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Kim EK, Martin V, Krishnamurthy R. Orotidine-Containing RNA: Implications for the Hierarchical Selection (Systems Chemistry Emergence) of RNA. Chemistry 2017; 23:12668-12675. [PMID: 28708927 DOI: 10.1002/chem.201702912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 02/05/2023]
Abstract
The prebiotic synthesis of canonical nucleobases from HCN is a cornerstone for the RNA world hypothesis. However, their role in the primordial pathways to RNA is still debated. The very same process starting from HCN also gives rise to orotic acid, which (via orotidine) plays a crucial role in extant biology in the de novo synthesis of uridine and cytidine, the informational base-pairs in RNA. However, orotidine itself is absent in RNA. Given the prebiotic and biological relevance of orotic acid vis-à-vis uracil, we investigated orotidine-containing RNA oligonucleotides and show that they have severely compromised base-pairing properties. While not unexpected, these results suggest that the emergence of extant RNA cannot just be a consequence of the plausible prebiotic formation of its chemical constituents/building blocks. In combination with other investigations on alternative prebiotic nucleobases, sugars, and linkers, these findings imply that the selection of the components of extant RNA occurred at a higher hierarchical level of an oligomer/polymer based on its functional properties-pointing to a systems chemistry emergence of RNA from a library of precursors.
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Affiliation(s)
- Eun-Kyong Kim
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
| | - Vincent Martin
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
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Complex formation of cadmium with sugar residues, nucleobases, phosphates, nucleotides, and nucleic acids. Met Ions Life Sci 2013; 11:191-274. [PMID: 23430775 DOI: 10.1007/978-94-007-5179-8_8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cadmium(II), commonly classified as a relatively soft metal ion, prefers indeed aromatic-nitrogen sites (e.g., N7 of purines) over oxygen sites (like sugar-hydroxyl groups). However, matters are not that simple, though it is true that the affinity of Cd(2+) towards ribose-hydroxyl groups is very small; yet, a correct orientation brought about by a suitable primary binding site and a reduced solvent polarity, as it is expected to occur in a folded nucleic acid, may facilitate metal ion-hydroxyl group binding very effectively. Cd(2+) prefers the guanine(N7) over the adenine(N7), mainly because of the steric hindrance of the (C6)NH(2) group in the adenine residue. This Cd(2+)-(N7) interaction in a guanine moiety leads to a significant acidification of the (N1)H meaning that the deprotonation reaction occurs now in the physiological pH range. N3 of the cytosine residue, together with the neighboring (C2)O, is also a remarkable Cd(2+) binding site, though replacement of (C2)O by (C2)S enhances the affinity towards Cd(2+) dramatically, giving in addition rise to the deprotonation of the (C4)NH(2) group. The phosphodiester bridge is only a weak binding site but the affinity increases further from the mono- to the di- and the triphosphate. The same also holds for the corresponding nucleotides. Complex stability of the pyrimidine-nucleotides is solely determined by the coordination tendency of the phosphate group(s), whereas in the case of purine-nucleotides macrochelate formation takes place by the interaction of the phosphate-coordinated Cd(2+) with N7. The extents of the formation degrees of these chelates are summarized and the effect of a non-bridging sulfur atom in a thiophosphate group (versus a normal phosphate group) is considered. Mixed ligand complexes containing a nucleotide and a further mono- or bidentate ligand are covered and it is concluded that in these species N7 is released from the coordination sphere of Cd(2+). In the case that the other ligand contains an aromatic residue (e.g., 2,2'-bipyridine or the indole ring of tryptophanate) intramolecular stack formation takes place. With buffers like Tris or Bistris mixed ligand complexes are formed. Cd(2+) coordination to dinucleotides and to dinucleoside monophosphates provides some insights regarding the interaction between Cd(2+) and nucleic acids. Cd(2+) binding to oligonucleotides follows the principles of coordination to its units. The available crystal studies reveal that N7 of purines is the prominent binding site followed by phosphate oxygens and other heteroatoms in nucleic acids. Due to its high thiophilicity, Cd(2+) is regularly used in so-called thiorescue experiments, which lead to the identification of a direct involvement of divalent metal ions in ribozyme catalysis.
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Bastian M, Sigel H. Stability and Structure of Binary and Ternary Metal Ion Complexes of Orotidinate 5′-Monophosphate (OMP3-) in Aqueous Solution. J COORD CHEM 2009. [DOI: 10.1080/00958979109408247] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Matthias Bastian
- a Institute of Inorganic Chemistry, University of Basel , Spitalstrasse 51, CH-4056 , Basel , Switzerland
| | - Helmut Sigel
- a Institute of Inorganic Chemistry, University of Basel , Spitalstrasse 51, CH-4056 , Basel , Switzerland
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Lewis CA, Wolfenden R. Indiscriminate binding by orotidine 5'-phosphate decarboxylase of uridine 5'-phosphate derivatives with bulky anionic c6 substituents. Biochemistry 2007; 46:13331-43. [PMID: 17967036 DOI: 10.1021/bi700796t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Orotidine 5'-phosphate (OMP) decarboxylase appears to act upon its substrate without the intervention of metals or other cofactors and without the formation of covalent bonds between the enzyme and the substrate. Crystallographic information indicates that substrate binding forces the substrate's scissile carboxylate group into the neighborhood of several charged groups at the active site. It has been proposed that binding might result in electrostatic stress at the substrate's C6 carboxylate group in such a way as to promote decarboxylation by destabilizing the enzyme-substrate complex in its ground state. If that were the case, one would expect uridine 5'-phosphate (UMP) derivatives with bulky anionic substituents at C6 to be bound weakly compared with UMP, which is unsubstituted at C6. Here, we describe the formation of anionic 5,6-dihydro-6-sulfonyl derivatives by spontaneous addition of sulfite to UMP and to OMP. These sulfite addition reactions, which are slowly reversible and are not catalyzed by the enzyme, result in the appearance of one (or, in the case of OMP, two) bulky anionic substituents at the 6-carbon atom of UMP. These inhibitors are bound with affinities that surpass the binding affinity of UMP. We are led to infer that the active site of OMP decarboxylase is remarkably accommodating in the neighborhood of C6. These are not the properties that one would expect of an active site with a rigid structure that imposes sufficient electrostatic stress on the substrate to produce a major advancement along the reaction coordinate.
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Affiliation(s)
- Charles A Lewis
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Yurenko YP, Zhurakivsky RO, Ghomi M, Samijlenko SP, Hovorun DM. How many conformers determine the thymidine low-temperature matrix infrared spectrum? DFT and MP2 quantum chemical study. J Phys Chem B 2007; 111:9655-63. [PMID: 17655217 DOI: 10.1021/jp073203j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A comprehensive conformational analysis of isolated 2'-beta-deoxy-thymidine (T), canonical DNA nucleoside, has been performed by means of ab initio calculations at the MP2/6-311++G(d,p)//DFT B3LYP/6-31G(d,p) level of theory. At 298.15 K, all 92 conformers of isolated dT are within a 7.49 kcal/mol Gibbs energy range. Syn orientation for the base and South (S) conformers for the sugar dominate at this temperature: syn/anti = 61.6%:38.4% and S/N = 74.5%:25.5%. However, at 420 K, the majority of conformers contain anti base and the population of North (N) sugars increases: syn/anti = 38.0%:62.0% and S/N = 59.5%:40.5%. The whole conformational parameters (P, chi, gamma, delta, beta, epsilon, nu max) were analyzed as well as the energies of the OH...O intramolecular H-bonds on the basis of nu(OH) stretching vibrations. Convolution of calculated IR spectra of all of the T conformers appears consistent with its low-temperature matrix spectrum (Ivanov et al. Low Temp. Phys. 2003, 29, 809). The maximal discrepancy in frequencies between calculated and experimental spectra is less than 1%. A conclusion was made that for reliable reconstruction of the isolated nucleoside IR spectrum the quasi whole set of conformers should be taken into consideration. In essence, this result opens up a possibility to reconstruct IR spectra of isolated nucleosides at physiological temperatures with rather satisfactory probability.
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Affiliation(s)
- Yevgen P Yurenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, vul. Zabolotnoho 150, 03143 Kyiv, Ukraine
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Wada T, Sato H, Inoue Y. External reversible control of recognition behavior of alpha-peptide ribonucleic acid (alpha-PRNA) through anti-syn orientational switching of the nucleobase induced by borate esterification of the cis-2',3'-diol. Biopolymers 2004; 76:15-20. [PMID: 14997470 DOI: 10.1002/bip.10563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A novel nucleic acid model using peptide ribonucleic acid (PRNA), which contains 5'-amino-5'-deoxypyrimidine ribonucleoside as a recognition site for nucleic acids, has been designed, synthesized and applied to the external reversible control of recognition behavior of the complementary polynucleotide through the orientational switching of the nucleobase induced by borate.
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Wada T, Minamimoto N, Inaki Y, Inoue Y. Peptide Ribonucleic Acids (PRNA). 2. A Novel Strategy for Active Control of DNA Recognition through Borate Ester Formation. J Am Chem Soc 2000. [DOI: 10.1021/ja9935456] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takehiko Wada
- Contribution from the Department of Molecular Chemistry and Department of Material and Life Science, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan and Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan
| | - Narutoshi Minamimoto
- Contribution from the Department of Molecular Chemistry and Department of Material and Life Science, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan and Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan
| | - Yoshiaki Inaki
- Contribution from the Department of Molecular Chemistry and Department of Material and Life Science, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan and Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan
| | - Yoshihisa Inoue
- Contribution from the Department of Molecular Chemistry and Department of Material and Life Science, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan and Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan
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Wada T, Minamimoto N, Inaki Y, Inoue Y. Conformational and Orientational Switching of Uridine Derivatives by Borates. CHEM LETT 1998. [DOI: 10.1246/cl.1998.1025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Mishchuk YR, Hovorun DM. Intramolecular hydrogen bonds and structural nonrigidity of pyrimidine nucleosides. ACTA ACUST UNITED AC 1998. [DOI: 10.7124/bc.0004e0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ya. R. Mishchuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - D. M. Hovorun
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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Bastian M, Sigel H. Stability and structure of the Mg2+, Ca2+ and Cu2+ complexes of orotidinate 5′-monophosphate (OMP)3− in various aqueous 1,4-dioxane mixtures. Inorganica Chim Acta 1991. [DOI: 10.1016/s0020-1693(00)90399-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Synthesis of nucleosides of uronic acids V. Synthesis and antivirus activity of nucleosides of D-xyluronic acid. Pharm Chem J 1988. [DOI: 10.1007/bf00759055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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2′-deoxynucleoside uronic acids from the ascidian Aplidium (= Amaroucium) fuscum (Drasche, 1883). ACTA ACUST UNITED AC 1986. [DOI: 10.1016/0305-0491(86)90263-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Billich A, Stockhove U, Witzel H. Synthesis, conformation and enzymatic properties of 1-(beta-D-allofuranosyl)uracil and some derivatives. Nucleic Acids Res 1983; 11:7611-24. [PMID: 6316265 PMCID: PMC326506 DOI: 10.1093/nar/11.21.7611] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A new route for the synthesis of 1-(beta-D-allofuranosyl)uracil ("allo-uridine") and the corresponding 6'-deoxy-derivative ("6'-deoxy-allo-uridine") as well as for 1-(beta-D-altrofuranosyl) uracil ("altro-uridine") is described. NMR studies of allo-uridine revealed a preferred conformation with the base in anti-position, C-2'-endo-pucker of the sugar moiety, the 5'-OH-group above the furanose ring and the 5'-CH2OH-group in a gt position with the OH-group in the plane of the furanose ring. The same conformation is found for the 5'- and 6'-phosphate, indicated by the influence of the phosphate group on the H-6 signal. Allo-uridine is phosphorylated by the phosphotransferases from carrot and from malt sprouts only in the 6'-position. The phosphate ester is hydrolysed by unspecific phosphatases but not by 5'-nucleotidase. A (3' leads to 6')-dinucleoside phosphate is formed by pancreatic ribonuclease with 2',3'-cyclic cytidylic acid and allo-uridine. It is split by nuclease S1, but not by snake-venom phosphodiesterase. It has no primer activity for polynucleotide phosphorylase. All-uridine 6'-diphosphate could not be prepared enzymatically by nucleotide kinase or by chemical methods, where 5',6'-cyclic phosphates are formed, which are hydrolysed exclusively to 6'-monophosphates.
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Uhl W, Reiner J, Gassen HG. On the conformation of 5-substituted uridines as studied by proton magnetic resonance. Nucleic Acids Res 1983; 11:1167-80. [PMID: 6828379 PMCID: PMC325784 DOI: 10.1093/nar/11.4.1167] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The proton magnetic resonance (pmr) spectra of 10 basemodified uridine derivatives x5Urd have been measured at 3 degrees, 30 degrees, and 60 degrees C in order to correlate the electronic effects of different substituents with the molecular conformation of the respective nucleosides. The results presented demonstrate the close relation between conformational parameters and the electron-affinity of the substituents as reflected by their Hammett constants. Going from electron-donating to electron-accepting groups, the portion of N-conformer in the ribose N in equilibrium S equilibrium increases from 44% to about 90%. In addition the percentage of gauche-gauche rotamer as measured for the exocyclic groups changes from about 30% in nh52Urd to more than 80% in no52Urd.
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Meyer W, Follmann H. Synthese und Eigenschaften von 5′-Desoxynucleosid-5′-carbonsäuren und ihren Derivaten. ACTA ACUST UNITED AC 1980. [DOI: 10.1002/cber.19801130719] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Wegner G, Jochims JC. Barrieren der behinderten Rotation um dieN-glycosidische Bindung, IV. 1-(β-D-Ribofuranosyl)isocyanursäuren. ACTA ACUST UNITED AC 1979. [DOI: 10.1002/cber.19791120604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Young PR, Kallenbach NR. Secondary structure in polyuridylic acid. Non-classical hydrogen bonding and the function of the ribose 2'-hydroxyl group. J Mol Biol 1978; 126:467-79. [PMID: 745237 DOI: 10.1016/0022-2836(78)90053-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Ludwig W, Follmann H. The specificity of ribonucleoside triphosphate reductase. Multiple induced activity changes and implications for deoxyribonucleotide formation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 82:393-403. [PMID: 624279 DOI: 10.1111/j.1432-1033.1978.tb12034.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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