Formation Of Nucleotides Research Articles

Function of active site residues in the dUTPase from Epstein‐Barr Virus

Epstein‐Barr Virus, which causes infectious mononucleosis, contributes to many diseases such as Burkitt lymphoma and other cancers. The viral genome encodes a dUTPase, an enzyme that catalyzes the reaction of dUTP + H2O to dUMP + PPi + H+. This is an intermediate reaction involved in the formation of the thymidine nucleotide. The dUTPase found in humans is a trimeric enzyme containing three active sites while the viral enzyme is monomeric. Due to variation in the structures of the human and viral proteins, there may be differences in each enzyme's catalytic activity. Our results demonstrate the importance of a metal cofactor for activity of the viral enzyme. The role of active site residues in substrate binding and the catalysis of dUTP to dUMP is being examined by site‐directed mutagenesis. Characterization of the EBV dUTPase may facilitate the discovery of inhibitors. Inhibition of dUTPase decreases the formation of thymidine nucleotides creating a high dUTP/dTTP ratio. Uracil becomes incorporated into DNA in place of thymine which causes mutations that may be detrimental to cell survival. Selectively inhibiting the dUTPase from Epstein‐Barr Virus provides a mechanism to target cells infected with the virus without damaging uninfected cells.Support or Funding InformationUWL Undergraduate Research and Creativity GrantThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Integrated synthesis of nucleotide and nucleosides influenced by amino acids

Research on prebiotic chemistry and the origins of nucleic acids and proteins has traditionally been focussed on only one or the other. However, if nucleotides and amino acids co-existed on the early Earth, their mutual interactions and reactivity should be considered explicitly. Here we set out to investigate nucleotide/nucleoside formation by simple dehydration reactions of constituent building blocks (sugar, phosphate, and nucleobase) in the presence of different amino acids. We demonstrate the simultaneous formation of glycosidic bonds between ribose, purines, and pyrimidines under mild conditions without catalysts or activated reagents, as well as nucleobase exchange, in addition to the simultaneous formation of nucleotide and nucleoside isomers from several nucleobases. Clear differences in the distribution of glycosylation products are observed when glycine is present. This work demonstrates that reaction networks of nucleotides and amino acids should be considered when exploring the emergence of catalytic networks in the context of molecular evolution.

Beginning of Life on Planets

Beginning of life on a planet including earth would occur with the formation of nucleotides from such precursors as linear polyphosphate anion, D-ribose, and heterocyclic bases in presence of metasilicate anion of composition (SiO32-)n, metaborate anion of composition (BO2)nn-, and enstatite (MgSiO3). These complex silicates and borates might have acted as catalysts as well as moulds for the production of the nucleotides of DNA/RNA.

Red Blood cell IMPDH activity in adults and children with or without azathioprine: Relationship between thiopurine metabolites, ITPA and TPMT activities.

Inosine monophosphate dehydrogenase (IMPDH) is considered as the limiting enzyme of thiopurine metabolism for the formation of 6-thioguanine nucleotides (6-TGN). No data are available on the influence of RBC IMPDH activity on the metabolism of thiopurine drugs in individuals with IBD. The aims of this study were as follows: (a) to carry out a phenotypic study of RBC IMPDH activity in adults and children treated or not with azathioprine (AZA) for autoimmune diseases, and (b) to investigate the relationship between the activities of IMPDH, thiopurine metabolites, inosine triphosphatase (ITPA) and thiopurine methyltransferase (TPMT). IMPDH activity was determined in 97 adults and 67 children treated or not with AZA. 6-Thioguanine nucleotides (6-TGN), 6-methylmercaptopurine nucleotide (6-MeMPN) levels, and ITPA as well as TPMT activities were measured in RBCs by HPLC. Using the Gaussian mixture model, distribution of IMPDH activity was evaluated. Influence of age, sex and AZA treatment on IMPDH activity was also assessed. A bimodal distribution in IMPDH activity was found with 87% of patients exhibiting normal activity and 13% of patients with high activity. No influence of age, sex and AZA therapy was found. There is no relationship between TPMT, ITPA and IMPDH activities. A negative correlation between IMPDH activity and 6-MeMPN was shown in adults and children (rs=-0.335 P=0.014 and rs=-0.383 P=0.012, respectively). Our results suggest that AZA-treated patients exhibiting lower IMPDH activity could have higher Me-6MPN levels with higher risk of hepatotoxicity. We demonstrated that RBC matrix could be an interesting alternative to lymphocyte matrix to monitor thiopurine metabolites and enzyme activity.

Photoresponsive Supramolecular Nanotubes: Shrinkable Nanotubes for Duplex Formation of Short Nucleotides (Small 34/2018)

Photoresponsive Supramolecular Nanotubes: Shrinkable Nanotubes for Duplex Formation of Short Nucleotides (Small 34/2018)

Shrinkable Nanotubes for Duplex Formation of Short Nucleotides.

Molecular monolayer nanotubes produced by self-assembly of an amphiphile modified with a 2-nitrobenzyl group as a photoresponsive unit are able to encapsulate dinucleotides via electrostatic attraction. Upon photoirradiation, the 18 nm inner diameter of the nanotubes shrinks to less than 2 nm as a result of photochemical cleavage of the 2-nitrobenzyl group in the amphiphile. This shrinking of the nanotube channels leads to a propulsive release of the dinucleotides into the bulk solution and simultaneously accelerates formation of the dinucleotide duplexes. The larger nanotube channels without photoirradiation merely release each dinucleotide into the bulk solution, indicating that the squeezing via transportation in the narrow nanotube channels is necessary for duplex formation. In addition to the size effect, water with a lower polarity confined within the narrow nanotube channels helps to stabilize the energetically unfavorable hydrogen-bonded base pair between the dinucleotides. This system should enable researchers to perform biological reactions that occur only in specific environments and conditions in living organisms.

Luminescence determination of microRNAs based on the use of terbium(III) sensitized with an enzyme-activated guanine-rich nucleotide.

A method is reported for the fluorometric quantitation of microRNA. It is making use of a luminescent probe deribed from terbium(III) ion whose fluorescence is sensitized with a guanine-rich (G-rich) nucleotide. The probe has a large Stokes' shift and strong and sharp emission bands. The assay relies on the wide substrate specificity of terminal deoxynucleotidyl transferase (TdTase), which catalyzes the formation of long G-rich nucleotides when using microRNA primer as a trigger to start the polymerization. The addition of Tb(III) induces the formation of a G-quadruplex from the G-rich nucleotide, and this strongly enhances the green fluorescence of Tb(III) (peaking at 545nm upon photoexcitation at 290nm). Specifically, microRNA-21 was chosen as the analyte. The fluorescence intensity of Tb(III) increases linearly in the 1 pM to 1nM microRNA concentration range, and the detection limit is as low as 0.11 pM. The method can distinguish between family members of microRNA and performs excellently even when applied to extracts of cancer cells. Graphical abstract A fluorometric technique is reported for the determination of microRNA. It is based on signal enhancement based on the sensitization of terbium(III) via a guanine-rich nucleotide sequence. Klenow Fragment exo- (KFexo-) generates DNA sequence at the 3'-OH of microRNA, and terminal deoxynucleotidyl transferase (TdTase) catalyzes the formation of long G-rich nucleotides.

The role of folate and one-carbon metabolism in brain development and hydrocephalus: a literature review

Folate metabolism has been known to influence the development of the nervous system, as found in the case of neural tube defects. Folates are a group of compounds involved in one-carbon metabolism, which is necessary for the formation of purine and thymidine nucleotides, as well as methionine and methyl donors. In addition to the well-documented role of folates within the pathogenesis of neural tube defects, current literature provides evidence that folate imbalances may play a significant role in the development and effects of hydrocephalus. This review considers the possibility that folate imbalances in hydrocephalic cerebrospinal fluid may be responsible for the neurological deficit seen in patients with this condition. Understanding the details of this potential imbalance may provide further insight into novel treatment options for hydrocephalus in the future.

A novel ruthenium (II)-derived organometallic compound, TQ-6, potently inhibits platelet aggregation: Ex vivo and in vivo studies

Arterial thrombosis plays a key role in cardiovascular diseases. Hence, developing more effective antithrombotic agents is necessary. We designed a ruthenium (II)-derived complex, [Ru(η6-cymene)2-(1H-benzoimidazol-2-yl)-quinoline Cl]BF4 (TQ-6), as a new antiplatelet drug. TQ-6 (0.3 µM) exhibited extremely strong inhibitory activity against platelet aggregation, Src, and Syk phosphorylation stimulated by agonists in human platelets. In collagen-activated platelets, TQ-6 also inhibited ATP-release, [Ca+2]i, P-selectin expression, FITC-PAC-1 binding, and hydroxyl radical formation, as well as the phosphorylation of phospholipase Cγ2, protein kinase C, mitogen-activated protein kinases, and Akt. Neither FITC-JAQ1 nor FITC-triflavin binding or integrin β3 phosphorylation stimulated by immobilized fibrinogen were diminished by TQ-6. Furthermore, TQ-6 had no effects in cyclic nucleotide formation. Moreover, TQ-6 substantially prolonged the closure time in whole blood, increased the occlusion time of thrombotic platelet plug formation and bleeding time in mice. In conclusion, TQ-6 has a novel role in inhibiting platelet activation through the inhibition of the agonist receptors-mediated inside-out signaling such as Src-Syk-PLCγ2 cascade and subsequent suppression of granule secretion, leading to disturb integrin αIIbβ3-mediated outside-in signaling, and ultimately inhibiting platelet aggregation. Therefore, TQ-6 has potential to develop as a therapeutic agent for preventing or treating thromboembolic disorders.

Die Kontrolle zyklischer Nukleotide mittels Licht

Sensory photoreceptors underpin diverse adaptive responses in nature and serve as genetically encoded, light-gated actuators in optogenetics. Photoactivated nucleotide cyclases (PACs) enable light-dependent control over the formation of cyclic nucleotides (cNMPs). Conversely, the engineered, red-light-activated phosphodiesterase LAPD mediates the hydrolytic breakdown of cNMPs. In combination, PACs and LAPD hence unlock precise and graded control over intracellular cNMPs and associated processes.

Walking over 4 Gya: Chemical Evolution from Photochemistry to Mineral and Organic Chemistries Leading to an RNA World.

Here we overview the chemical evolution of RNA molecules from inorganic material through mineral-mediated RNA formation compatible with the plausible early Earth environments. Pathways from the gas-phase reaction to the formation of nucleotides, activation and oligomerization of nucleotides, seem to be compatible with specific environments. However, how these steps interacted is not clear since the chemical conditions are frequently different and can be incompatible between them; thus the products would have migrated from one place to another, suitable for further chemical evolution. In this review, we summarize certain points to scrutinize the RNA World hypothesis.

Two Experiments in Abiogenesis

Two new papers on prebiotic chemistry are reviewed by James Tour. The first claims to find further support for the RNA World hypothesis and the second suggests that nucleotide formation and selection may have been robust processes on the prebiotic Earth. Tour expresses skepticism on both counts.

Spontaneous formation and base pairing of plausible prebiotic nucleotides in water.

The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life.

Stepwise Hydration of 2-Aminooxazole: Theoretical Insight into the Structure, Finite Temperature Behavior and Proton-Induced Charge Transfer.

It was recently suggested that 2-aminooxazole (AO) could contribute to the formation of RNA nucleotides on primitive earth. In this article we have considered by means of computational modeling the influence of microhydration on the structural and spectral properties of this potential prebiotic molecule. The stable structures of AO(H2O)n were obtained first by sampling the potential energy landscapes of clusters containing up to n = 20 water molecules, using a simple but reasonably accurate force field and replica-exchange molecular dynamics simulations. Through reoptimization using an explicit description of electronic structure at the level of density functional theory with the M06-2X functional, the formation energies, ionization energies and electron affinities were determined in the vertical and adiabatic treatments, as well as vibrational and optical spectra covering the far-IR, mid-IR, and lower part of the UV ranges. The results generally show a clear segregation between the aminooxazole solute and the water molecules, a water cluster being formed near the nitrogen and amino group side leaving the hydrocarbon side dry even at temperatures corresponding to the liquid state. The spectral signatures generally concur and show distinct contributions of the solute and solvent, spectral shifts to lower energies being in agreement with earlier calculations in bulk solvent. We have also investigated the importance of microhydration on the charge transfer cross section upon collision with a proton, thereby extending an earlier investigation on the bare AO molecule. The presence of water molecules generally reduces the propensity for charge transfer at small sizes, but the influence of the solvent steadily decreases in larger droplets.

Synthesis of barbituric acid containing nucleotides and their implications for the origin of primitive informational polymers.

Given that all processes in modern biology are encoded and orchestrated by polymers, the origin of informational molecules had to be a crucial and significant step in the origin of life on Earth. An important molecule in this context is RNA that is thought to have allowed the transition from chemistry to biology. However, the RNA molecule is comprised of intramolecular bonds which are prone to hydrolysis, especially so under the harsh conditions of the early Earth. Furthermore, the formation of nucleotides with extant bases and their subsequent polymerization have both been problematic, to say the least. Alternate heterocycles, in contrast, have resulted in nucleosides in higher yields, suggesting a viable and prebiotically relevant solution to the longstanding "nucleoside problem". In the present study, we have synthesized a nucleotide using ribose 5'-monophosphate (rMP) and barbituric acid (BA), as the base analog, using dry-heating conditions that are thought to be prevalent in several regimes of the early Earth. Polymerization of the resultant monomers, i.e. BA-nucleotides, was also observed when dehydration-rehydration cycles were carried out at low pH and high temperature. The resulting RNA-like oligomers have intact bases unlike in reactions that were carried out with canonical nucleotides, which resulted in abasic sites under acidic conditions due to cleavage of the N-glycosidic linkages. Furthermore, the incorporation of BA directly into preformed sugar-phosphate backbones was also observed when rMP oligomers were subjected to heating with BA. The results from our aforementioned experiments provide preliminary evidence that BA could have been a putative precursor of modern nucleobases, which could have been incorporated into primitive informational polymers that predated the molecules of an RNA world. Moreover, they also highlight that the prebiotic soup, which would have been replete with alternate heterocycles, could have allowed the sampling of other such heterocycles, which would have had a selective advantage under pertinent selection pressures. Importantly, these kinds of processes have implications for shaping the prebiotic landscape that allowed for the emergence of primitive informational polymers of the pre-RNA world(s), prior to the emergence of a putative RNA world.

Adhesion promotion of thick polyphosphate-poly(allylamine) films onto polyolefin substrates by plasma polymers

The adhesion of thick poly(allylamine)-polyphosphate layers (1 μm) deposited by the wet-chemical layer-by-layer (LbL) technique onto polyethylene or polystyrene (each 100 μm) was very low. To promote the adhesion of these LbL deposited layers, the polyolefin substrates were oxidized at the surface by short exposure to the oxygen plasma (2 or 5 s) and subsequently coated with an interlayer of plasma-deposited poly(allylamine) or poly(allyl alcohol) (100 nm). The plasma polymer interlayers have improved strongly the adhesion between polyolefin substrates and polyphosphate coatings. Such phosphate coatings are interesting for life sciences (nucleotide formation) but also for fire retardancy in combination with N-rich compounds such as melamine. The intention was to prefer chemical hydrogen bonds for adhesion promoting because of their high binding energy. Therefore the introduced oxygen-containing groups at the polyolefin surface could interact with the OH or NH2 groups of the adhesion-promoting plasma polymer interlayer. These groups were also able to interact strongly with the poly(allylamine)-polyphosphate topcoating. The coated polyolefins were investigated using Fourier transform infrared spectroscopy in attenuated total reflectance mode (FTIR-ATR), X-ray photoelectron spectroscopy, thermogravimetric analyses and atomic force spectroscopy, and 90° peel test.

Adsorption of nucleic Acid bases, ribose, and phosphate by some clay minerals.

Besides having a large capacity for taking up organic molecules, clay minerals can catalyze a variety of organic reactions. Derived from rock weathering, clay minerals would have been abundant in the early Earth. As such, they might be expected to play a role in chemical evolution. The interactions of clay minerals with biopolymers, including RNA, have been the subject of many investigations. The behavior of RNA components at clay mineral surfaces needs to be assessed if we are to appreciate how clays might catalyze the formation of nucleosides, nucleotides and polynucleotides in the “RNA world”. The adsorption of purines, pyrimidines and nucleosides from aqueous solution to clay minerals is affected by suspension pH. With montmorillonite, adsorption is also influenced by the nature of the exchangeable cations. Here, we review the interactions of some clay minerals with RNA components.

Functionalized anodic aluminum oxide membrane-electrode system for enzyme immobilization.

A nanoporous membrane system with directed flow carrying reagents to sequentially attached enzymes to mimic nature’s enzyme complex system was demonstrated. Genetically modified glycosylation enzyme, OleD Loki variant, was immobilized onto nanometer-scale electrodes at the pore entrances/exits of anodic aluminum oxide membranes through His6-tag affinity binding. The enzyme activity was assessed in two reactions—a one-step “reverse” sugar nucleotide formation reaction (UDP-Glc) and a two-step sequential sugar nucleotide formation and sugar nucleotide-based glycosylation reaction. For the one-step reaction, enzyme specific activity of 6–20 min–1 on membrane supports was seen to be comparable to solution enzyme specific activity of 10 min–1. UDP-Glc production efficiencies as high as 98% were observed at a flow rate of 0.5 mL/min, at which the substrate residence time over the electrode length down pore entrances was matched to the enzyme activity rate. This flow geometry also prevented an unwanted secondary product hydrolysis reaction, as observed in the test homogeneous solution. Enzyme utilization increased by a factor of 280 compared to test homogeneous conditions due to the continuous flow of fresh substrate over the enzyme. To mimic enzyme complex systems, a two-step sequential reaction using OleD Loki enzyme was performed at membrane pore entrances then exits. After UDP-Glc formation at the entrance electrode, aglycon 4-methylumbelliferone was supplied at the exit face of the reactor, affording overall 80% glycosylation efficiency. The membrane platform showed the ability to be regenerated with purified enzyme as well as directly from expression crude, thus demonstrating a single-step immobilization and purification process.

Molecular Mechanism of Diaminomaleonitrile to Diaminofumaronitrile Photoisomerization: An Intermediate Step in the Prebiotic Formation of Purine Nucleobases

The photoinduced isomerization of diaminomaleonitrile (DAMN) to diaminofumaronitrile (DAFN) was suggested to play a key role in the prebiotically plausible formation of purine nucleobases and nucleotides. In this work we analyze two competitive photoisomerization mechanisms on the basis of state-of-the-art quantum-chemical calculations. Even though it was suggested that this process might occur on the triplet potential-energy surface, our results indicate that the singlet reaction channel should not be disregarded either. In fact, the peaked topography of the S1 /S0 conical intersection suggests that the deexcitation should most likely occur on a sub-picosecond timescale and the singlet photoisomerization mechanism might effectively compete even with a very efficient intersystem crossing. Such a scenario is further supported by the relatively small spin-orbit coupling of the S1 and T2 states in the Franck-Condon region, which does not indicate a very effective triplet bypass for this photoreaction. Therefore, we conclude that the triplet reaction channel in DAMN might not be as prominent as was previously thought.

Nucleotidyl cyclase activity of soluble guanylyl cyclase in intact cells

Soluble guanylyl cyclase (sGC) is activated by nitric oxide (NO) and generates the second messenger cyclic GMP (cGMP). Recently, purified sGC α1β1 has been shown to additionally generate the cyclic pyrimidine nucleotides cCMP and cUMP. However, since cyclic pyrimidine nucleotide formation occurred only the presence of Mn2+ but not Mg2+, the physiological relevance of these in vitro findings remained unclear. Therefore, we studied cyclic nucleotide formation in intact cells. We observed NO-dependent cCMP- and cUMP formation in intact HEK293 cells overexpressing sGC α1β1 and in RFL-6 rat fibroblasts endogenously expressing sGC, using HPLC–tandem mass spectrometry. The identity of cCMP and cUMP was unambiguously confirmed by HPLC–time-of-flight mass spectrometry. Our data indicate that cCMP and cUMP play second messenger roles and that Mn2+ is a physiological sGC cofactor.