Capillary electrophoresis for detection of inherited disorders of purine and pyrimidine metabolism: a selective approach

We developed a capillary electrophoresis method as a diagnostic tool for purine and pyrimidine metabolic disorders. Optimal conditions allowed the separation of the major diagnostic metabolites in urine samples within an analysis time of 10 min and with a separation efficiency of about 350,000 theoretical plates/m. The diagnostically important metabolites (adenine, adenosine, 2-deoxyadenosine, 2-deoxyguanosine, 2,8-dihydroxyadenine, guanosine, hypoxanthine, orotidine, orotic acid, and creatinine) were detectable at concentrations of 1.0-5.7 micromol/L. The method gives a linear calibration curve for tested purine and pyrimidine derivatives within the range of 5-500 micromol/L (r > 0.996) The coefficients of variation for the within- and between-day imprecisions were less than 3.2 and 5.8%, respectively. Characteristic abnormalities were detected in the electropherograms of urine samples from patients with purine and pyrimidine enzyme deficiencies. We provide electrophoretic and spectral characteristics of intermediates in purine and pyrimidine metabolism and possible artifacts from medication and their UV-absorbing compounds. Our method allows the detection of the majority of inborn errors of purine and pyrimidine metabolism.     

Parallel solution-phase synthesis of a 2,6,8,9-tetrasubstituted purine library via a sulfur intermediate

Purine analogues exhibiting a wide range of pharmacological activities have been considered a privileged structure in medicinal chemistry. In addition, the purine core consisting of four points of structural diversity is a well-sought scaffold in combinatorial chemistry. Although most of the efforts have been focused on 2,6,9-, 6,8,9-, or 2,8,9-trisubstituted purines, syntheses of 2,6,8,9-tetrasubstituted purines are rare. This paper presents a parallel solution phase approach for the synthesis of fully substituted purines via a 6-sulfur-substituted pyrimidine as the key intermediate. This strategy combining construction and modification of the purine ring thus increases the structural diversity of the final products. Sequential substitution of chlorines in 4,6-dichloro-2-methyl-5-nitropyrimidine with primary amine and benzylmercaptan afforded the 4-(substituted)amino-6-benzylthio-5-nitropyrimidine, which was readily converted to its diaminopyrimidine analogue by reduction of the nitro group. The diaminopyrimidine intermediate was cyclized to construct the purine ring with a C-8 substituent. Eventual oxidation of sulfur to sulfone and subsequent displacement by a primary or secondary amine provided the desired 2,6,8,9-tetrasubstituted purine analogues. This synthetic methodology was validated with the synthesis of a 216-member purine library.     

Probing the reactivity of nebularine N1-oxide. A novel approach to C-6 C-substituted purine nucleosides

A novel approach to the synthesis of purine nucleoside analogues, featuring the reaction of the C6-N1-O⁻ aldonitrone moiety of 9-ribosyl-purine (nebularine) N1-oxide with some representative dipolarophiles, as well as Grignard reagents, is reported. Addition of Grignard reagents to the electrophilic C-6 carbon of the substrate allows a facile access to C-6 C-substituted purine nucleosides without using metal catalysts. 1,3-Dipolar cycloaddition processes lead to novel nucleoside analogues via opening, degradation or ring-enlargement of the pyrimidine ring of the base system of the first-formed isoxazoline or isoxazolidine cycloadduct.     

A New Variant of Emissive RNA Alphabets

A new fluorescent ribonucleoside alphabet (^mthN) consisting of pyrimidine and purine analogues, all derived from methylthieno[3,4-d]pyrimidine as the heterocyclic core, is described. Large bathochromic shifts and high microenvironmental susceptibility of their emission relative to previous alphabets derived from thieno[3,4-d]pyrimidine (^thN) and isothiazole[4,3-d]pyrimidine (^tzN) scaffolds are observed. Subjecting the purine analogues to adenosine deaminase, guanine deaminase and T7 RNA polymerase indicate that, while varying, all but one enzyme tolerate the corresponding ^mthN/^mthNTP substrates. The robust emission quantum yields, high photophysical responsiveness and enzymatic accommodation suggest that the ^mthN alphabet is a biophysically viable tool and can be used to probe the tolerance of nucleoside/tide-processing enzymes to structural perturbations of their substrates.     

Emissive RNA alphabet

A fluorescent ribonucleoside alphabet consisting of highly emissive purine ((th)A, (th)G) and pyrimidine ((th)U, (th)C) analogues, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, is described. Structural and biophysical analyses demonstrated that the emissive analogues are faithful isomorphic nucleoside surrogates. Photophysical analysis established that the nucleosides offer highly desirable qualities, including visible emission, high quantum yield, and responsiveness to environmental perturbations, traits entirely lacking in their native counterparts.     

Determination of purines and pyrimidines in beer samples by capillary zone electrophoresis

Ten purine and pyrimidine bases were separated using capillary zone electrophoresis (CZE) with direct UV detection at 254 nm as well as mass spectrometric (MS) detection using an electrospray ionization (ESI) interface. For this purpose a carrier electrolyte composition compatible with both methods of detection containing 300 mM diethylamine (DEA) was selected. Limits of detection were in the range between 0.1 and 0.3 mg l⁻¹ and calibration plots were found to be linear over at least two orders of magnitude. The applicability of the developed method for the analysis of real samples was demonstrated for some beer samples. A series of “Lager” beer samples from different breweries in Europe as well as a number of completely different types of beers were investigated with respect to their content in the selected purine and pyrimidine bases using the developed CE method with UV detection at 254 nm.     

Synthesis and conformational analysis of new cyclobutane-fused nucleosides

[structure: see text]. A stereselective synthesis of 3-oxabicyclo[3.2.0]heptane nucleoside analogues, which were designed as conformational mimics of the anti-HIV agents 2',3'-didehydro-2',3'-dideoxythimidine (stavudine, d4T) and 2',3'-didehydro-2',3'-dideoxyadenosine (d4A), is described. The target compounds were prepared by condensation of a common intermediate bicyclic acetate, derived from a homochiral 2(5H)-furanone, with pyrimidine and purine bases under modified Vorbrüggen conditions. The conformational behavior of the synthesized nucleoside analogues was studied by NMR spectroscopy and X-ray crystallography.     

Synthesis of 9-[(2-hydroxy-1-phosphonylethoxy)ethyl]guanine, 1-[(2-hydroxy-1-phosphonylethoxy)ethyl]cytosine and 9-[(2-hydroxy-1-phosphonylethoxy)ethyl] adenine

The acyclic nucleoside phosphonate analogues, 9-[(2-hydroxy-1-phosphonylethoxy)ethyl]guanine 6 , 1-[(2-hydroxy-1-phosphonylethoxy)ethyl]cytosine 7 and 9-[(2-hydroxy-1-phosphonylethoxy)ethyl]adenine 8 , have been prepared by the coupling of a tosylate of the phosphonate side chain 12 with a purine or pyrimidine base followed by deprotection of the blocking groups.     

Synthesis of novel chiral compounds of purine and pyrimidine bases

The physiologically active groups such as purine and pyrimidine bases are introduced to the asymmetric ynthesis. The optically pure compounds bearing purine and pyrimidine bases (5a—5e) were prepared via the asymetric Michael addition reaction of purines and pyrimidines as Michael donators with the chiral source 5-(R)-[(1R, 2S, 5R)-menthyloxy]-2(5H)-furanone (3a), which was prepared from the natural chiral auxiliary (-)-menthol. The synthetic method was studied in detail and the new compounds were identified on the basis of their analytical data and spectroscopic data, such as [α]_D~(20), IR, UV, ~1H NMR, ~(13)C NMR and MS. The absolute configuration of 5a was established by X-ray crystallography. The results provided an efficient synthetic route to chiral purines and pyrimidine analogues, and offered chiral sources for further research on the physiologically active compounds of chiral nucleotides.     

Direct multicomponent analysis of beer samples constituents using micellar electrokinetic capillary chromatography

A capillary electrophoretic method was developed using micellar electrokinetic capillary chromatography (MEKC) with diode-array detection to analyze simultaneously 26 beer constituents in a single procedure, including alcohols, iso-alpha-acids, amino acids, flavonoids, isoflavonoids, a vitamin, purine and pyrimidine bases. After filtration, sample components were separated with an uncoated capillary and a 25 mM sodium borate and 110 mM SDS buffer at pH 10.5. Analyses were run at 14 kV and 8 s of hydrodynamic injection with UV detection at 210 nm and 270 nm. The proposed method was successfully applied to the direct determination of beer constituents without any sample cleanup procedures.     

A new concept for the preparation of beta-L- and beta-D-2',3'-dideoxynucleoside analogues

[reaction: see text] A new method for the synthesis of 2',3'-dideoxynucleoside analogues has been developed. An electrochemical activation of 2-substituted furans is followed by the coupling with a pyrimidine or purine base. This gives planar furyl nucleosides as key intermediates, which are hydrogenated cis-selectively to give the corresponding beta-2',3'-dideoxynucleosides as racemic mixtures. An enzymatic kinetic resolution gives rise to beta-D- and beta-L-configured derivatives in high optical purity. This is exemplified by the synthesis of beta-D- and beta-L-3'-deoxythymidine.     

Retention Behavior of Nucleic Acid Bases and Purine Derivatives on Titania

The retention of nucleic acid bases and purine derivatives on titania was studied using a 0.4 mM acetic acid–sodium acetate buffer (pH 6.0) and 70% aqueous methanol as mobile phases. We observed that the retention strength of tested analytes on titania was dependent on the structural differences between pyrimidine and purine skeletons and the variety and number of substituents. The retention order was purine derivatives with methyl groups, pyrimidine bases and purine derivatives with hydrophilic functional groups, which were retained most strongly on titania. We concluded that the retention of each analyte was caused by the analyte’s hydrophobicity in the case of purine derivatives with methyl groups and pyrimidine bases. In the case of purine and its derivatives with hydrophilic functional groups, it was considered that the retention was dependent on the analyte’s ability to form chelates, and the variety and number of functional groups on C6 and C2.     

Use of biological fluids for the rapid diagnosis of potentially lethal inherited disorders of human purine and pyrimidine metabolism

Inherited purine and pyrimidine disorders may be associated with serious, sometimes life-threatening consequences. Early and accurate diagnosis is essential. Difficulties encountered when using existing high pressure liquid chromatographic (HPLC) methods led to the development of an improved method based on prior fractionation of urine. The advantages are as follows. 1. Production of fingerprints demonstrating altered urinary excretion patterns characteristic of any one of ten different disorders, in 30 minutes. 2. Positive identification and quantification by comparison with established methods (using conventional chromatography, electrophoresis and UV spectrophotometry) in addition to specific retention times and characteristic UV absorbance ratios at two separate wavelengths (245 and 280 nm) by HPLC. 3. Direct analysis of all the purines and pyrimidines normally found in human body fluids as well as identification of abnormal compounds. 4. Short time between successive analyses while maintaining excellent resolution between compounds of interest and column longevity. 5. Improved separation of the different adenine-based compounds encountered in some disorders, plus demonstration of potential interference by dietary or drug metabolites. 6. Applicability to the monitoring of therapy involving a variety of different purine and pyrimidine analogues. Particular attention should be paid to sample preparation. Plasma profiles will confirm the diagnosis in some, but not all, of these disorders.     

Highly stereoselective synthesis of novel cyclobutane-fused azanucleosides

Stereoselective syntheses of several 3-azabicyclo[3.2.0]heptane nucleoside analogues have been efficiently completed starting from a homochiral a,b-unsaturated-g-lactam. The target compounds were prepared by condensation of a common bicyclic acetate intermediate with pyrimidine and purine bases under modified Vorbrüggen conditions. The anti-HIV activity of the newly synthesized azanucleosides has been evaluated.     

Synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] modified nucleosides and oligonucleotides.

A versatile synthetic route has been developed for the synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] (abbreviated as 2'-O-DMAOE) modified purine and pyrimidine nucleosides and their corresponding nucleoside phosphoramidites and solid supports. To synthesize 2'-O-DMAOE purine nucleosides, the key intermediate B (Scheme 1) was obtained from the 2'-O-allyl purine nucleosides (13a and 15) via oxidative cleavage of the carbon-carbon bond to the corresponding aldehydes followed by reduction. To synthesize pyrimidine nucleosides, opening the 2,2'-anhydro-5-methyluridine 5 with the borate ester of ethylene glycol gave the key intermediate B. The 2'-O-(2-hydroxyethyl) nucleosides were converted, in excellent yield, by a regioselective Mitsunobu reaction, to the corresponding 2'-O-[2-[(1,3-dihydro-1,3-dioxo-2H-isoindol-2-yl)oxy]ethyl] nucleosides (18, 19, and 20). These compounds were subsequently deprotected and converted into the 2'-O-[2-[(methyleneamino)oxy]ethyl] derivatives (22, 23, and 24). Reduction and a second reductive amination with formaldehyde yielded the corresponding 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] nucleosides (25, 26, and 27). These nucleosides were converted to their 3'-O-phosphoramidites and controlled-pore glass solid supports in excellent overall yield. Using these monomers, modified oligonucleotides containing pyrimidine and purine bases were synthesized with phosphodiester, phosphorothioate, and both linkages (phosphorothioate and phosphodiester) present in the same oligonucleotide as a chimera in high yields. The oligonucleotides were characterized by HPLC, capillary gel electrophoresis, and ESMS. The effect of this modification on the affinity of the oligonucleotides for complementary RNA and on nuclease stability was evaluated. The 2'-O-DMAOE modification enhanced the binding affinity of the oligonucleotides for the complementary RNA (and not for DNA). The modified oligonucleotides that possessed the phosphodiester backbone demonstrated excellent resistance to nuclease with t(1/2) > 24 h.     

Eutectic phase polymerization of activated ribonucleotide mixtures yields quasi-equimolar incorporation of purine and pyrimidine nucleobases

The RNA world hypothesis requires a plausible mechanism by which RNA itself (or precursor RNA-like polymers) can be synthesized nonenzymatically from the corresponding building blocks. Simulation experiments have exploited chemically reactive mononucleotides as monomers. Solutions of such monomers in the prebiotic environment were likely to be very dilute, but in experimental simulations of polymerization reactions dilute solutions of activated mononucleotides in the millimolar range hydrolyze extensively, and only trace amounts of dimers and trimers are formed. We report here that random medium-size RNA analogues with mixed sequences (5- to 17-mers with traces of longer products) can be synthesized in ice eutectic phases that are produced when dilute solutions of activated monomers and catalysts (Mg(II) and Pb(II)) are frozen and maintained at -18 degrees C for periods up to 38 days. Under these conditions, the monomers are concentrated as eutectics in an ice matrix. Hydrolysis of the activated mononucleotides was suppressed at low-temperature ranges, and polymerization was enhanced with yields up to 90%. Analysis of the mixed oligomers established that incorporation of both purine and pyrimidine bases proceeded at comparable rates and yields. These results suggest that ice deposits on the early Earth could have facilitated the synthesis of short- and medium-size random sequence RNA analogues and thereby provided a microenvironment suitable for the formation of biopolymers or their precursors.     

Reactions of trimethylsilyl fluorosulfonyldifluoroacetate with purine and pyrimidine nucleosides

Difluorocarbene, generated from trimethylsilyl fluorosulfonyldifluoroacetate (TFDA), reacts with the uridine and adenosine substrates preferentially at the enolizable amide moiety of the uracil ring and the 6-amino group of the purine ring. 2′,3′-Di-O-benzoyl-3′-deoxy-3′-methyleneuridine reacts with TFDA to produce 4-O-difluoromethyl product derived from an insertion of difluorocarbene into the 4-hydroxyl group of the enolizable uracil ring. Reaction of the difluorocarbene with the adenosine substrates having the unprotected 6-amino group in the purine ring produced the 6-N-difluoromethyl derivative, while reaction with 6-N-benzoyl protected adenosine analogues gave the difluoromethyl ether product derived from the insertion of difluorocarbene into the enol form of the 6-benzamido group. Treatment of the 6-N-phthaloyl protected adenosine analogues with TFDA resulted in the unexpected one-pot conversion of the imidazole ring of the purine into the corresponding N-difluoromethylthiourea derivatives. Treatment of the suitably protected pyrimidine and purine nucleosides bearing an exomethylene group at carbons 2′, 3′ or 4′ of the sugar rings with TFDA afforded the corresponding spirodifluorocyclopropyl analogues but in low yields.     

Furan Decorated Nucleoside Analogues as Fluorescent Probes: synthesis, photophysical evaluation and site-specific incorporation

The synthesis and photophysical evaluation of modified nucleoside analogues in which a five-membered heterocycle (furan, thiophene, oxazole, and thiazole) is attached to the 5-position of 2′-deoxyuridine are reported. The furan-containing derivative is identified as the most promising responsive nucleoside of this family due to its emission quantum efficiency and degree of sensitivity to its microenvironment. The furan moiety was then attached to the 5-position of 2′-deoxycytidine as well as the 8-position of adenosine and guanosine. Photophysical evaluation of these four furan-containing nucleoside analogues reveals distinct differences in the absorption, emission, and quantum efficiency depending upon the class of nucleoside (pyrimidine or purine). Comparing the photophysical properties of all furan-containing nucleosides, identifies the furan thymidine analogue, 5-(fur-2-yl)-2′-deoxyuridine, as the best candidate for use as a responsive fluorescent probe in nucleic acids. 5-(Fur-2-yl)-2′-deoxyuridine was then converted to the corresponding phosphoramidite and site specifically incorporated into DNA oligonucleotides with greater than 88% coupling efficiency. Such furan-modified oligonucleotides form stable duplexes upon hybridization to their complementary DNA strands and display favorable fluorescent features.     

Synthesis and structure of palladium(II) mixed complexes with DNA purine or pyrimidine bases and imidazole derivatives. Part I

Summary Palladium(II) mixed ligand complexes with purine or pyrimidine and imidazole derivatives were prepared and characterized by i.r., Raman and electronic spectroscopy. The compounds have the general formula [Pd(L₁)(L₂)(X₂)]; where L₁ = adenine, guanine, hypoxanthine, cytosine, 2-aminopyrimidine, 4(6)-hydroxypyrimidine; L₂ = N-methylimidazole, N-ethylimidazole or N-propylimidazole; X = Cl or Br. The complexes are square planar with cis-halogens. The purine, pyrimidine and imidazole bases act as monodentate ligands coordinated via the N(7) of purine and N(3) of pyrimidine and imidazole.     

A Stereoselective Approach to β-l-Arabino Nucleoside Analogues: Synthesis and Cyclization of Acyclic 1',2'-synN,O-Acetals

Reported herein is a novel and versatile strategy for the stereoselective synthesis of unnatural β-l-arabinofuranosyl nucleoside analogues from acyclic N,OTMS-acetals bearing pyrimidine and purine bases. These unusual acetals undergo a C1' to C4' cyclization where the OTMS of the acetal serves as the nucleophile to generate 2'-oxynucleosides with complete retention of configuration at the C1' acetal center. N,OTMS-acetals are obtained diastereoselectively from additions of silylated nucleobases onto acyclic polyalkoxyaldehydes in the presence of MgBr(2)·OEt(2). The strategy reported is addressing important synthetic challenges by providing stereoselective access to unnatural l-nucleosides starting from easily accessible pools of d-sugars and, as importantly, by allowing the formation of the sterically challenging 1',2'-cis nucleosides. A wide variety of nucleoside analogues were synthesized in 7-8 steps from easily accessible d-xylose.