Synthesis of 2′-deoxy-2′-fluororibo- and 2′-deoxy-2′,2′-difluororibonucleosides derived from 6-(het)aryl-7-deazapurines

A series of novel sugar-modified derivatives of cytostatic 6-hetaryl-7-deazapurine ribonucleosides (2′-deoxy-2′-fluororibo- and 2′-deoxy-2′,2-difluororibonucleosides) bearing an aryl or hetaryl group in position 6, was prepared and screened for biological activity. The fluororibo derivatives were prepared by aqueous palladium catalyzed cross-coupling reactions of the corresponding 6-chloro-7-deazapurine 2′-deoxy-2′-fluororibonucleoside 11 with (het)arylboronic acids. The key intermediate 11 was prepared by a six-step sequence from the corresponding arabinonucleoside by selective protection of 3′- and 5′-hydroxyls by acid-labile groups followed by stereoselective S_N2 fluorination and deprotection. The difluororibo-series was prepared by non-stereoselective glycosidation of 6-chloro-7-deazapurine with benzoyl-protected 2-deoxy-2,2-difluoro-d-erythro-pentofuranosyl-1-mesylate followed by cross-couplings, separation of anomers and deprotection. The title nucleosides did not show considerable cytostatic or antiviral activity.     

Probing hydrogen bonding and ion-carbonyl interactions by solid-state 17O NMR spectroscopy: G-ribbon and G-quartet

We report solid-state 17O NMR determination of the 17O NMR tensors for the keto carbonyl oxygen (O6) of guanine in two 17O-enriched guanosine derivatives: [6-17O]guanosine (G1) and 2',3',5'-O-triacetyl-[6-17O]guanosine (G2). In G1.2H2O, guanosine molecules form hydrogen-bonded G-ribbons where the guanine bases are linked by O6...H-N2 and N7...H-N7 hydrogen bonds in a zigzag fashion. In addition, the keto carbonyl oxygen O6 is also weakly hydrogen-bonded to two water molecules of hydration. The experimental 17O NMR tensors determined for the two independent molecules in the asymmetric unit of G1.2H2O are: Molecule A, CQ=7.8+/-0.1 MHz, etaQ=0.45+/-0.05, deltaiso=263+/-2, delta11=460+/-5, delta22=360+/-5, delta33=-30+/-5 ppm; Molecule B, CQ=7.7+/-0.1 MHz, etaQ=0.55+/-0.05, deltaiso=250+/-2, delta11=440+/-5, delta22=340+/-5, delta33=-30+/-5 ppm. In G1/K+ gel, guanosine molecules form extensively stacking G-quartets. In each G-quartet, four guanine bases are linked together by four pairs of O6...H-N1 and N7...H-N2 hydrogen bonds in a cyclic fashion. In addition, each O6 atom is simultaneously coordinated to two K+ ions. For G1/K+ gel, the experimental 17O NMR tensors are: CQ=7.2+/-0.1 MHz, etaQ=0.68+/-0.05, deltaiso=232+/-2, delta11=400+/-5, delta22=300+/-5, delta33=-20+/-5 ppm. In the presence of divalent cations such as Sr2+, Ba2+, and Pb2+, G2 molecules form discrete octamers containing two stacking G-quartets and a central metal ion, that is, (G2)4-M2+-(G2)4. In this case, each O6 atom of the G-quartet is coordinated to only one metal ion. For G2/M2+ octamers, the experimental 17O NMR parameters are: Sr2+, CQ=6.8+/-0.1 MHz, etaQ=1.00+/-0.05, deltaiso=232+/-2 ppm; Ba2+, CQ=7.0+/-0.1 MHz, etaQ=0.68+/-0.05, deltaiso=232+/-2 ppm; Pb2+, CQ=7.2+/-0.1 MHz, etaQ=1.00+/-0.05, deltaiso=232+/-2 ppm. We also perform extensive quantum chemical calculations for the 17O NMR tensors in both G-ribbons and G-quartets. Our results demonstrate that the 17O chemical shift tensor and quadrupole coupling tensor are very sensitive to the presence of hydrogen bonding and ion-carbonyl interactions. Furthermore, the effect from ion-carbonyl interactions is several times stronger than that from hydrogen-bonding interactions. Our results establish a basis for using solid-state 17O NMR as a probe in the study of ion binding in G-quadruplex DNA and ion channel proteins.     

The self-assembly of a lipophilic guanosine nucleoside into polymeric columnar aggregates: the nucleoside strucutre contains sufficient information to drive the process towards a strikingly regular polymer

Lipophilic guanosine derivatives act as self-assembled ionophores. In the presence of alkali metal ions in organic solvents, these G derivatives can form tubular polymeric structures. The molecular aggregates formed by 3',5'-didecanoyl-2'-deoxyguanosine (1) have been characterised by SANS and NMR spectroscopy. The polymer is structured as a pile of stacked G quartets held together by the alkali metal ions that occupy the column's central channel. The deoxyribose moieties, with their alkyl substituents, surround the stacked G quartets, and the nucleoside's long-chain alkyl tails are in intimate contact with the organic solvent. In this polymeric structure, there is an amazing regularity in the rotamers around the glycosidic bond within each G quartet and in the repeat sequence of the G quartets along the columns. In hydrocarbon solvents, these columnar aggregates form lyomesophases of the cholesteric and hexagonal types.     

Studies directed toward synthesis of guanosine 8,5''-imino cyclonucleosides and derivatives—I

8,5'-Aminimino bridging in the guanosine series using 5'-O-tosyl (1) and 5'-O-mesyl derivatives (2) of 2',3'-O-isopropylidene-8-bromoguanosine (5) and hydrazine gave N³,5'-cyclized product 3 and the N⁵,5'-cyclonucleoside of 4-carboxyhydrazido-5-amino-2-bromoimidazole 4. To exclude the N³,5'-cyclization through ionization in the base moiety, a N²-dimethylaminomethylidene-N¹-methoxymethylene derivative 7 was synthesized from 5 through the N²-protected compound 6. 7 was converted into the N²-dimethylaminomethy analogue 8, which with hydrazine yielded first the N²-deprotected form of 8 (9). 8 or 9 with hydrazine under forcing conditions gave an 8,5'-aminimino-N¹-methox derivative 10. Oxidation of 10 with sodium metaperiodate or sodium nitrite yielded 8,5'-imino-N¹-methoxymethyleneguanosine (11a) and 8,5'-imino-N¹-methoxymethylenexanthosine derivative 11b, respectively. 11a was deprotected to 8,5'-imino-N¹-methoxymethyleneguanosine 12.     

Self-assembly of N2-modified guanosine derivatives: formation of discrete G-octamers

In the presence of Na(+) ions, two N(2)-modified guanosine derivatives, N(2)-(4-n-butylphenyl)-2',3',5'-O-triacetylguanosine (G1) and N(2)-(4-pyrenylphenyl)-2',3',5'-O-triacetylguanosine (G2), are found to self-associate into discrete octamers that contain two G-quartets and a central ion. In each octamer, all eight guanosine molecules are in a syn conformation and the two G-quartets are stacked in a tail-to-tail fashion. On the basis of NMR spectroscopic evidence, we hypothesize that the pi-pi-stacking interaction between the N(2)-side arms (phenyl in G1 and pyrenyl in G2) can considerably stabilize the octamer structure. For G1, we have used NMR spectroscopic saturation-transfer experiments to monitor the kinetic ligand exchange process between monomers and octamers in CD(3)CN. The results show that the activation energy (E(a)) of the ligand exchange process is 31 +/-5 kJ mol(-1). An Eyring analysis of the saturation transfer data yields the enthalpy and entropy of activation for the transition state: DeltaH(not =)=29 +/-5 kJ mol(-1) and DeltaS(not =)=-151 +/-10 J mol(-1) K(-1). These results are consistent with an associative mechanism for ligand exchange.     

Bromination at C-5 of Pyrimidine and C-8 of Purine Nucleosides with 1,3-Dibromo-5,5-dimethylhydantoin

Treatment of the protected and unprotected nucleosides with 1,3-dibromo-5,5- dimethylhydantoin in aprotic solvents such as CH(2)Cl(2), CH(3)CN, or DMF effected smooth bromination of uridine and cytidine derivatives at C-5 of pyrimidine rings as well as adenosine and guanosine derivatives at C-8 of purine rings. Addition of Lewis acids such as trimethylsilyl trifluoromethanesulfonate enhanced efficiency of bromination.     

Gas-phase formation of radical cations of monomers and dimers of guanosine by collision-induced dissociation of Cu(II)-guanosine complexes

An electrosprayed water/methanol solution of guanosine and Cu(NO3)2 was observed to give rise to gas-phase copper complexed ions of [CuLn]*2+, [CuL(MeOH)n]*2+, and [CuG n(NO3)]*+, as well as the ions [L]*+, [L+H]+, [G]*+, and [G+H]+ (L=guanosine, G=guanine). The Collision-Induced Dissociation (CID) of [CuL3]*2+ and [CuL(MeOH)n]*2+ (n=2, 3) generates guanosine radical cations [L]*+, while dimeric guanosine radical cations [L2]*+ are generated in the dissociation of [CuL4]*2+. Protonated guanosine [L+H]+ is one of the main products in the primary dissociation of [CuL2]*2+, while the dissociation of the higher-order [CuG2]*2+ produces the [G]*+ radical cation. The guanosine dimer radical cation, [L2]*+ presumably arises from the interaction of two guanosine molecules via proton and hydrogen bonding and is observed to dissociate into [L+H]+ and [L-H]* at low energies. We propose that the first two ligands bind strongly with Cu(II) through N7 and O6 to form a [CuL2]*2+ complex with a four-coordinated planar structure and that a third ligand binds loosely with copper to form [CuL3]*2+. Additional ligation observed in the formation of [CuLn]*2+ (n相似文献   

Highly Specific Recognition of Guanosine Using Engineered Base-Excised Aptamers

Purines and their derivatives are highly important molecules in biology for nucleic acid synthesis, energy storage, and signaling. Although many DNA aptamers have been obtained for binding adenine derivatives such as adenosine, adenosine monophosphate, and adenosine triphosphate, success for the specific binding of guanosine has been limited. Instead of performing new aptamer selections, we report herein a base-excision strategy to engineer existing aptamers to bind guanosine. Both a Na⁺-binding aptamer and the classical adenosine aptamer have been manipulated as base-excising scaffolds. A total of seven guanosine aptamers were designed, of which the G16-deleted Na⁺ aptamer showed the highest bindng specificity and affinity for guanosine with an apparent dissociation constant of 0.78 mm . Single monophosphate difference in the target molecule was also recognizable. The generality of both the aptamer scaffold and excised site were systematically studied. Overall, this work provides a few guanosine binding aptamers by using a non-SELEX method. It also provides deeper insights into the engineering of aptamers for molecular recognition.     

An Efficient and Simple Entry to N-Substituted beta-Enamino Acid Derivatives from 2-Alkyl-2-oxazolines and 2-Alkyl-2-thiazolines

Reaction of azaenolates of 2-alkyl-oxa(thia)zolines 6 with imidoyl chlorides 7 as electrophiles to furnish masked N-substituted beta-enamino acid derivatives 1-2 in 70-90% yield is described. Alternative routes are discussed. Compounds 1-2 generally appear in one tautomeric form, imino or enamino, depending on the nature of the imidoyl chloride. The configuration of the enamino moiety (Z) and the conformation (s-cis) of compounds 1-2 obtained were established by an NMR study and unequivocally set by nuclear Overhauser effect difference experiments. An X-ray structure of compound 1e is also reported, showing a strong intramolecular NH.N hydrogen bond. Ab initio calculations (HF/3-21G and HF/3-21+G) have been carried out on several representative examples (1e, 1p, and 1l) in an attempt to support and provide the correct geometry of these derivatives. Structural considerations among the possible isomers of compounds 1 are discussed. From these studies it was concluded that the theoretical calculations agree with the experimental results. In addition, a very simple one-pot procedure for the preparation of masked N-substituted alpha-alkylated beta-enamino acid derivatives 2 from 6, 7, and different alkyl halides (R(3)Y) is described.     

Guanosine tetra- and pentaphosphate analysis: PEI-cellulose thin-layer purification and luciferin-luciferase liquid scintillation quantitation

A system is presented that can separate and quantitate in picomole amounts various guanosine tetra and penta phosphates namely guanosine 5′ triphosphate, 3′ diphosphate (pppGpp), guanosine 5′ tetraphosphate (ppppG), and diguanosine 5′ tetraphosphate (GppppG). It was found to be inactive with guanosine 5′ diphosphate, 3′ diphosphate (ppGpp), and a synthetic compound pCppG.The analytical detection system uses a crude firefly luciferin-luciferase system in which the various derivatives probably transphosphorylate ADP to produce the ATP necessary to emit light with the luciferin-luciferase system.The system should be useful in quantitating reactions in which guanosine tetraphosphates and pentaphosphates are involved. Their role is apparently one of control at either RNA polymerase or ribosomal levels and should be important in further research in molecular biology.     

Factors that influence the antiproliferative activity of half sandwich Ru(II)-[9]aneS3 coordination compounds: activation kinetics and interaction with guanine derivatives

Half sandwich Ru(ii)-[9]aneS3 complexes ([9]aneS3 = 1,4,7-trithiacyclononane) are being studied for their antiproliferative activity. We investigated here the activation kinetics of three such complexes, namely [Ru([9]aneS3)(en)Cl](PF(6)) (1), [Ru([9]aneS3)(bpy)Cl](PF(6)) (2) and [Ru([9]aneS3)(pic)Cl] (3) (en = 1,2-diaminoethane, pic = picolinate), and their interaction with DNA model bases. The aim of the study was to assess how they are affected by the nature and charge of the chelating ligand. The model reactions of 1-3 with the guanine derivatives 9-methylguanine (9MeG), guanosine (Guo), and guanosine 5'-monophosphate (5'-GMP) were studied by NMR spectroscopy. All reactions lead, although with different rates and to different extents, to the formation of monofunctional adducts with the guanine derivatives N7-bonded to the Ru center. Two products, the complexes [Ru([9]aneS3)(en)(9MeG-N7)](PF(6))(2) (4) and [Ru([9]aneS3)(pic)(9MeG-N7)](PF(6)) (10), were structurally characterized also by X-ray crystallography. The structure of 4 is stabilized by strong intramolecular H-bonding between an NH of en and the carbonyl O6 of 9MeG. The kinetics of aquation and anation of complexes 2 and 3, as well as the kinetics and the mechanism of the reaction of complexes 1-3 with the biologically more relevant 5'-GMP ligand were studied by UV-Vis spectroscopy. The rate of the reaction of 1-3 with 5'-GMP depends on the nature of the chelating ligand rather than on the charge of the complex, decreasing in the order 3≈2 > 1. The measured enthalpies and entropies of activation (ΔH(≠) > 0, ΔS(≠) < 0) support an associative mechanism for the substitution process.     

Synthesis of novel push-pull-type solvatochromic 2′-deoxyguanosine derivatives with longer wavelength emission

We synthesized novel push-pull-type fluorescent guanosine derivatives, ^CNG and ^AcG containing 1,6- and 2,7-disubstituted pyrene chromophores. 1,6-Disubstituted pyrene derivatives, 1,6-^CNG (3b) and 1,6-^AcG (3c), exhibited highly solvatochromic fluorescence emission at longer wavelength (∼540 nm). The environmentally sensitive fluorescent deoxyguanosines such as 3b and 3c can be used as powerful tools for structural studies of nucleic acids and molecular diagnostics.     

Selective interactions of a few acridinium derivatives with single strand DNA: study of photophysical and DNA binding interactions

Novel acridinium derivatives 1-3, wherein steric factors have been varied systematically through substitution at the ninth position of the acridinium ring, were synthesized and their interactions with single strand and double strand DNA have been investigated through photophysical, biophysical, and microscopic techniques. The acridinium derivative 1 exhibited quantitative fluorescence yields (phi f approximately =1) and high lifetime of 35 ns, while significantly lower fluorescence yields of 0.11 and 0.02 and lifetimes of 3.5 and 1.2 ns were observed for 2 and 3, respectively. The derivatives 1 and 2 having 2-methylphenyl and 2,4-dimethylphenyl substituents at the ninth position of the acridinium ring showed selective interactions with single strand DNA (ssDNA) with association constants of KssDNA = 6.3-6.6 x 10(4) M(-1), while negligible interactions were observed with double strand DNA (dsDNA). In contrast, the derivative 3 with 2,6-dimethylphenyl substitution showed negligible interactions with both ssDNA and dsDNA. Studies with a series of 19-mer oligonucleotides indicate that these derivatives exhibit significant selectivity for the sequences rich in guanosine (ca. 3-fold) as compared to the cytosine-rich sequences. These derivatives with high water solubility and the ability to distinguish between ssDNA and dsDNA through changes in fluorescence emission can be used as fluorescent probes for understanding the role of ssDNA in various biological processes and to study various DNA-ligand interactions.     

Transfer ribonucleic acids

Transfer ribonucleic acids (tRNAs)

1 Abbreviations used according to IUPAC-IUB convention: tRNA = transfer ribonucleic acid; tRNA_yeast = mixture of tRNAs from yeast; tRNA^Phe = phenylalanine specific tRNA; Phe-tRNA = tRNA esterified (“charged”) with Phe; mRNA = messenger RNA; DNA = deoxyribonucleic acid; U = uridine; A = adenosine; C = cytidine; G = guanosine; pA = 5′-adenylic acid; Ap or A- = 3′-adenylic acid; m²′G = 2′-O-methyl guanosine; m⁷G = 7-methyl guanosine; mG = N(2)-dimethyl guanosine; other methylated nucleosides are abbreviated analogously; abbreviations of other odd nucleosides are given with Fig. 2; p or – signifies phosphate; RNase = ribonuclease; DEAE = diethylaminoethyl; fMet = N-formayl methionine.

occur in all living organisms. In biological protein synthesis they accept activated amino acids which are then transferred to growing peptide chains. With molecular weights lying between 25000 and 30000, tRNAs are easily within the reach of today's physical, chemical, and biochemical methods. The primary structures of several tRNAs as well as some relationships between structure and function have been elucidated. Three-dimensional structure, specificity, and mechanism of action are the subjects of present research efforts.     

Unsaturated didehydrodeoxycytidine drugs. 1. Impact of C=C positions in the sugar ring

The chemical names of a pair of recently synthesized antitumor drugs are given in the present study as 1',2'-didehydro-3',4'-deoxycytidine and 3',4'-didehydro-2',4'-deoxycytidine. The order of stabilities, geometries, and ionization potentials of the unsaturated sugar-modified cytidine derivatives is investigated quantum mechanically. Our density functional theory calculations based on the B3LYP/6-311++G** model reveal that 3',4'-didehydro-2',4'-deoxycytidine (SD-C2) is slightly more stable than its isomer, 1',2'-didehydro-3',4'-deoxycytidine, by an energy of 5.28 kJ x mol(-1) in isolation. The isomers structurally differ by only the C=C location in the sugar ring. However, the compounds exhibit an unusual orientation with a less puckered sugar ring; that is, 3',4'-didehydro-2',4'-deoxycytidine is determined to be a beta-nucleoside, which is a C1'-endo, north conformer with an anticlinal sugar ring, whereas 1',2'-didehydro-3',4'-deoxycytidine is neither an alpha-nucleoside nor a beta-nucleoside but is a C4'-endo, south conformer with an antiperiplanar sugar ring. The present study further indicates that the C=C double bond location imposes significant effects on their ionization potentials (IPs) and other important molecular properties such as molecular electrostatic potential (MEP). In addition, inner shell binding energy spectral variations with respect to the C=C bond exhibit more site dependence. The valence shell binding energy spectral changes are, on the other hand, significant and delocalized. The latter indicates that such changes in valence space are not isolated effects but are within the entire nucleoside. Finally, the present study suggests that the nearly 0.6 eV difference in the first ionization potentials (highest occupied molecular orbital) of the isomers is sufficiently large to identify them by further spectroscopic measures.     

Structural Selection in G‐Quartet‐Based Hydrogels and Controlled Release of Bioactive Molecules

A guanosine‐5′‐hydrazide can entrap biologically interesting molecules such as acyclovir, vitamin C, and vancomycin into its hydrogel network. Controlled release of these molecules was monitored by ¹H NMR spectroscopy. The hydrazide may potentially form mixed G–G quartets with analogous compounds containing a guanine group. ¹H NMR spectroscopy was used to study the inclusion of various guanine derivatives into the hydrogel. The structural selectivity was found to depend strongly on both the shape and the charge of the additive and may arise from the strong cohesion of the supramolecular architecture of the gel and the resulting resistance to perturbation by foreign bodies. Hydrogels thus offer a promising medium for highly selective, controlled release of bioactive substances.     

7-Functionalized 7-deazapurine ribonucleosides related to 2-aminoadenosine, guanosine, and xanthosine: glycosylation of pyrrolo[2,3-d]pyrimidines with 1-O-acetyl-2,3,5-tri-O-benzoyl-D-ribofuranose

[reaction: see text] The Silyl-Hilbert-Johnson reaction as well as the nucleobase-anion glycosylation of a series of 7-deazapurines has been investigated, and the 7-functionalized 7-deazapurine ribonucleosides were prepared. Glycosylation of the 7-halogenated 6-chloro-2-pivaloylamino-7-deazapurines 9b-d with 1-O-acetyl-2,3,5-tri-O-benzoyl-D-ribofuranose (5) gave the beta-D-nucleosides 11b-d (73-75% yield), which were transformed to a number of novel 7-halogenated 7-deazapurine ribonucleosides (2b-d, 3b-d, and 4b-d) related to guanosine, 2-aminoadenosine, and xanthosine. 7-Alkynyl derivatives (2e-i, 3e-h, or 4g) have been prepared from the corresponding 7-iodonucleosides 2d, 3d, or 4d employing the palladium-catalyzed Sonogashira cross-coupling reaction. The 7-halogenated 2-amino-7-deazapurine ribonucleosides with a reactive 6-chloro substituent (18b-d) were synthesized in an alternative way using nucleobase-anion glycosylation performed on the 7-halogenated 2-amino-6-chloro-7-deazapurines 13b-d with 5-O-[(1,1-dimethylethyl)dimethylsilyl]-2,3-O-(1-methylethylidene)-alpha-D-ribofuranosyl chloride (17). Compounds 18b-d have been converted to the nucleosides 19b-d carrying reactive substituents in the pyrimidine moiety. Conformational analysis of selected nucleosides on the basis of proton coupling constants and using the program PSEUROT showed that these ribonucleosides exist in a preferred S conformation in solution.     

Using diffusion NMR to characterize guanosine self-association: insights into structure and mechanism

This paper presents results from a series of pulsed field gradient (PFG) NMR studies on lipophilic guanosine nucleosides that undergo cation-templated assembly in organic solvents. The use of PFG-NMR to measure diffusion coefficients for the different aggregates allowed us to observe the influences of cation, solvent and anion on the self-assembly process. Three case studies are presented. In the first study, diffusion NMR confirmed formation of a hexadecameric G-quadruplex [G 1](16)4 K(+)4 pic(-) in CD(3)CN. Furthermore, hexadecamer formation from 5'-TBDMS-2',3'-isopropylidene G 1 and K(+) picrate was shown to be a cooperative process in CD(3)CN. In the second study, diffusion NMR studies on 5'-(3,5-bis(methoxy)benzoyl)-2',3'-isopropylidene G 4 showed that hierarchical self-association of G(8)-octamers is controlled by the K(+) cation. Evidence for formation of both discrete G(8)-octamers and G(16)-hexadecamers in CD(2)Cl(2) was obtained. The position of this octamer-hexadecamer equilibrium was shown to depend on the K(+) concentration. In the third case, diffusion NMR was used to determine the size of a guanosine self-assembly where NMR signal integration was ambiguous. Thus, both diffusion NMR and ESI-MS show that 5'-O-acetyl-2',3'-O-isopropylidene G 7 and Na(+) picrate form a doubly charged octamer [G 7](8)2 Na(+)2 pic(-) 9 in CD(2)Cl(2). The anion's role in stabilizing this particular complex is discussed. In all three cases the information gained from the diffusion NMR technique enabled us to better understand the self-assembly processes, especially regarding the roles of cation, anion and solvent.