rearrangement process by loss of formaldehyde. The proposed mechanism is supported with the aid of three newly synthesized adefovir derivatives and with accurate mass measurement. Other fragmentations by loss of a pivaloyl group, loss of water, C-P bond cleavage and C-O bond cleavage were also observed for adefovir derivatives. It was concluded that the compounds containing a >POO-CHR-OCO- group generally displayed a rearrangement reaction by loss of RCHO in collision-induced dissociation, and the process generally required an activation energy lower than for a direct bond cleavage.

[Fourier transform infrared spectra analysis of nucleic acid in human breast tissue]

DNA molecular constitution is damaged to result in the inductive variation of base structure in female breast tissue under the influence of physical factors and chemical factors. The present research indicated that the FTIR spectra can reflect sensitively the change in the constitution. Our findings indicated that normal, benign and cancerous breast tissues are different in constitution and content of protein, nucleic acid and sugar, comparing the FTIR spectra, deconvolution spectra and date analysis. The result indicated that the content of collagen protein and nucleic acid increased obviously in cancerous tissue, while the content of glycoprotein increased gradually except mucinous carcinoma. After extracting nucleic acid of breast tissue, we further investigated the difference of constitution and content of base and phosphate by comparing normal, benign and cancerous breast tissues. The spectra and spectral data showed that the degree of hydrogen-bonding of base ring guanine (Gue) increased in cancerous tissue, base ring adenine (Ade) presented mostly in oxydic 8-OH-Ade via the attack of the *OH in cancerous breast, the peak position shifted to higher wave number with enhancing of C=N vibration, and the content of phosphate increased. After deconvolution, the ratio A1080/A1050 showed that the amount of PO2- relative to C-O increased from normal to cancerous breast tissues. It provided a important basis to study the mechanism of cancerization from molecular biology and molecular medicine.

Simultaneous separation and determination of active components in Cordyceps sinensis and Cordyceps militarris by LC/ESI-MS

A simple and rapid isocratic LC/MS coupled with electrospray ionization (ESI) method for simultaneous separation and determination of adenine, hypoxanthine, adenosine and cordycepin in Cordyceps sinensis (Cs) and its substitutes was developed. 2-Chloroadenosine was used as internal standard for this assay. The optimum separation for these analytes was achieved using the mixture of water, methanol and formic acid (85:14:1, v/v/v) as a mobile phase and a 2.0 x 150 mm Shimadzu VP-ODS column. Selective ion monitoring (SIM) mode ([M+H]+ at m/z 136, 137, 268, 252 and 302) was used for quantitative analysis of above four active components. The regression equations were liner in the range of 1.4-140.0 microg ml(-1) for adenine, 0.6-117.5 microg ml(-1) for hypoxanthine, 0.5-128.5 microg ml(-1) for adenosine and 0.5-131.5 microg ml(-1) for cordycepin. The limits of quantitation (LOQ) and detection (LOD) were, respectively 1.4 and 0.5 microg ml(-1) for adenine, 0.6 and 0.2 microg ml(-1) for hypoxanthine, 0.5 and 0.1 microg ml(-1) for adenosine and cordycepin. The recoveries of four constituents were from 93.5 to 107.0%. The nucleoside contents of various types of natural Cs and its substitutes were determined and compared with this developed method.

Adenine and RNA in mineral samples. Surface-enhanced Raman spectroscopy (SERS) for picomole detections

Studies on the interactions of biological macromolecules with mineral surfaces are crucial for the detecting biomarkers. But before this can be done for real samples like rocks or sediments, rational methods based on mineral models plus known amounts of nucleic acids must be developed. The methods must be very sensitive, as the amount of bound macromolecule may be very small. Surface-enhanced Raman spectroscopy (SERS) is perfect for detecting picomolar amounts of nucleic acid materials. In this study, the models used were adenine and GAAA hairpin for nucleic acids materials and a clay (montmorillonite) plus colloidal silver (used for SERS detection) for mineral supports. We have shown that OH(-) anions compete with adenine and the adenyl residues in the GAAA loop for adsorption onto nano-sized silver particles in basic medium. The GAAA adenyl moieties are less well adsorbed onto either clay or silver than is adenine. Also, the transfer of either adenine or the RNA hairpin from the clay to the silver aggregates is pH-dependent. Contact between adenine and the montmorillonite also seems to disperse adenine aggregates. The clay could also increase the flexibility of the RNA hairpin so that it is released from the clay at pH 10, and the affinity of its adenyl moieties for the metallic substrate is enhanced.

[2,8-dihydoroxyadenine (DHA) urolithiasis: a case report]

We report a case of 2,8-dihydroxyadenine (DHA) urolithiasis in a 28-year old female. She was admitted to our hospital complaining of a sudden pain in the left lumbar region. Abdominal X-ray (kidney-ureter-bladder; KUB) and computed tomography (CT) demonstrated a radiolucent left ureteral (8 x 6 mm2) and a renal (15 x 10 mm2) stone. In the repetitive procedure of transurethral ureterolithothripsy (TUL) and extracorporeal shock wave lithotripsy (ESWL), the stones had been removed successfully. The spectrophotometric analysis of the stone fragments revealed an absorption spectrum for 2,8-DHA. Adenine phosphoribosyltransferase (APRT) enzyme activity was lowered to 0.8 nmol/hr/mg protein. Thus, we diagnosed the illness as 2,8-DHA urolithiasis originating from APRT deficiency. A molecular analysis of the APRT gene by the polymerase chain reaction (PCR) method revealed the genotype to be APRT*J/APRT*Q0.

Direct electrochemistry of DNA, guanine and adenine at a nanostructured film-modified electrode

A nanostructured film electrode, a multi-wall carbon nanotubes (MWNT)-modified glassy carbon electrode (GCE), is described for the simultaneous determination of guanine and adenine. The properties of the MWNT-modified GCE were investigated by scanning electron microscopy (SEM) and cyclic voltammetry. The oxidation peak currents of guanine and adenine increased significantly at the MWNT-modified GCE in contrast to those at the bare GCE. The experimental parameters were optimized and a direct electrochemical method for the simultaneous determination of guanine and adenine was proposed. Using the MWNT-modified GCE, a sensitive and direct electrochemical technique for the measurement of native DNA was also developed, and the value of (G+C)/(A+T) of HCl-digested DNA was detected.

Synthesis of antisense oligonucleotides with minimum depurination

The removal of 4,4'-dimethoxytrityl (DMTr) groups from oligonucleotides at low pH and the acid lability of the glycosidic linkage of purine nucleotides constitute an inherent conflict in preparative oligonucleotide chemistry. The use of a mildly acidic NaOAc buffer (10 mM, pH 3.0-3.2) allows adjustment of the pH in a range where the progress of the DMTr removal reaction can be monitored conveniently by HPLC and the optimum reaction time can be calculated. As a result, oligonucleotides with minimum depurination are obtained.

Mechanisms for the formation of major oxidation products of adenine upon 365-nm irradiation with 2-methyl-1,4-naphthoquinone as a sensitizer

Recently we reported the isolation and characterization of N6-formyl- and N6-acetyladenine from 365-nm irradiation of dinucleoside monophosphates d(ApA), d(ApC), and d(CpA) in the presence of 2-methyl-1,4-naphthoquinone (menadione) (Wang et al. Biochem. Biophys. Res. Commun. 2002, 291, 1252-7). In this article we investigated the mechanisms for the formation of the two major products by carrying out photoirradiation with isotopically labeled menadione and 2,3-dimethyl-1,4-naphthoquinone. HPLC and electrospray ionization (ESI)-mass spectrometry (MS) and tandem MS studies of the products unambiguously established that the carbonyl group in the products arises from the photosensitizer: The N6-formyl group comes from oxidation of the methyl group and the N6-acetyl group stems from the methyl group and the adjacent ring carbon in menadione. From above results, we proposed mechanisms for the formation of the two products.

Electrochemical biosensor for the interaction of DNA with the alkylating agent 4,4'-dihydroxy chalcone based on guanine and adenine signals

The interaction of an alkylating agent, 4,4'-dihydroxy chalcone (DHC) with calf thymus double stranded DNA (dsDNA) and calf thymus single stranded DNA (ssDNA) was studied electrochemically based on the oxidation signals of guanine and adenine by using differential pulse voltammetry (DPV) at carbon paste electrode (CPE). As a result of the alkylation of DHC between the base pairs in dsDNA, the voltammetric signal of guanine and adenine greatly decreased. After the interaction of DHC with ssDNA, a higher decrease in the oxidation signals of guanine and adenine was observed under the same conditions. The partition coefficients of DHC at dsDNA and ssDNA modified CPEs were calculated. The interactions of DHC with synthetic polynucleotides, such as polyguanylic acid and polyadenylic acid were also observed. In addition, the detection limit and the reproducibility were determined by using DPV. The interaction of DHC with dsDNA in solution-phase was also investigated and the results were compared with the ones obtained by surface immobilized dsDNA. The application of electrochemical DNA biosensor for monitoring the DNA-alkylating agent interactions was explored.

Expression of the human RNA-binding protein HuR in Trypanosoma brucei increases the abundance of mRNAs containing AU-rich regulatory elements

The salivarian trypanosome Trypanosoma brucei infects mammals and is transmitted by tsetse flies. The mammalian 'bloodstream form' trypanosome has a variant surface glycoprotein coat and relies on glycolysis while the procyclic form from tsetse flies has EP protein on the surface and has a more developed mitochondrion. We show here that the mRNA for the procyclic-specific cytosolic phosphoglycerate kinase PGKB, like that for EP proteins, contains a regulatory AU-rich element (ARE) that destabilises the mRNA in bloodstream forms. The human HuR protein binds to, and stabilises, mammalian mRNAs containing AREs. Expression of HuR in bloodstream-form trypanosomes resulted in growth arrest and in stabilisation of the EP, PGKB and pyruvate, phosphate dikinase mRNAs, while three bloodstream-specific mRNAs were reduced in abundance. The synthesis and abundance of unregulated mRNAs and proteins were unaffected. Our results suggest that regulation of mRNA stability by AREs arose early in eukaryotic evolution.

Teleost introns are characterized by a high A+T content

We previously observed that Antarctic fish genes contain intron sequences of high A+T content (60-70% average A+T) which are in stark contrast with adjacent protein coding-sequences. Here, we report that this disparity in intron/exon base composition is a common feature among teleosts. We analyzed 483 teleost genomic DNA sequences, containing 2583 introns, from 80 teleost genera that populate polar, temperate, or tropical habitats. Eighty-nine percent of teleost introns display an A+T content between 50-84% A+T with a mean of 60% A+T. In contrast, only 37% of teleost exons have an A+T content greater-than 50% with a mean of 48% A+T. A comparison to homologous mammalian genes showed a striking difference; in this case, introns and exons have similar base compositions, averaging 45-47% A+T. This indicates that most teleost genes exhibit a large difference in base composition between their introns and exons. There was no correlation of teleost intron A+T content to intron length or habitat temperature range. Thus, teleost intron sequences tend to show the common feature of being much higher in A+T content then neighboring exons.

A study of fast and metastable dissociations of adenine-thymine binary-base oligonucleotides by using positive-ion MALDI-TOF mass spectrometry

In the present study, fast and metastable dissociations of a number of adenine-thymine binary-base oligonucleotides under the conditions of UV matrix-assisted laser desorption/ionization mass spectrometry were investigated. 2-Aminobenzoic acid/ammonium fluoride (ABA/NH4F) matrix system was used. The spectra obtained under metastable and fast dissociation conditions exhibit distinctive dissociation products. From the post-source-decay analysis, all oligonucleotides underwent predominantly metastable dissociations at the 3' C-O linkages to form [a(n)-B]+ and w(n)+ complimentary ion series. Based on the present results, the so-called "[wn+80]+" ions were postulated to be the complimentary [Z(8-n)AH]+ ions rather than the expected phosphate rearrangement products. In addition, these oligonucleotides were found to generate fast dissociation products of b(n)+, d(N)+, w(N)+ and y(N)+ ions through backbone cleavages at 5' C-O, 5' O-P, 3' C-O and 3' P-O linkages, respectively. Product ion series formed under PSD conditions were not observed. The implications of this mutually exclusive occurrence of the two sets of fragment ions under fast and metastable conditions using ABA/NH4F matrix would be discussed. A model of ion activation under UV-MALDI conditions was also proposed.

[Determination of the base contents of liver DNA of rats by reversed-phase high performance liquid chromatography]

The base contents of liver deoxyribonucleic acid (DNA) of rats living at an altitude of 2.3 km were determined by reversed-phase high performance liquid chromatography. At first, 0.05 mol/L KH2PO4(pH 4.0) was used to dissolve the DNA acid hydrolysis products with 8-bromoguanosine (Br8G) as an internal standard. Then the DNA hydrolysis products with Br8G were chromatographed on a Supelcosil LC-18 column with UV detection at 254 nm and eluted by the mobile phase of MeOH-0.05 mol/L KH2PO4(pH 4.0) (20:80, V/V) at the flow rate of 0.8 mL/min. Under these conditions, several bases were separated effectively. From the results, the relatively constant proportions of the bases in DNA were found. The contents were 17.4% of cytosine (C), 28.8% of adenine (A), 23.3% of guanine (G) and 25.3% of thymine (T). RSDs of the determination of these bases were 1.7%, 1.5%, 1.3% and 2.1%, respectively. At the same time the methylation level of liver DNA of the rats determined by the internal standard method was 6.2%.

Preparation and spectroscopic studies of an inclusion complex of adenine with beta-cyclodextrin in solution and in the solid state

The interaction between adenine and beta-CD has been investigated in solution and in the solid state by several analytical techniques, primarily by 1H-NMR, 2D ROESY and fluorescence spectra, and secondarily by other important techniques, for example, Fourier transform infrared spectroscopy (FT-IR) and differential scanning calorimetry (DSC). The association constant and 1:1 nature of the complex between adenine and beta-CD in solution were determined by fluorescence spectroscopy. A spatial configuration for the complex in solution is proposed from analysis of the 1H-NMR and 2D ROESY data. The Fourier transform infrared spectroscopy (FT-IR) and differential scanning calorimetry (DSC) data are consistent with the formation of an inclusion complex. In addition, a solid inclusion complex of adenine with beta-CD was synthesized by the coprecipitation method.

In situ localisation of cytokinins in the shoot apical meristem of Sinapis alba at floral transition

In plants of Sinapis alba L. induced to flower by one long day (LD), previous work showed that the phloem sap feeding the shoot apex is enriched in cytokinins of the isopentenyladenine (iP)-type between 9 and 25 h after start of the LD [P. Lejeune et al. (1994) Physiol Plant 90:522-528]. We have checked the hypothesis that the cytokinin content of the shoot apical meristem (SAM) should increase in response to floral induction by one LD using histoimmunolocalisation techniques and rabbit antiserum against isopentenyladenosine or zeatin riboside. The free bases iP and zeatin are present only in apical tissues containing dividing cells. At 30 h after the start of an inductive LD, a markedly increased iP immune reaction is observed in SAM tissues while the level of zeatin is not modified. Our results are in line with the data obtained by analysis of phloem sap.

Charcoal affects early development and hormonal concentrations of somatic embryos of hybrid larch

Embryogenic tissue of hybrid larch (Larix x marschlinsii Coaz) was multiplied on Medium M (modified MSG medium supplemented with the plant growth regulators (PGRs) 2,4-dichlorophenoxyacetic acid (2,4-D; 9 microM) and N-6-benzyladenine (2.25 microM)). After 1 week, cultures were transferred to either MSG lacking PGRs (Medium C-) or MSG lacking PGRs but supplemented with 1% activated charcoal (Medium C+). Embryos were sampled after 1 week on Medium M, C- or C+. Embryos were analyzed by ELISA for abscisic acid (ABA), abscisic acid-glucose ester, 2,4-D, indole-3-acetic acid (IAA), indole-3-aspartate (IAAsp), zeatin (Z), zeatin riboside (ZR), isopentenyladenine (iP) and isopentenyladenosine (iPA). Transfer of embryos to Medium C+ reduced the embryo concentrations of 2,4-D and iPA, but resulted in elevated concentrations of IAA, IAAsp, ABA, Z, ZR and iP. Charcoal reduced 2,4-D concentrations of embryos by an order of magnitude greater than PGR-free medium alone. Charcoal affected embryo concentrations of five of the eight PGRs quantified. Use of either C+ or C- medium as part of the maturation protocols also affected germination and plantlet establishment of the embryos. A 1-week treatment on Medium C+ positively influenced plantlet establishment and generally reduced variability during both germination and plantlet establishment.

Major adenine products from 2-methyl-1,4-naphthoquinone-sensitized photoirradiation at 365 nm

In this article we report the isolation and characterization of major products of adenine in dinucleoside monophosphates upon 2-methyl-1,4-naphthoquinone (menadione)-sensitized UVA irradiation. Our results show that the major products form via the coupling between the menadione moiety and the exocyclic amino group of adenine. Similar reactions were not observed for cytosine. To our knowledge, this is the first report about the direct reaction between a DNA base and a photosensitizer under 365-nm ultraviolet light irradiation. Our results are consistent with previous observation showing that N(6) radical formed on adenine upon UVA irradiation.

A colorimetric assay for the quantitation of free adenine applied to determine the enzymatic activity of ribosome-inactivating proteins

Adenine quantitation is required for a variety of applications. To date, the prevalent method for quantifying free adenine, in a variety of applications, is the detection of fluorescent-derivatized adenine by HPLC. For the present study, we developed a high-throughput, nonradioactive, enzyme-based colorimetric adenine quantitation assay that is performed in one multireaction incubation step. The assay does not require adenine derivatization and is designed for microplates. The key step is the conversion of adenine to adenosine monophosphate by adenine phosphoribosyl transferase. Subsequent reactions finally produce three inorganic phosphate ions per adenine molecule. Phosphate is quantitated by the color-generating phosphorylysis of a particular purine derivate. Ribosome-inactivating proteins that release adenine from polynucleotides are often used to investigate intracellular protein trafficking and are important for the design of immunotoxins. We therefore used ricin, dianthin, saporin, and a variety of saporin fusion proteins to show that this method is suitable for quantifying adenine release using different substrates. The measured rate of adenine release and substrate specificity are comparable to those determined by HPLC and radioactive detection techniques.

Elimination voltammetry of adenine and cytosine mixtures

The elimination voltammetry with linear scan (EVLS) was used to study adenine and cytosine reduction signals at the mercury electrode. In comparison with the linear scan voltammetry (which provides only one unresolved peak), two elimination functions provide good resolution of individual peaks and significant increase of sensitivity. The first elimination function eliminates the kinetic current (I(k)) and conserves the diffusion current (I(d)). The second elimination function eliminates kinetic and charging currents (I(k) and I(c)) simultaneously and conserves the diffusion current (I(d)). Both functions give two well-resolved peaks of adenine and cytosine in a wide concentration range, while the linear sweep voltammetry gives badly resolved peaks due to hydrogen evolution. The best resolution of peaks is observed in acetate buffer at pH 3.8 and the detection limit for both substances is 500 nM. The concentration dependence of EVLS peak heights for one substance at the constant concentration of the other substance is linear. The peak potentials differ in these elimination functions. The difference in EVLS peak potentials gives the possibility to evaluate alpha n(a). Elimination voltammetry with linear scan contributes to the resolution of cathodic signals of purine and pyrimidine bases at very negative potentials near supporting electrolyte discharge.

The adsorption of nucleotides and polynucleotides on montmorillonite clay

The binding of adenine derivatives to Na(+)-montmorillonite increases in the order 5'AMP, 3'-AMP, 5'ADP < adenosine < purine, adenine. With the exception of cytosine, cytosine derivatives bind less strongly than the corresponding adenine derivatives in the order 5'-CMP < cytidine < cytosine. There is little difference in the binding of uracil derivatives and these compounds bind less strongly than the corresponding adenine analogs. It is concluded that the adenine ring in adenine derivatives is protonated by the acidic montmorillonite surface and binding is a consequence of the electrostatic interaction between the protonated base and the negative charges on the surface of the montmorillonite. Different binding trends were observed with Cu(2+)-montmorillonite with AMP binding more strongly than adenosine and UMP binding more strongly than uridine. It is concluded that ligation to the Cu2+ is a major force in the binding of nucleotides to Cu(2+)-montmorillonite and are not readily washed from the clay. Factors contributing to the binding are discussed. Watson-Crick hydrogen bonding of 5'-AMP to poly(U) and 5'GMP to poly(C) was observed when the homopolymers are bound to the surface of the clay. No association of 5'-UMP to poly(U) bound to clay was detected. The possible role of montmorillonite clays in the prebiotic formation of RNA is discussed.