Uracil Moiety Research Articles

Handedness Enantioselection of Carbon Nanotubes Using Helical Assemblies of Flavin Mononucleotide

In order to truly unlock advanced applications of single-walled carbon nanotubes (SWNTs), one needs to separate them according to both chirality and handedness. Here we show that the chiral D-ribityl phosphate chain of flavin mononucleotide (FMN) induces a right-handed helix that enriches the left-handed SWNTs for all suspended (n,m) species. Such enantioselectivity stems from the sp(3) hybridization of the N atom anchoring the sugar moiety to the flavin ring. This produces two FMN conformations (syn and anti) analogous to DNA. Electrostatic interactions between the neighboring uracil moiety and the 2'-OH group of the side chain provide greater stability to the anti-FMN conformation that leads to a right-handed FMN helix. The right-handed twist that the FMN helix imposes to the underlying nanotube, similar to "Indian burn", causes diameter dilation of only the left-handed SWNTs, whose improved intermolecular interactions with the overlaying FMN helix, impart enantioselection.

A reliable Pd-mediated hydrogenolytic deprotection of BOM group of uridine ureido nitrogen

The benzyloxymethyl (BOM) group has been utilized widely in syntheses of a variety of natural and non-natural products. The BOM group is also one of few choices to protect uridine ureido nitrogen. However, hydrogenolytic cleavage of the BOM group of uridine derivatives has been unreliably performed via heterogeneous conditions using Pd catalysts. One of the undesirable by-products formed by Pd-mediated hydrogenation conditions is the over-reduced product in which the C5–C6 double bond of the uracil moiety was saturated. To date, we have generated a wide range of uridine-containing antibacterial agents, where the BOM group has been utilized in their syntheses. In screening of deprotection conditions of the BOM group of uridine ureido nitrogen under Pd-mediated hydrogenation conditions, we realized that the addition of water to the iPrOH-based hydrogenation conditions can suppress the formation of over-reduced uridine derivatives and the addition of HCO2H (0.5%) dramatically improve the reaction rate. An optimized hydrogenation condition described here can be applicable to the BOM-deprotections of a wide range of uridine derivatives.

Enhancement of photovoltaic properties in supramolecular polymer networks featuring a solar cell main-chain polymer H-bonded with conjugated cross-linkers

Stille polymerization was employed to synthesize a low-band-gap (LBG) conjugated main-chain polymer PBTH consisting of bithiazole, dithieno[3,2-b:2′,3′-d]pyrroles (DTP), and pendent melamine derivatives. Novel supramolecular polymer networks PBTH/C and PBTH/F were developed by mixing proper molar amounts of polymer PBTH (containing melamine pendants) to be hydrogen-bonded (H-bonded) with complementary uracil-based conjugated cross-linkers C and F (i.e., containing two symmetrical uracil moieties connected with carbazole and fluorene units through triple bonds). The formation of multiple H-bonds between polymer PBTH and cross-linkers C or F was confirmed by FT-IR measurements. In contrast to polymer PBTH, the supramolecular design with multiple H-bonds can enhance the photovoltaic properties of polymer solar cell (PSC) devices containing H-bonded polymer networks PBTH/C and PBTH/F by tuning their light harvesting capabilities, HOMO energy levels, and crystallinities. Initially, the power conversion efficiency (PCE) values of PSC devices containing supramolecular polymer networks PBTH/C and PBTH/F as electron donors and [6,6]-phenyl-C71-butyric acid methyl ester (PC70BM) as an electron acceptor (polymer:PC70BM = 1:1 w/w) are found to be 0.97 and 0.68%, respectively, in contrast to 0.52% for polymer PBTH. The highest PCE value of 1.56% with a short-circuit current densities (Jsc) value of 7.16 mA/cm2, a open circuit voltages (Voc) value of 0.60 V, and a fill factor (FF) of 0.36 was further optimized in the PSC device containing a supramolecular polymer network PBTH/C as polymer:PC70BM = 1:2 w/w. These results indicate that supramolecular design is an effective route towards better photovoltaic properties of Voc, Jsc, and PCE values in polymer solar cells.

Design and controlled emission properties of bioorganometallic compounds composed of uracils and organoplatinum(ii) moieties

The bioorganometallic platinum(II) compounds PtU6 and PtU5 were designed by the conjugation of the corresponding uracil derivative and the organoplatinum(II) compound [4-octyloxy-(C^N^N)PtCl]. The single crystal X-ray structure determination of PtU6 revealed the formation of the dimeric structure through intermolecular hydrogen bonds between the uracil moieties of two independent molecules, wherein each hydrogen-bonded dimer was connected through Pt(II)-Pt(II) and π-π interactions. The tuning of the emission properties of the organoplatinum(II) compounds was achieved by changing the direction of hydrogen bonding sites and the molecular scaffold having two 2,6-dihexamidopyridine moieties as a complementary hydrogen bonding site for the uracil moiety, which depends on the regulation of the aggregated structures, to induce the Pt(II)-Pt(II) and π-π interactions.

Modulation of charge-transfer complexes assisted by complementary hydrogen bonds of nucleobases: TCNQ complexes of a uracil-substituted EDO-TTF

A hydrogen bond functionalized ethylenedioxytetrathiafulvalene (EDO-TTF) derivative having an n-butyluracil moiety was synthesized. In the crystal structure, the Watson–Crick-type complementary hydrogen bonds of the uracil moiety formed a pair of donor molecules, which further aggregated by S⋯S interactions and π-stacks of the TTF moiety to construct a two-dimensional sheet. In the charge-transfer complex formation with tetracyanoquinodimethane, the crystallization conditions modulated the subtle balance between Watson–Crick and reverse Watson–Crick types of complementary hydrogen-bonded pairs, controlling stoichiometry, ionicity and molecular packing of the complexes. A highly conducting mixed valence complex with the Watson–Crick-type hydrogen bonds was yielded by the quick evaporation of reaction solvent, and a low-conducting neutral complex forming reverse Watson–Crick-type hydrogen bonds was obtained by the slow vapor diffusion method.

Palladium-catalyzed synthesis of benzo[ c]pyrimido[1,6- a]azepine scaffold from Morita–Baylis–Hillman adducts: intramolecular 6-arylation of uracil nucleus

Palladium-catalyzed intramolecular arylation at the C-6 position of uracil moiety was examined. Morita–Baylis–Hillman adducts bearing an uracil moiety at the primary position served an efficient way to a benzo[ c]pyrimido[1,6- a]azepine scaffold.

FTIR and Raman spectra and fundamental frequencies of 5-halosubstituted uracils: 5-X-uracil (X = F, Cl, Br and I)

FTIR and Raman spectra of 5-halosubstituted uracils (5-X-uracil; X = F, Cl, Br and I) were recorded in the region 200–4000 cm −1. Assuming under the C s point group, the distribution of normal mode of vibrations between the two species as planar (a′) and non-planar (a″) are given by 21a′ + 9a″, of which also correspond to the 30 modes of uracil moiety and the electro negativity of halogen group substitution causes some where mixing/shifting in their modes with other modes. The ring breathing and kekule stretching modes are observed in lower magnitudes compared to those of uracil which could be due to mass effect of halogen atom in place of the hydrogen atom. The C–X (X = F, Cl, Br and I) stretching frequency is distinctly separated from the CH/NH ring stretching frequencies on the pyrimidine ring. All other bands have also been assigned different fundamentals/overtones/combinations.

Direct Evidence for Tautomerization of the Uracil Moiety within the Pb2+/Uridine-5′-monophosphate Complex: A Combined Tandem Mass Spectrometry and IRMPD study

The structure of the [Pb(UMP)-H](+) (UMP = uridine-5'-monophosphate) complex was studied in the gas phase by combining electrospray ionization (ESI), tandem mass spectrometry, and mid-infrared multiple photon dissociation (IRMPD) spectroscopy. The results obtained show that Pb(2+) ions interact not only with the deprotonated phosphate group but also with a carbonyl group of the nucleobase moiety by folding of the mononucleotide, resulting in macrochelates that are not likely to be present in solution. Comparison between the IRMPD and DFT-computed spectra suggests that the ESI-generated complex likely corresponds to a mixture of several structures, and establishes the enolic tautomers as the most abundant species for the [Pb(UMP)-H](+) ion, while the very weak IRMPD signal observed at ∼1763 cm(-1) points to a minor population of oxo forms. Our data also suggest that losing the nucleobase residue under CID conditions does not necessarily mean a lack of interaction between the metal and the nucleobase moiety, as commonly reported in the literature for large oligonucleotides.

Evaluation of the Role of the Vaccinia Virus Uracil DNA Glycosylase and A20 Proteins as Intrinsic Components of the DNA Polymerase Holoenzyme

The vaccinia virus DNA polymerase is inherently distributive but acquires processivity by associating with a heterodimeric processivity factor comprised of the viral A20 and D4 proteins. D4 is also an enzymatically active uracil DNA glycosylase (UDG). The presence of an active repair protein as an essential component of the polymerase holoenzyme is a unique feature of the replication machinery. We have shown previously that the A20-UDG complex has a stoichiometry of ∼1:1, and our data suggest that A20 serves as a bridge between polymerase and UDG. Here we show that conserved hydrophobic residues in the N' terminus of A20 are important for its binding to UDG. Our data argue against the assembly of D4 into higher order multimers, suggesting that the processivity factor does not form a toroidal ring around the DNA. Instead, we hypothesize that the intrinsic, processive DNA scanning activity of UDG tethers the holoenzyme to the DNA template. The inclusion of UDG as an essential holoenzyme component suggests that replication and base excision repair may be coupled. Here we show that the DNA polymerase can utilize dUTP as a substrate in vitro. Moreover, uracil moieties incorporated into the nascent strand during holoenzyme-mediated DNA synthesis can be excised by the viral UDG present within this holoenzyme, leaving abasic sites. Finally, we show that the polymerase stalls upon encountering an abasic site in the template strand, indicating that, like many replicative polymerases, the poxviral holoenzyme cannot perform translesion synthesis across an abasic site.

Pyrimidine Nucleotides with 4-Alkyloxyimino and Terminal Tetraphosphate δ-Ester Modifications as Selective Agonists of the P2Y4 Receptor

P2Y(2) and P2Y(4) receptors are G protein-coupled receptors, activated by UTP and dinucleoside tetraphosphates, which are difficult to distinguish pharmacologically for lack of potent and selective ligands. We structurally varied phosphate and uracil moieties in analogues of pyrimidine nucleoside 5'-triphosphates and 5'-tetraphosphate esters. P2Y(4) receptor potency in phospholipase C stimulation in transfected 1321N1 human astrocytoma cells was enhanced in N(4)-alkyloxycytidine derivatives. OH groups on a terminal δ-glucose phosphoester of uridine 5'-tetraphosphate were inverted or substituted with H or F to probe H-bonding effects. N(4)-(Phenylpropoxy)-CTP 16 (MRS4062), Up(4)-[1]3'-deoxy-3'-fluoroglucose 34 (MRS2927), and N(4)-(phenylethoxy)-CTP 15 exhibit ≥10-fold selectivity for human P2Y(4) over P2Y(2) and P2Y(6) receptors (EC(50) values 23, 62, and 73 nM, respectively). δ-3-Chlorophenyl phosphoester 21 of Up(4) activated P2Y(2) but not P2Y(4) receptor. Selected nucleotides tested for chemical and enzymatic stability were much more stable than UTP. Agonist docking at CXCR4-based P2Y(2) and P2Y(4) receptor models indicated greater steric tolerance of N(4)-phenylpropoxy group at P2Y(4). Thus, distal structural changes modulate potency, selectivity, and stability of extended uridine tetraphosphate derivatives, and we report the first P2Y(4) receptor-selective agonists.

Antimicrobial activity of pyrimidinophanes with thiocytosine and uracil moieties

Reactions of pyrimidinophanes with two 6-methylthiocytosine and one 5(6)-alkyluracil moieties bridged with each other by polymethylene spacers with methyl or nonyl p-toluenesulfonate, p-toluenesulfonic acid, methanesulfonate and trifluorosulfonate afforded amphiphilic macrocyclic bis- p-toluene-, methane- and trifluorosulfonates. Despite the presence of several reaction centers in the initial pyrimidinophane molecules, protonation and methylation occurred only at the N 1 atom (with quaternization) of the 6-methylthiocytosine moieties. The bacteriostatic and fungistatic activity of the products was estimated. Macrocyclic tosylates exhibit a remarkable selectivity towards Staphylococcus aureus, with MIC values comparable with a reference drug. Bacteriostatic activity of the amphiphilic pyrimidinophanes depends on the size of the macrocycles, and the highest activity corresponds to definite lengths of polymethylene bridges. Besides, the antimicrobial activity of the screened pyrimidine derivatives depends on their topology. While macrocyclic tosylates are more active against bacteria than against fungi, acyclic tosylate with the same structural fragments shows a dramatical decrease of MIC towards mold and yeast with respect to the corresponding macrocycle. It is found that macrocyclic and acyclic tosylates in high dilutions decrease the extracellular lipase activity.

Effect of the methylation of uracil and/or glycine on their mutual interaction

In order to simulate the hydrogen bonding and proton transfer (PT) in protein-DNA/RNA interactions, a series of simplified models were employed and investigated in the gas phase. These models included various neutral, anionic and cationic glycine-uracil dimers, and their methylated derivatives generated by the mono- or dimethylation of glycine and/or uracil moieties of the dimer. The results reveal that the only process that can occur in the neutral complexes is a double-PT process leading to proton exchange between the two moieties (i.e., point mutation). The first methyl substitute can reduce the activation energy of the PT process and thus promote the isomerization of the two moieties; further methylation can reduce the isomerization in only some of the cases. In the anionic complexes, only the one-way PT (i.e., amino acid → nucleic acid base) process is energetically favorable, and this PT process is an interesting barrier-free one (BFPT), with the attached electron locating itself at the base moiety. Methylation will disfavor BFPT, but it cannot alter the nature of BFPT. In the cationic complexes, three different PT processes can occur. These processes can transform mutually by adjusting either or both of the methylated sites and methyl number, indicating that the methylation can regulate the dynamics of these PT processes.

A QM/QM Investigation of the hUNG2 Reaction Surface: The Untold Tale of a Catalytic Residue

Human uracil-DNA glycosylase (hUNG2) is a base excision repair enzyme that removes the damaged base uracil from DNA through hydrolytic deglycosylation of the nucleotide. In the present study, the mechanism of hUNG2 is thoroughly investigated using ONIOM(MPWB1K/6-31G(d):PM3) active-site models to generate reaction potential energy surfaces. Active-site models that differ in the hydrogen-bonding arrangement of the nucleophilic water molecule and/or protonation state of His148 are considered. The large barrier calculated using the model with a cationic His148 verifies that this residue is neutral in the early stages of the reaction. The reaction pathways predicted by two models with a neutral His148 are consistent with a wealth of experimental data on the enzyme, including mutational studies, which supports our approach. On the basis of our calculations, we propose a complete mechanism for the chemical step of hUNG2. In the first part of the reaction, His268, Asn204, and a water molecule work together to stabilize the negative charge forming on the uracil moiety. Subsequently, either Asp145 or His148 can act as the general base that activates the water nucleophile depending on the binding orientation of the water molecule in the active site. However, we propose that His148 preferentially acts as the general base. Therefore, in agreement with previous proposals, we assign the primary function of Asp145 to electrostatic stabilization of the positive charge developing on the sugar moiety during the reaction, which is also consistent with a growing theory that the primary function of active-site carboxylate groups present in many glycosylases is transition state stabilization. Most importantly, our work explains, for the first time, the role of His148 in the chemical step and provides additional support for the inclusion of this amino acid in the list of residues (Asp145 and His268) essential to the chemical step of the hUNG2 mechanism.

Structural Modifications of UMP, UDP, and UTP Leading to Subtype-Selective Agonists for P2Y2, P2Y4, and P2Y6 Receptors

A large series of derivatives and analogues of the uracil nucleotides UMP, UDP, and UTP with modifications in various positions of the uracil moiety and/or the phosphate groups were synthesized and evaluated at human P2Y(2), P2Y(4), and P2Y(6) receptors. 2-(Ar)alkylthio substitution of UMP and UDP was best tolerated by the P2Y(2) receptor. 2-Phenethylthio-UMP (13e) showed an EC(50) value of 1.3 μM at P2Y(2) and >70-fold selectivity versus P2Y(4) and P2Y(6) receptors. Substitution of the 2-keto group in UMP by NH (13g, iso-CMP) resulted in the first potent and selective P2Y(4) agonist (EC(50) 4.98 μM, >20-fold selective vs P2Y(2) and P2Y(6)). In contrast, replacement of the 2-keto function in UDP by NH yielded a potent P2Y(2) agonist (12g, iso-CDP, EC(50) = 0.604 μM, >100-fold selective). In an attempt to obtain metabolically stable UTP analogues, β,γ-dichloro- and β,γ-difluoro-methylene-UTP derivatives were synthesized. The triphosphate modifications were much better tolerated by P2Y(2), and in some cases also by P2Y(6), than by P2Y(4) receptors. 4-Thio-β,γ-difluoromethylene-UTP (14g) was a potent P2Y(2) agonist with an EC(50) value of 0.134 μM and >50-fold selectivity. N3-Phenacyl-β,γ-dichloromethylene-UTP (14b) proved to be a potent P2Y(6) receptor agonist (EC(50) 0.142 μM) with high selectivity versus P2Y(4) (50-fold) and moderate selectivity versus P2Y(2) receptors (6-fold).

ウラシル部位を有する有機白金(II)錯体の組織化に基づく発光

ウラシル部位を有する有機白金(II)錯体の組織化に基づく発光

Redox-active tubular frameworks with TTF: self-assemblies by complementary hydrogen-bonds and π-stacks of TTF-phenyluracil

Tubular frameworks of a tetrathiafulvalene (TTF) based electron-donor with a N1-phenyluracil moiety were constructed by strong self-assembling abilities. The uracil moiety formed the reversed Watson–Crick type hydrogen-bond pair. The TTF moiety exhibited C–H⋯X hydrogen-bonds, S⋯S interactions, and uniform π-stack. The phenyl group formed a herring-bone array by the edge-to-face interaction. These multiple intermolecular interactions established channels of ca. 4 × 8 A. The cavities were filled with crystalline solvent molecules (tetrahydrofuran and pyridine), which were fixed on the framework by the C–H⋯X hydrogen-bonds.

Identification of a Napsamycin Biosynthesis Gene Cluster by Genome Mining

Napsamycins are potent inhibitors of bacterial translocase I, an essential enzyme in peptidoglycan biosynthesis, and are classified as uridylpeptide antibiotics. They comprise an N-methyl diaminobutyric acid, an ureido group, a methionine and two non-proteinogenic aromatic amino acid residues in a peptide backbone that is linked to a 5'-amino-3'-deoxyuridine by an unusual enamide bond. The napsamycin gene cluster was identified in Streptomyces sp. DSM5940 by using PCR probes from a putative uridylpeptide biosynthetic cluster found in S. roseosporus NRRL15998 by genome mining. Annotation revealed 29 hypothetical genes encoding for resistance, regulation and biosynthesis of the napsamycins. Analysis of the gene cluster indicated that the peptide core structure is assembled by a nonlinear non-ribosomal peptide synthetase (NRPS)-like mechanism that involves several discrete single or didomain proteins. Some genes could be assigned, for example, to the synthesis of the N-methyl diaminobutyric acid, to the generation of m-tyrosine and to the reduction of the uracil moiety. The heterologous expression of the gene cluster in Streptomyces coelicolor M1154 resulted in the production of napsamycins and mureidomycins as demonstrated by LC-ESI-MS and MS/MS analysis. The napsamycin gene cluster provides a molecular basis for the detailed study of the biosynthesis of this class of structurally unusual compounds.

Expression in E. coli and characterization of the catalytic domain of Botrytis cinerea chitin synthase

BackgroundChitin synthase 3a (CHS3a) from Botrytis cinerea (Bc) catalyses the multiple transfer of N-acetylglucosamine (GlcNAc) residues to the growing chitin chain. Chitin, a β-1,4 linked GlcNAc homopolymer, is an essential cell wall component of filamentous fungi. Chitin synthase, processive membranous protein, has been recognized as a promising target for new antifungicides. Enzymatic characterizations of chitin synthases have been limited, mainly because purity and amounts of integral enzyme obtained after purification procedures have not been sufficient.FindingsWe undertook the preparation of two BcCHS3a fragment proteins, containing only the central domain and devoid of the N-terminal and transmembrane C-terminal regions. The central domain of CHS3a, named SGC (Spsa GntI Core), is conserved in all UDP-glycosyltransferases and it is believed to contain the active site of the enzyme. CHS3a-SGC protein was totally expressed as inclusion bodies in Escherichia coli. We performed recombinant CHS3a-SGC purification in denaturing conditions, followed by a refolding step. Although circular dichroism spectra clearly exhibited secondary structures of renatured CHS3a-SGC, no chitin synthase activity was detected. Nevertheless CHS3a-SGC proteins show specific binding for the substrate UDP-GlcNAc with a dissociation constant similar to the Michaelis constant and a major contribution of the uracil moiety for recognition was confirmed.ConclusionsMilligram-scale quantities of CHS3a-SGC protein with native-like properties such as specific substrate UDP-GlcNAc binding could be easily obtained. These results are encouraging for subsequent heterologous expression of full-length CHS3a.

Synthesis and characterization of bioorganometallic conjugates composed of NCN-pincer platinum(II) complexes and uracil derivatives

The conjugation of the NCN-pincer platinum(II) complexes as an oraganometallic compound and the uracil derivatives as a nucleobase was demonstrated to give the corresponding bioorganometallics. The NCN-pincer ligands bearing the 6-ethynyl-1-octyluracil, 5-ethynyl-1-octyluracil, and the furanopyrimidine moiety were synthesized. In a crystal state, the NCN-pincer ligand bearing the 6-ethynyl-1-octyluracil moiety was found to form a hydrogen-bonded dimer through intermolecular hydrogen bonds between the uracil moieties, which was connected through π–π interaction between the uracil and benzene moieties of the NCN-pincer ligand. The reaction of the NCN-pincer ligand bearing the 6-ethynyl-1-octyluracil moiety with [Pt(tolyl-4) 2(SEt 2)] 2 led to the formation of the NCN-pincer platinum(II) complex bearing the 6-ethynyl-1-octyluracil moiety. The NCN-pincer platinum(II) complex bearing the furanopyrimidine moiety was obtained by the reaction of the NCN-pincer ligand bearing the furanopyrimidine moiety with [Pt(tolyl-4) 2(SEt 2)] 2. The single-crystal X-ray structure determination of the NCN-pincer platinum(II) complex bearing the furanopyrimidine moiety revealed the formation of the furanopyrimidine ring and the π stack dimer between the furanopyrimidine and benzene moieties of the NCN-pincer ligand in the crystal packing. The NCN-pincer platinum(II) complexes bearing the 6-ethynyl-1-octyluracil moiety or the furanopyrimidine moiety exhibited emission in both solution and solid states.

Synthesis and sensing properties of a new carbazole fluorosensor for detection of abacavir

An abacavir-targeted fluorosensor based on the carbazole moiety has been synthesised and characterised. Recognition of abacavir is by base pairing between a uracil moiety present in the fluorosensor and the guanine moiety of abacavir. The fluorosensor exhibits five-fold quenching in the presence of 50 μM abacavir. Its sensitivity to abacavir is superior to that of other reverse transcriptase inhibitors: zidovudine, lamivudine and didanosine. Due to its high sensitivity, this fluorosensor has the potential to be used in multi-analyte array-based detection platforms as well as in microfluidics systems.