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The Emerging Field of RNA Nanotechnology
Published in Lajos P. Balogh, Nano-Enabled Medical Applications, 2020
RNA is a polymer made up of four different nucleotides: adenine, cytosine, guanine and uridine. RNA possesses not only Watson–Crick base pairing but also noncanonical base pairing which promotes folding into rigid structural motifs distinct from the structure of single-stranded DNA. The noncanonical property facilitates loop-receptor interactions and allows the creation of synthetic ribozymes [16, 17]. It also allows the formation of special structural motifs [18–20]. Tertiary interactions mediate GNRA/receptor interactions [10], and formation of micrometer sized RNA filaments [10–12, 21, 24] (Fig. 5.2g–j). Currently, an RNA up to 80 nucleotides can be synthesized commercially. An 80-nucleotide RNA can display up to 1048 (480) different structures with unique shapes involving non-canonical interactions. Such a huge pool of rich structural conformations would ease the search for viable partners in particle assemblies, substrate binding, building architectures, and manufacture engineering.
Assembly of nucleobases into rings and cages via metal ions
Published in Journal of Coordination Chemistry, 2022
Bernhard Lippert, Pablo J. Sanz Miguel
Two cases of octanuclear metal nucleobase complexes, both having “wheel” structures and composed of eight Cu2+ ions and eight pym nucleosides, need to be mentioned: a uridine complex [106] and a cytidine complex [107]. These compounds not only involve CuII binding to the heterocyclic nucleobases (N3,O2 chelation in case of cytidine, N3 binding to uridine), but also to deprotonated sugar moieties (singly deprotonated with cytidine; twofold deprotonated in case of uridine). Thus, cytidine has a charge of −1, whereas uridine has one of −3, as N3 is deprotonated as well. As a result, and ignoring anions coordinated to the Cu centers, the cytidine wheel is formally a + 8 cation, whereas the uridine wheel is formally a −8 anion. In both ions the metals occupy corners of a distorted square antiprism, with closest Cu–Cu distances being in the order of 3 Å. There is yet another feature common to both structures, namely the presence of a metal hexaqua cation in the center, [Na(H2O)6]+ in the uridine complex, and [Cu(H2O)6]2+ in the cytidine complex.
Enhanced shortcut nitrogen removal and metagenomic analysis of functional microbial communities in a double sludge system treating ammonium-rich wastewater
Published in Environmental Technology, 2020
Jia Miao, Yunhong Shi, Danfei Zeng, Guangxue Wu
Starch could produce α-D-Glucose-1P through the ‘metabolic pathway of starch and sucrose’ (ko00500), and then pyruvate was produced through ‘Glycolysis’ (ko00100). It was noteworthy that α-D-Glucose-6P was an intermediate product of ‘Glycolysis’ and it could synthesize uridine diphosphonate glucose (UDP-Glucose) through ‘Amino sugars and ribose metabolic pathway’ (ko00520). In addition, UDP-Glucose was the precursor of glycogen synthesis and it could be further metabolized to pyruvate through ‘Ascorbate metabolic pathway’ (ko00053). Besides, pyruvate could be degraded to generate NADH through ‘Pyruvate metabolic pathway’ (ko00620) or ‘Tricarboxylic acid cycle (TCA)’ (ko00020). Accordingly, there were two potential pathways of starch metabolism. One was that it could be directly metabolized to produce NADH, and the other was that it was metabolized firstly to synthesize UDP-Glucose and then degraded to produce NADH. This was coincident with the results of typical cycle study in SBRDN. Peptone, as the initial breakdown product of protein, could be degraded through all amino acid metabolic pathways (ko00250, ko00260, ko00270, ko00280, ko00310, ko00330, ko00340, ko00350, ko00360 and ko00380) to produce pyruvate or intermediates of TCA, and then was further metabolized.
Structural studies on Ba(II) adducts of the cytosine nucleobase and its derivative 1-Methylcytosine*
Published in Journal of Coordination Chemistry, 2018
Nadia Marino, Rosaria Bruno, Donatella Armentano, Giovanni De Munno
Focusing on Mg(II) and Ca(II), some X-ray structures are known, three Mg2+ complexes with the nucleobase cytosine [46,54] and some Ca2+ complexes, three with cytosine [46, 54, 57-59], eight with cytidine [60–62] and only one, reported by us, with cytidine-5′-phosphate [54]. On the contrary, only four Ba2+ compounds, with either cytidine-5′-monophosphate, uridine-5′-monophosphate, guanosine-5′-monophosphate or adenosine-5′-phosphate, have been structurally characterized [63–66]. These studies helped to establish that the coordination mode/s of such biomolecules toward alkaline-earth metal ions mainly depend on the nature of the metal ion in terms of affinity and size.