Building Blocks Of Nucleic Acids Research Articles

Multicomponent Synthesis of C(8)-Substituted Purine Building Blocks of Peptide Nucleic Acids from Prebiotic Compounds.

We have explored the reaction of a three-components mixture of aminomalononitrile, urea and α-amino acid methyl esters for the multicomponent synthesis substituted purines resembling PNA's building blocks. 2,6-diamino-purines, 6-amino-3,9-dihydro-2H-purin-2-one (iso-guanines), and 3,9-dihydro-6H-purin-6-one derivatives, selectively decorated at C(8)-position of the purine ring with different amino acid residues, were obtained from acceptable to good yields. The regio-selectivity of the transformation was controlled by the use of urea in the ternary mixture and by the annulation agent involved in the ring-closure of amino-imidazole carbonitrile intermediates. Solvent free conditions, microwave irradiation and simple one-carbon containing reagents further satisfied the major requirement of atom economy and sustainable chemistry. Due to the prebiotic nature of the three-components mixture and of annulation agents, it also embodies the possibility for the synthesis of novel PNAs bearing purine nucleobases decorated at C(8)-position of the imidazole ring as alternative RNA analogues in molecular evolution.

Application of Mass Spectrometry for Analysis of Nucleobases, Nucleosides and Nucleotides in Tea and Selected Herbs: A Critical Review of the Mass Spectrometric Data.

The main and most commonly known biological function of nucleobases, nucleosides, and nucleotides is usually associated with the fact that they are the building blocks of nucleic acids. However, these compounds also belong to plant secondary metabolites, although in that role they have attracted less attention than the others, e.g., terpenes, phenolics, or alkaloids. The former compounds are also important constituents of the human diet, e.g., as ingredients of tea and herbs, endowing them with specific taste qualities and pharmacological activities. Liquid chromatography-mass spectrometry seems to be the most important analytical method that permits the identification and determination of nucleobases, nucleosides, and nucleotides, along with the other metabolites. The main goal of this review is to discuss in detail the aspects of mass spectrometric detection of nucleobases, nucleosides, and nucleotides in tea and selected herbs. An important conclusion is that the identification of the compounds of interest should be performed not only on the basis of [M + H]+/[M - H]- ions but should also be confirmed by the respective product ions; however, as discussed in detail in this review, it may sometimes be problematic. It also clear that all difficulties that may be encountered when analyzing plant material are caused by the complexity of the analyzed samples and the need to analyze different classes of compounds, and this review absolutely does not debase any of the mentioned papers.

Prebiotic N-(2-Aminoethyl)-Glycine (AEG)-Assisted Synthesis of Proto-RNA?

Quantum mechanical calculations are used to explore the thermodynamics of possible prebiotic synthesis of the building blocks of nucleic acids. Different combinations of D-ribofuranose (Ribf) and N-(2-aminoethyl)-glycine (AEG) (trifunctional connectors (TCs));the nature of the Ribf, its anomeric form, and its ring puckering (conformation); and thenature of the nucleobases (recognition units (RUs)) are considered. The combinatorial explosion of possible nucleosides has been drastically reduced on physicochemical grounds followed by a detailed thermodynamic evaluation of alternative synthetic pathways. The synthesis of nucleosides containing N-(2-aminoethyl)-glycine (AEG) is predicted to be thermodynamically favored suggesting a possible role of AEG as a component of an ancestral proto-RNA that may have preceded today's nucleic acids.A new pathway for the building of free nucleotides (exemplified by 5'-uridine monophosphate (UMP)) and of AEG dipeptides is proposed. This new pathway leads to a spontaneous formation of free UMP assisted by an AEG nucleoside in an aqueous environment. This appears to be a workaround to the "water problem" that prohibits the synthesis of nucleotides in water.

Vibrational circular dichroism of adenosine crystals

Adenosine is one of the building blocks of nucleic acids and other biologically important molecules. Spectroscopic methods have been among the most utilized techniques to study adenosine and its derivatives. However, most of them deal with adenosine in solution. Here, we present the first vibrational circular dichroism (VCD) spectroscopic study of adenosine crystals in solid state. Highly regular arrangement of adenosine molecules in a crystal resulted in a strongly enhanced supramolecular VCD signal originating from long-range coupling of vibrations. The data suggested that adenosine crystals, in contrast to guanosine ones, do not imbibe atmospheric water. Relatively large dimensions of the adenosine crystals resulted in scattering and substantial orientational artifacts affecting the spectra. Several strategies for tackling the artifacts have been proposed and tested. Atypical features in IR absorption spectra of crystalline adenosine (e.g., extremely low absorption in mid-IR spectral range) were observed and attributed to refractive properties of adenosine crystals.

Ultrafast excited state dynamics of isocytosine unveiled by femtosecond broadband time-resolved spectroscopy combined with density functional theoretical study.

Isocytosine, having important applications in antivirus and drug development, is among the building blocks of Hachimoji nucleic acids. In this report, we present an investigation of the excited state dynamics of isocytosine in both protic and aprotic solvents, which was conducted by a combination of methods including steady-state spectroscopy, femtosecond broadband time-resolved fluorescence, and transient absorption. These methods were coupled with density functional and time-dependent density functional theory calculations. The results of our study provide the first direct evidence for a highly efficient nonradiative mechanism achieved through internal conversion from the ππ* state of the isocytosine keto-N(3)H form occurring within subpicoseconds and picoseconds following photo-excitation. Our study also unveils a crucial role of solvent, particularly solute-solvent hydrogen bonding, in determining the tautomeric composition and regulating the pathways and dynamics of the deactivation processes. The deactivation processes of isocytosine in the solvents examined are found to be distinct from those of cytosine and the case known for isocytosine in the gas phase mainly due to different tautomeric forms involved. Overall, our findings demonstrate the high photo-stability of isocytosine in the solution and showcase the remarkable effect of covalent modification in altering the spectral character and excited state dynamics of nucleobases.

Screening and application of purine degrading Limosilactobacillus fermentum LF-1 from Huangjiu fermentation broth.

As the important building blocks of nucleic acids, purines are alkaloids and responsible for hyperuricemia and gout. The purine content in Huangjiu is higher, and mainly exists in the form of free bases, which is easier to be absorbed by human body. However, the currently available reports on purine in Huangjiu mainly focus on detection methods and content survey. No studies on the regulation of the purine content in Huangjiu have been reported. Eighty-four strains, with the degradation capacity of purine, were screened from the fermentation broth of Huangjiu. In detail, the isolated lactic acid bacteria (LAB) strain 75 # showed the strongest degradation ability of guanosine, inosine and four purines, which reduce their levels by 83.4% (guanosine), 97.4% (inosine), 95.1% (adenine), 95.0% (guanine), 94.9% (hypoxanthine) and 65.9% (xanthine), respectively. Subsequently, the LAB strain 75# was identified to be Limosilactobacillus fermentum by 16S rRNA gene sequencing, which was named as Limosilactobacillus fermentum LF-1 and applied to the fermentation of Huangjiu in the laboratory. Compared with the fermentation broth of Huangjiu without adding L. fermentum LF-1, the content of purine compounds in the fermentation broth inoculated with L. fermentum LF-1 was reduced by 64.7%. In addition, the fermented Huangjiu had richer flavor compounds, and the physicochemical indices were in accordance with the national standard of Chinese Huangjiu. The screened strain L. fermentum LF-1 may be a promising probiotic for the development of a novel that can efficiently degrade purine in Huangjiu. © 2023 Society of Chemical Industry.

Effect of Nucleotides on the Phase and Crystal Structure of Synthetic Calcium Carbonate

The interactions of organic hereditary materials (i.e., DNA and RNA) with inorganic minerals are of key importance in many fields of research, from archeology and paleontology to medicine. It was previously shown that the building blocks of the main structural biomacromolecules, amino acids and monosaccharides, can be incorporated into the crystal lattice of calcium carbonate (CaCO3), the most abundant biomineral. Here, we continue this reductionist approach and study how the mineral host is affected when grown in the presence of mono- or triphosphate nucleotides─the building blocks of nucleic acids. We show that the nucleotides facilitate the stabilization of the amorphous polymorph of CaCO3, as well as promote the formation of vaterite, its least thermodynamically stable anhydrous crystalline phase. We use high-resolution powder X-ray diffraction, and a variety of chemical analysis tools, to demonstrate the mechanism by which nucleotides become incorporated within the vaterite lattice.

Yeast-extracted nucleotides and nucleic acids as promising feed additives for European sea bass (Dicentrarchus labrax) juveniles

Nowadays functional ingredients have a significant potential for improving current low fish meal (FM) aquafeed formulation in sustaining growth and enhancing animal robustness for Mediterranean aquaculture. Among them, nucleotides (NT) and nucleic acids (NA) drew attention for their application in the last two decades. NT are organic molecules involved in many life-supporting pathways, and are the building blocks of NA, which stand as genetic repositories. NT are naturally present in organic ingredients, and among them FM is known to be one of the highest NT sources. When this NT source is seriously limited, fish might be under the minimum NT requirements, especially in fast growing life stages of carnivorous species. Hence, a trial on European sea bass juveniles was carried out, testing two dietary FM levels (FM10, FM20 as 10% and 20% FM, respectively) supplemented with 500 mg kg-1 yeast-originate NT or NA dose over 80 days. Thereafter, fish were exposed to one week of sub-optimal thermal and dissolved oxygen condition (30°C and 4.0 mg/L O2) to further explore the effect of NT and NA inclusion on immune response and gut microbiome alteration. At the end of the growth period NT increased feed intake at both FM dietary levels. FM20 combined with NA and NT further improved growth performance, enhancing lipid efficiency and increased anti-inflammatory TGF-β. After sub-optimal environmental conditions both NT and NA exerted prebiotic functions on gut microbiome by promoting beneficial lactic acid bacteria such as Weissella and Leuconostoc. At the same time NT in 10% FM diet increased the abundance of Bacillus taxon. In conclusion, the combination of NT/NA included at 500 mg kg-1 was able to promote growth when included in 20% FM level, assuming higher nutritional NT requirement when combined with 10% FM. On the other hand, NT/NA added in 10% FM upregulate proinflammatory IL-1β and favor beneficial gut bacterial taxa.

Analytical characterization of nucleotides and their concentration variation in drinking water treatment process

Nucleotides, as the basic building blocks of nucleic acids, widely exist in aqueous environment. In this study, we developed a solid phase extraction-high performance liquid chromatography-tandem mass spectrometry (SPE-UPLC-MS/MS) method for the analysis of 5′-adenosine monophosphate (AMP), 5′-uridine monophosphate (UMP), 5′-cytidine monophosphate (CMP) and 5′-guanosine monophosphate (GMP). The method achieved limits of detection (LODs) of 0.1–1.0 ng/L, and recoveries of 85–95% for the four tested nucleotides. The occurrence and concentrations of the four nucleotides in water from eight representative drinking water treatment and distribution systems in China were determined using this method. All four nucleotides were detectable in water treatment plant (WTP) influent and effluent, at concentrations of up to 30 ng/L and with occurrence frequency of around 90%. The concentrations of identified nucleotides increased 3–10 times after 10 km of water age in the water distribution system. Biological filters and coagulation increased the concentrations of nucleotides, conversely, active carbon, ozonation, and ultrafiltration membrane removed nucleotides in water. The effects of active carbon and coagulation were further confirmed using laboratory-controlled experiment. In addition, monochlorinated nucleotides were identified as the chlorination products of nucleotides.

Reverse C-glycosidase reaction provides C-nucleotide building blocks of xenobiotic nucleic acids

C-Analogues of the canonical N-nucleosides have considerable importance in medicinal chemistry and are promising building blocks of xenobiotic nucleic acids (XNA) in synthetic biology. Although well established for synthesis of N-nucleosides, biocatalytic methods are lacking in C-nucleoside synthetic chemistry. Here, we identify pseudouridine monophosphate C-glycosidase for selective 5-β-C-glycosylation of uracil and derivatives thereof from pentose 5-phosphate (d-ribose, 2-deoxy-d-ribose, d-arabinose, d-xylose) substrates. Substrate requirements of the enzymatic reaction are consistent with a Mannich-like addition between the pyrimidine nucleobase and the iminium intermediate of enzyme (Lys166) and open-chain pentose 5-phosphate. β-Elimination of the lysine and stereoselective ring closure give the product. We demonstrate phosphorylation-glycosylation cascade reactions for efficient, one-pot synthesis of C-nucleoside phosphates (yield: 33 – 94%) from unprotected sugar and nucleobase. We show incorporation of the enzymatically synthesized C-nucleotide triphosphates into nucleic acids by RNA polymerase. Collectively, these findings implement biocatalytic methodology for C-nucleotide synthesis which can facilitate XNA engineering for synthetic biology applications.

Quantitation of uridine and L-dihydroorotic acid in human plasma by LC–MS/MS using a surrogate matrix approach

Uridine and L-dihydroorotate (DHO) are important intermediates of de novo as well as salvage pathways for the biosynthesis of pyrimidines, which are the building blocks of nucleic acids - DNA and RNA. These metabolites are known to be significant biomarkers of pyrimidine synthesis during the development of DHODH inhibitor drugs for treatment of several cancers and immunological disorders. Here we are reporting a validated LC-MS/MS assay for the quantitation of uridine and DHO in K2EDTA human plasma. Due to presence of endogenous uridine and DHO in the biological matrix, a surrogate matrix approach with bovine serum albumin (BSA) solution was used. Human plasma samples were spiked with stable isotope labeled internal standards, processed by protein precipitation, and analyzed using LC–MS/MS. Parallelism was successfully demonstrated between human plasma (the authentic matrix) and BSA (the surrogate matrix). The linear analytical ranges of the assay were set at 30.0–30,000 ng/mL for uridine and 3.00–3,000 ng/mL for DHO. This validated LC–MS/MS method demonstrated excellent accuracy and precision. The overall accuracy was between 91.9 % and 106 %, and the inter-assay precision (%CV) were less than 4.2 % for uridine in human plasma. The overall accuracy was between 92.8 % and 106 %, and the inter-assay precision (%CV) were less than 7.2 % for DHO in human plasma. Uridine and DHO were found to be stable in human plasma for at least 24 h at room temperature, 579 days when stored at -20 °C, 334 days when stored at -70 °C, and after five freeze/thaw cycles. The assay has been successfully applied to human plasma samples to support clinical studies.Novel Aspect: A surrogate matrix approach to quantify endogenous uridine and DHO concentrations in human plasma

Mapping primordial reaction networks

Prebiotic Chemistry Chemists seeking to understand the origins of life have published a wide range of reactions that may have yielded the building blocks of proteins, nucleic acids, and lipids from simple precursors. Wolos et al. scoured the literature to document each such reaction class and then wrote software that applied the reactions first to the simplest compounds such as cyanide, water, and ammonia, and then iteratively to each successive generation of products. The resulting network predicted a variety of previously unappreciated routes to biochemically relevant compounds, several of which the authors validated experimentally. Science , this issue p. [eaaw1955][1] [1]: /lookup/doi/10.1126/science.aaw1955

Synthetic connectivity, emergence, and self-regeneration in the network of prebiotic chemistry.

The challenge of prebiotic chemistry is to trace the syntheses of life's key building blocks from a handful of primordial substrates. Here we report a forward-synthesis algorithm that generates a full network of prebiotic chemical reactions accessible from these substrates under generally accepted conditions. This network contains both reported and previously unidentified routes to biotic targets, as well as plausible syntheses of abiotic molecules. It also exhibits three forms of nontrivial chemical emergence, as the molecules within the network can act as catalysts of downstream reaction types; form functional chemical systems, including self-regenerating cycles; and produce surfactants relevant to primitive forms of biological compartmentalization. To support these claims, computer-predicted, prebiotic syntheses of several biotic molecules as well as a multistep, self-regenerative cycle of iminodiacetic acid were validated by experiment.

History of DNA Sequencing

Abstract The nucleotides are the building blocks of nucleic acids and determining their sequential arrangement had always been an integral part of biological research. Since the past seven decades, researchers from multi-disciplinary fields has been working together to innovate the best sequencing methods. Various methods had been proposed, from some oligonucleotides to the whole genome sequencing, and the growth had gone through adolescence to the mature phase where it is now capable of sequencing the whole genome at a low cost and within a short time frame. DNA sequencing has become a key technology in every discipline of biology and medicine. This review aims to highlight the evolution of DNA sequencing techniques and the machines used, including their principles and key achievements.

107 Roles of Amino Acids in One-carbon Metabolism and Nutition.

The critical importance of non-essential and conditionally-essential amino acids for physiological function is perhaps best exemplified in one-carbon metabolism (OCM), a complex metabolic process whereby chemical groups containing a single carbon atom are used as biosynthetic building blocks. OCM is required for the synthesis of three of the building blocks of nucleic acids (adenine, guanine, thymidine). In addition, OCM provides methyl groups for many methyltransferases. OMC involves two vitamins (folate, Vitamin B12) and amino acids such as serine and glycine which serve as sources of the one-carbon groups. As much as 70% of the whole-body labile methyl groups (S-adenosylmethionine) produced by OMC in piglets is utilized for creatine synthesis. Formate plays a critical role in OCM. Formate, produced in mitochondria from serine and other substrates is released to the cytosol where it is incorporated into 10-formyl-THF. This may be directly incorporated into purines or reduced to 5,10-methylene-THF which is used either for thymidine synthesis or for the production of methyl groups. We have measured formate in serum from a variety of animals (mice, rats, sheep, pigs, humans) and find substantial concentrations, (25–50 µM), in all cases. An important exception is in late pregnant fetal lambs and fetal rats, where we found very high formate concentrations (200–400 µM) in the fetal circulation. Serine concentrations in the fetal circulation are also very high almost 10-fold higher than in the pregnant ewe. Formate concentrations in the human umbilical cord are 70% higher than in the mother. These data suggest an important role for formate in fetal development. We examined this possibility by examining the fate of formate in fetal sheep. Label from 13C-formate infused into the fetal circulation is incorporated into methionine. This requires that formate serves as a substrate for OCM in fetal sheep. Formate is a new frontier in OCM.

Luminescent Ultralong Microfibers Prepared through Supramolecular Self-Assembly of Lanthanide Ions and Thymidine in Water.

Luminescent materials are of great interest in many fields, such as fluorescent sensing and medical imaging. Here, the construction of lanthanide-based luminescent ultralong microfibers through supramolecular self-assembly (SSA) is reported. Nucleosides (thymidine in particular), the building blocks of nucleic acids, were used as new ligands to mediate the formation of luminescent microfibers in water. The length of microfibers from thymidine-lanthanide ion (Eu and Tb) SSA was on the centimeter scale. Notably, the microfibers exhibited strong luminescence because the lanthanide ions had been chelated, sensitized and effectively protected by thymidine molecules in water. Only when the stoichiometric ratio of lanthanide ion to thymidine was 1:3 and the pH of the solution was 7, are luminescent microfibers formed. Other nucleosides, such as adenosine, cytidine, and guanosine, could not form microfibers with the lanthanide ions. This work opens a new avenue for constructing nucleoside-lanthanide SSA architectures, which hold great potential in biological and optical related applications.

The Origin of Life on Earth and the Design of Alternative Life Forms

To understand the origin of life on Earth, and to evaluate the potential for life on exoplanets, we must understand the pathways that lead from chemistry to biology. Recent experiments suggest that a chemically rich environment that provides the building blocks of membranes, nucleic acids and peptides, along with sources of chemical energy, could result in the emergence of replicating, evolving cells. The broad scope of synthetic chemistry suggests that it may be possible to design and construct artificial life forms based upon a very different biochemistry than that of existing biology.

Gas-Phase Conformations and N-Glycosidic Bond Stabilities of Sodium Cationized 2'-Deoxyguanosine and Guanosine: Sodium Cations Preferentially Bind to the Guanine Residue.

2'-Deoxyguanosine (dGuo) and guanosine (Guo) are fundamental building blocks of DNA and RNA nucleic acids. In order to understand the effects of sodium cationization on the gas-phase conformations and stabilities of dGuo and Guo, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and complementary electronic structure calculations are performed. The measured IRMPD spectra of [dGuo+Na]+ and [Guo+Na]+ are compared to calculated IR spectra predicted for the stable low-energy structures computed for these species to determine the most favorable sodium cation binding sites, identify the structures populated in the experiments, and elucidate the influence of the 2'-hydroxyl substituent on the structures and IRMPD spectral features. These results are compared with those from a previous IRMPD study of the protonated guanine nucleosides to elucidate the differences between sodium cationization and protonation on structure. Energy-resolved collision-induced dissociation (ER-CID) experiments and survival yield analyses of protonated and sodium cationized dGuo and Guo are performed to compare the effects of these cations toward activating the N-glycosidic bonds of these nucleosides. For both [dGuo+Na]+ and [Guo+Na]+, the gas-phase structures populated in the experiments are found to involve bidentate binding of the sodium cation to the O6 and N7 atoms of guanine, forming a 5-membered chelation ring, with guanine found in both anti and syn orientations and C2'-endo (2T3 or 3T2) puckering of the sugar. The ER-CID results, IRMPD yields and the computed C1'-N9 bond lengths indicate that sodium cationization activates the N-glycosidic bond less effectively than protonation for both dGuo and Guo. The 2'-hydroxyl substituent of Guo is found to impact the preferred structures very little except that it enables a 2'OH···3'OH hydrogen bond to be formed, and stabilizes the N-glycosidic bond relative to that of dGuo in both the sodium cationized and protonated complexes.

Gene expression control by Bacillus anthracis purine riboswitches.

In all kingdoms of life, cellular replication relies on the presence of nucleosides and nucleotides, the building blocks of nucleic acids and the main source of energy. In bacteria, the availability of metabolites sometimes directly regulates the expression of enzymes and proteins involved in purine salvage, biosynthesis, and uptake through riboswitches. Riboswitches are located in bacterial mRNAs and can control gene expression by conformational changes in response to ligand binding. We have established an inverse reporter gene system in Bacillus subtilis that allows us to monitor riboswitch-controlled gene expression. We used it to investigate the activity of five potential purine riboswitches from Bacillus anthracis in response to different purines and pyrimidines. Furthermore, in vitro studies on the aptamer domains of the riboswitches reveal their variation in guanine binding affinity ranging from namomolar to micromolar. These data do not only provide insight into metabolite sensing but can also aid in engineering artificial cell regulatory systems.

Anti-fatigue effects of dietary nucleotides in mice

ABSTRACTAs the building blocks of nucleic acids, nucleotides are conditionally essential nutrients that exhibit multifaceted activities. The present study aimed to evaluate the anti-fatigue effects of dietary nucleotides (NTs) on mice and explore the possible underlying mechanism. Mice were randomly divided into four experimental sets to detect different indicators. Each set of mice was then divided into four groups: (i) one control group and (ii) three NTs groups, which were fed diets supplemented with NTs at concentrations of 0%, 0.04%, 0.16%, and 0.64% (wt/wt). NTs could significantly increase the forced swimming time, enhance lactate dehydrogenase activity and hepatic glycogen levels, as well as delay the accumulation of blood urea nitrogen and blood lactic acid in mice after 30 days of treatment. NTs also markedly improved fatigue-induced alterations in oxidative stress biomarkers and antioxidant enzymes. Notably, NTs increased the mitochondrial energy metabolic enzyme activities in the skeletal muscles of mice. These results suggest that NTs exert anti-fatigue effects, which may be attributed to the inhibition of oxidative stress and the improvement of mitochondrial function in skeletal muscles. NTs could be used as a novel natural agent for relieving exercise fatigue.Abbreviations: ATP: adenosine triphosphate; BLA: blood lactic acid; GSH-Px: glutathione peroxidase; LDH: lactate dehydrogenase; MDA: malondialdehyde; NTs: dietary nucleotides; SDH: succinate dehydrogenase; SOD: superoxide dismutase; BUN: blood urea nitrogen