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Jeilani YA, Nguyen MT. Autocatalysis in Formose Reaction and Formation of RNA Nucleosides. J Phys Chem B 2020; 124:11324-11336. [PMID: 33269920 DOI: 10.1021/acs.jpcb.0c07070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding of the abiotic formation of nucleosides under geochemical conditions is currently a major scientific challenge. In this study, free radical pathways for formation of RNA nucleosides with canonical nucleobases are proposed for the first time. The pathways proceed with relatively low energy barriers for the formation of ribose as well as all RNA nucleosides. The formose reaction proceeds either with or without Ca2+ and CaOH+ cations. An autocalytic cycle for the formation of both glycolaldehyde and glyceraldehyde is identified when Ca2+ or CaOH+ cations are involved in the reaction. The results suggest that Ca2+ cations are not involved in the formation of ribose from glyceraldehyde. In addition, these pathways lead to the formation of dihydroxyacetone and d-erythrose. Calculated results show that the glycosidic bond can be formed abiotically between the d-ribose and the nucleobase, where d-ribose forms a cyclic free radical that subsequently reacts with the neutral nucleobase. Involvement of proper nucleobase tautomer is important for the formation of RNA nucleosides. Our approaches provide a solution for the long-standing question of how the glycosidic bond is formed under the abiotic conditions with low energy barriers. The pathways for formation of the sugars without a catalyst are relevant to the formation of sugars in interstellar clouds. On the other hand, the autocalysis in the formose reaction followed by the formation of the nucleosides is appropriate for the abiotic synthesis taking place in the presence of water in the early Earth environment. The Ca2+ and CaOH+ cations appear to be the first nonenzymatic catalytic systems for formation of biomolecules.
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Affiliation(s)
- Yassin Aweis Jeilani
- Department of Chemistry, University of Hail, Hail, 81451 Kingdom of Saudi Arabia.,Department of Chemistry and Biochemistry, Spelman College, Atlanta, Georgia 30314, United States
| | - Minh Tho Nguyen
- Computational Chemistry Research Group and Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, 700000 Vietnam
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2
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Akimsheva E, Dolinina E, Parfenyuk E. Interactions of sol-gel encapsulated acyclovir with silica matrix. Colloids Surf B Biointerfaces 2019; 178:103-110. [DOI: 10.1016/j.colsurfb.2019.02.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/06/2019] [Accepted: 02/26/2019] [Indexed: 10/27/2022]
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3
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Buchner F, Heggen B, Ritze HH, Thiel W, Lübcke A. Excited-state dynamics of guanosine in aqueous solution revealed by time-resolved photoelectron spectroscopy: experiment and theory. Phys Chem Chem Phys 2015; 17:31978-87. [DOI: 10.1039/c5cp04394h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time-resolved photoelectron spectroscopy is performed on aqueous guanosine solution to study its excited-state relaxation dynamics.
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Affiliation(s)
- Franziska Buchner
- Max-Born-Institut für nichtlineare Optik und Kurzzeitspektroskopie
- 12489 Berlin
- Germany
| | - Berit Heggen
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim/Ruhr
- Germany
| | - Hans-Hermann Ritze
- Max-Born-Institut für nichtlineare Optik und Kurzzeitspektroskopie
- 12489 Berlin
- Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim/Ruhr
- Germany
| | - Andrea Lübcke
- Max-Born-Institut für nichtlineare Optik und Kurzzeitspektroskopie
- 12489 Berlin
- Germany
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4
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Singh P, Deckert V. Local protonation control using plasmonic activation. Chem Commun (Camb) 2014; 50:11204-7. [DOI: 10.1039/c4cc04642k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Spatial control of a protonation reaction under ambient conditions is demonstrated utilizing localized surface plasmons.
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Affiliation(s)
- Pushkar Singh
- Leibniz Institute of Photonic Technology
- 07745 Jena, Germany
| | - Volker Deckert
- Leibniz Institute of Photonic Technology
- 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics
- Friedrich-Schiller University Jena
- 07743 Jena, Germany
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Nielsen JB, Thøgersen J, Jensen SK, Nielsen SB, Keiding SR. Vibrational dynamics of deoxyguanosine 5'-monophosphate following UV excitation. Phys Chem Chem Phys 2011; 13:13821-6. [PMID: 21720611 DOI: 10.1039/c1cp20918c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The relaxation dynamics of the DNA nucleotide deoxyguanosine 5'-monophosphate (dGMP) following 266 nm photoexcitation has been studied by transient IR spectroscopy with femtosecond time resolution. The induced dynamics of the amide I (carbonyl) stretch, the asymmetric guanine ring stretch and the phosphate asymmetric stretch are monitored in the region 1000-1800 cm(-1). Excitation and subsequent rapid internal conversion to a "hot" ground state is reflected by depletion of the vibrational ground states of the amide I stretch and guanine ring stretch. However, the vibrational ground state of the phosphate is left unperturbed, indicating the absence of vibrational coupling between the guanine ring system and the phosphate group. The vibrational ground state of the amide I is repopulated in 2.5 ps (±0.2 ps) while it takes 3.7 ps (±0.5 ps) to repopulate the guanine ring vibration. This article discusses two possible relaxation pathways of dGMP, as well as the implications of the weak phosphate dynamics.
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Affiliation(s)
- Jakob Brun Nielsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark.
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Fritzsche H. Infrarotspektroskopie und kernmagnetische Resonanz in der Nucleinsäureforschung. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/zfch.19720120102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Miannay FA, Gustavsson T, Banyasz A, Markovitsi D. Excited-state dynamics of dGMP measured by steady-state and femtosecond fluorescence spectroscopy. J Phys Chem A 2010; 114:3256-63. [PMID: 20085298 DOI: 10.1021/jp909410b] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The room-temperature fluorescence of 2'-deoxyguanosine 5'-monophosphate (dGMP) in aqueous solution is studied by steady-state and time-resolved fluorescence spectroscopy. The steady-state fluorescence spectrum of dGMP shows one band centered at 334 nm but has an extraordinary long red tail, extending beyond 700 nm. Both the fluorescence quantum yield and the relative weight of the 334 nm peak increase with the excitation wavelength. The initial fluorescence anisotropy after excitation at 267 nm is lower than 0.2 for all emission wavelengths, indicating an ultrafast S(2) --> S(1) internal conversion. The fluorescence decays depend strongly on the emission wavelength, getting longer with the wavelength. A rise time of 100-150 fs was observed for wavelengths longer than 450 nm, in accordance with a gradual red shift of the time-resolved spectra. The results are discussed in terms of a relaxation occurring mainly on the lowest excited (1)pi pi*-state surface toward a conical intersection with the ground state, in line with recent theoretical predictions. Our results show that the excited-state population undergoes a substantial "spreading out" before reaching the CI, explaining the complex dynamics observed.
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Affiliation(s)
- Francois-Alexandre Miannay
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM-CNRS URA 2453, CEA Saclay, F-91191 Gif-sur-Yvette, France
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Zhachkina A, Liu M, Sun X, Amegayibor FS, Lee JK. Gas-Phase Thermochemical Properties of the Damaged Base O6-Methylguanine versus Adenine and Guanine. J Org Chem 2009; 74:7429-40. [DOI: 10.1021/jo901479m] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Anna Zhachkina
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Min Liu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Xuejun Sun
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - F. Sedinam Amegayibor
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
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Er Y, Barnes TJ, Fornasiero D, Prestidge CA. The encapsulation and release of guanosine from PEGylated liposomes. J Liposome Res 2009; 19:29-36. [DOI: 10.1080/08982100802673940] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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McGovern DA, Quinn S, Doorley GW, Whelan AM, Ronayne KL, Towrie M, Parker AW, Kelly JM. Picosecond infrared probing of the vibrational spectra of transients formed upon UV excitation of stacked G-tetrad structures. Chem Commun (Camb) 2007:5158-60. [PMID: 18060127 DOI: 10.1039/b711172j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photophysical properties of stacked G-tetrads in diverse systems, including concentrated solutions of 5'-guanosine monophosphate (5'-GMP), polyguanylic acid (poly(G)) and the G-rich oligodeoxynucleotide sequence characteristic of human telomeric DNA, are probed by ps-TRIR and compared to those of the monomeric 5'-GMP.
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Affiliation(s)
- David A McGovern
- School of Chemistry and Centre for Chemical Synthesis and Chemical Biology, Trinity College, Dublin 2, Ireland
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Yao L, Cukier RI, Yan H. Catalytic mechanism of guanine deaminase: an ONIOM and molecular dynamics study. J Phys Chem B 2007; 111:4200-10. [PMID: 17394305 DOI: 10.1021/jp0673056] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The catalytic mechanism of Bacillus subtilis guanine deaminase (bGD), a Zn metalloenzyme, has been investigated by a combination of quantum mechanical calculations using the multilayered ONIOM method and molecular dynamics simulations. In contrast to a previously proposed catalytic mechanism, which requires the bound guanine to assume a rare tautomeric state, the ONIOM calculations showed that the active-site residues of the enzyme do not affect the tautomeric state of guanine, and consequently the bound guanine is a tautomer that is the most abundant in aqueous solution. Two residues, Glutamate 55 and Aspartate 114, were found to play important roles in proton shuttling in the reaction. The proposed reaction path is initiated by proton transfer from a Zn-bound water to protonate Asp114. This process may be quite complex and rather dynamic in nature, as revealed by the molecular dynamics (MD) simulations, whereby another water may bridge the Zn-bound water and Asp114, which then is eliminated by positioning of guanine in the active site. The binding of guanine stabilizes protonated Asp114 by hydrogen bond formation. Asp114 can then transfer its proton to the N3 of the bound guanine, facilitating the nucleophilic attack on C2 of the guanine by the Zn-bound hydroxide to form a tetrahedral intermediate. This occurs with a rather low barrier. Glu55 then transfers a proton from the Zn-hydroxide to the amino group of the reaction intermediate and, at this point, the C2-N2 bond has lengthened by 0.2 A compared to guanine, making C2-N2 bond cleavage more facile. The C2-N2 bond breaks forming ammonia, with an energy barrier of approximately 8.8 kcal/mol. Ammonia leaves the active site, and xanthine is freed by the cleavage of the Zn-O2 bond, with a barrier approximately 8.4 kcal/mol. Along this reaction path, the highest barrier comes from C2-N2 bond cleavage, while the barrier from the cleavage of the Zn-O2 bond is slightly smaller. The Zn-O2 bond can be broken without the assistance of water during the release of xanthine.
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Affiliation(s)
- Lishan Yao
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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Padermshoke A, Katsumoto Y, Aida M. Dimerization and Double Proton Transfer-Induced Tautomerism of 4(3H)-Pyrimidinone in Solution Studied by IR Spectroscopy and Quantum Chemical Calculations. J Phys Chem B 2006; 110:26388-95. [PMID: 17181298 DOI: 10.1021/jp065408i] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tautomerism and dimerization of 4(3H)-pyrimidinone (4(3H)Pyr) in carbon tetrachloride (CCl4) and chloroform (CHCl3) solutions were investigated using IR spectroscopy and quantum chemical calculations. The observed IR spectra in the NH and OH stretching regions clearly revealed the predominance of the keto tautomer in both solvent systems. The enol form only exists in a very small proportion in the CCl4 solution. The tautomeric constant for the two monomers KT[OH/NH] = 0.012 and DeltaE = 2.62 kcal/mol were estimated at 25 degrees C. This result was supported by the self-consistent reaction field/polarizable continuum (SCRF/PCM) calculation at the MP4(full, SDQ)/aug-cc-pVDZ level, which predicted DeltaE = 3.06 kcal/mol in CCl4. In the C=O stretching region, two bands were observed, suggesting the coexistence of two keto structures at equilibrium. The calculated IR spectra indicated that the bands at 1711 and 1675 cm(-1) arise from the keto monomer and keto-keto (KK) ring dimer, respectively. At elevated temperature, the populations of both the keto and enol monomers increased for the CCl4 solution. The present study revealed that the keto <--> enol tautomerization does not occur in the isolated monomer molecule. The double proton transfer (DPT) reaction in the KK ring dimer presumably plays a substantial role in the population increase of the enol monomer. To our knowledge, this may be the first observation of the tautomerization in a model base pair via the temperature-induced ground-state DPT reaction under a nonpolar liquid environment reported so far. This tautomerism can serve as a mimic circumstance for the spontaneous mutations induced by proton transfer in the DNA base pairs.
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Affiliation(s)
- Adchara Padermshoke
- Center for Quantum Life Sciences, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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13
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Liu J, Barrio JR, Satyamurthy N. Kinetics and mechanism of the defluorination of 8-fluoropurine nucleosides in basic and acidic media. J Fluor Chem 2006. [DOI: 10.1016/j.jfluchem.2006.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Jang YH, Goddard WA, Noyes KT, Sowers LC, Hwang S, Chung DS. pKaValues of Guanine in Water: Density Functional Theory Calculations Combined with Poisson−Boltzmann Continuum−Solvation Model. J Phys Chem B 2003. [DOI: 10.1021/jp020774x] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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MILES HT, FRAZIER J. INFRARED SPECTRA IN 2H2O SOLUTION OF GUANYLIC ACID HELICES AND OF POLY-G. ACTA ACUST UNITED AC 1996; 79:216-20. [PMID: 14114525 DOI: 10.1016/0926-6577(64)90057-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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Proton transfer reactions of nucleic acid bases: A semiempirical molecular orbital study. J CHEM SCI 1995. [DOI: 10.1007/bf02884440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Raman spectroscopic study of the interaction of metal ions with pyridine and maleimide — models for nucleic acids. J Mol Struct 1993. [DOI: 10.1016/0022-2860(93)80163-p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Abstract
(+-)-Carbovir [(+-)-9-[4 alpha-(hydroxymethyl)-cyclopent-2-ene-1 alpha-yl]guanine; NSC 614846] is a novel carbocyclic nucleoside analogue which has been shown to be a potent and selective inhibitor of HIV in vitro. As part of an effort to develop a parenteral formulation for subsequent clinical and toxicological evaluation of this compound, the aqueous solution stability of carbovir as a function of pH and temperature and various physicochemical properties of carbovir including its pKa, solubility versus pH and solvent composition, and octanol-water partition coefficient have been examined. Ultraviolet spectrophotometry indicated that carbovir has pKa values of 3.15 and 9.68, respectively, at 25 degrees C and 0.01 ionic strength. The aqueous solubility of carbovir over the pH range 7-10.5 was consistent with that expected of a weak acid with a pKa of 9.65 and an intrinsic solubility of 1.24 mg/mL. Due to the limited solubility of carbovir at physiological pH, methods for solubilizing carbovir in aqueous solution were explored, including propylene glycol-water cosolvents and complexation with hydroxypropyl-beta-cyclodextrin. As expected for carbovir, a semipolar compound with an octanol-water partition coefficient of 0.29, propylene glycol:water cosolvents were not highly effective in enhancing solubility. Complex formation between carbovir and 2-hydroxypropyl-beta-cyclodextrin was found to be more effective, with a K1:1 of 105 M-1 for the complexation. The pH profiles generated at 50, 70, and 90 degrees C were accounted for by acid-catalyzed degradation at low pH leading to the formation of guanine and a neutral degradation pathway which dominates above pH 4. Prototype lyophilized formulations containing (after reconstitution) 10 mg/mL of carbovir at a pH of 10.6 were developed and evaluated.
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Affiliation(s)
- B D Anderson
- Department of Pharmaceutics, College of Pharmacy, University of Utah, Salt Lake City 84112
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20
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Interaction of MgATP2− with DNA: Assessment of metal binding sites and DNA conformations by spectroscopic and thermal denaturation studies. Inorganica Chim Acta 1988. [DOI: 10.1016/s0020-1693(00)83863-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Sheina G, Stepanian S, Radchenko E, Blagoi Y. IR spectra of guanine and hypoxanthine isolated molecules. J Mol Struct 1987. [DOI: 10.1016/0022-2860(87)80024-8] [Citation(s) in RCA: 106] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Roy KB, Frazier J, Miles HT. Interaction of poly(X) with poly(U): alkali metal ion specificity suggests a four-stranded helix. Biopolymers 1983; 22:2021-34. [PMID: 6626690 DOI: 10.1002/bip.360220903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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23
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Piperaki P, Katsaros N, Katakis D. The interaction of oxomolybdenum(VI) with nucleic acid bases and nucleosides. Inorganica Chim Acta 1982. [DOI: 10.1016/s0020-1693(00)85037-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Yakovlev GI, Karpeisky MY, Bezborodova SI, Beletskaja OP, Sakharovsky VG. Guanyl-specific ribonuclease from the fungus Penicillium chrysogenum strain 152 and its complex with guanosine 3'-phosphate studied by nuclear magnetic resonance. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 109:75-85. [PMID: 6250840 DOI: 10.1111/j.1432-1033.1980.tb04769.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The method of proton magnetic resonance was used to obtain information on the active site of the guanyl-specific ribonuclease from Penicillium chrysogenum, strain 152A. Four pH-dependent signals in the aromatic region of the proton NMR spectrum of the enzyme were assigned to the C-2 and C-4 protons of the two histidine residues. To determine the pK values and the environment of the histidine residues the pH dependence of their chemical shifts was studied and experimental curves thus obtained were analyzed taking into account the effect of other dissociating groups of the enzyme. The pK values of the histidine residues were found to be equal to 7.92 +/- 0.04 and 7.86 +/- 0.09. The results of the calculations indicate that each histidine residue should interact with an acidic group (carboxylic) of the protein (pK 4.33 and 3.48) and the distance between two histidine residues does not exceed 0.85 nm. The rate constants for the quasi-first order reaction of deuterium exchange of the histidine residues (11.2 s-1 and 3.7 x-1) suggest that both residues are accessible, though to a different degree to solvent. Formation of a complex between the enzyme and guanosine 3'-phosphate (Guo3'P) is accompanied by the shift of the histidine pK toward the alkaline region by 0.5. The existence of the complex is controlled by dissociation of a histidine residue with pK 8.7 in alkaline medium and by protonation of the N-7 of Guo3'P (pK 2.4) in acid medium. Nuclear Overhauser effect measurements were used to determine the glycosidic torsion angle for the Guo3'P in the complex and to estimate the distances between the histidine residues of the enzyme and ribose ring of Guo-3'P. The results obtained suggest that the nucleotide in the complex has an anti conformation and the least exposed histidine is spaced not more than 0.5 nm from the C-1' proton of the nucleotide ribose ring. A model for the enzyme-nucleotide complex is presented.
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Egami F, Oshima T, Uchida T. Specific interaction of base-specific nucleases with nucleosides and nucleotides. MOLECULAR BIOLOGY, BIOCHEMISTRY, AND BIOPHYSICS 1980; 32:250-77. [PMID: 6255305 DOI: 10.1007/978-3-642-81503-4_21] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Inoue Y, Kuramochi T, Imakubo K. Protonation and quaternization of 1,N6-ethenoadenosine: What are the species responsible for the fluorescence of 1,N6-ethenoadenosine? Biopolymers 1979. [DOI: 10.1002/bip.1979.360180908] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kottmair N, Beck W. Tungsten carbonyl complexes of 2′,3′-O-isopropylideneguanosine and 6-mercaptopurine. Inorganica Chim Acta 1979. [DOI: 10.1016/s0020-1693(00)94691-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Arata Y, Kimura S, Matsuo H, Narita K. Proton magnetic resonance studies of ribonuclease T1. Assignment of histidine-40 peak and analysis of the active site. Biochem Biophys Res Commun 1976; 73:133-40. [PMID: 11795 DOI: 10.1016/0006-291x(76)90507-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Beck W, Kottmair N. Neue Übergangsmetallkomplexe mit Nuclein-Basen und Nucleosiden. ACTA ACUST UNITED AC 1976. [DOI: 10.1002/cber.19761090318] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Poly(8-aminoguanylic acid) has in neutral solution a novel ordered structure of high stability. The 8-amino group permits formation of three hydrogen bonds between two residues along the "top", or long axis, of the purines. The usual hydrogen bonding protons and Watson-Crick pairing sites are not involved in the association. The bonding scheme has a twofold rotation axis and is hemiprotonated at N(7). Poly(8NH2G) is converted by alkaline titration (pK = 9.7) to a quite different ordered structure, which is the favored form over the range approximately pH 10-11. The bonding scheme appears to be composed of a planar, tetrameric array of guanine residues, in which the 8-amino group does not participate in interbase hydrogen bonding. Poly (8NH2G) does not interact with poly(C) in neutral solution because of the high stability of the hemiprotonated G-G self-structure. Titration to the alkaline plateau, however, permits ready formation of a two-stranded Watson-Crick helix. In contrast to the monomer 8NH2GMP, poly(8NH2G) does not form a triple helix with poly(C) under any conditions. The properties of the ordered structures are interpreted in terms of a strong tendency of the 8-amino group to form a third interbase hydrogen bond, when this possibility is not prevented by high pH.
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Miles HT, Frazier J. Formation of a new 5'-guanylic acid helix in neutral solution. Biochem Biophys Res Commun 1972; 49:199-204. [PMID: 5077852 DOI: 10.1016/0006-291x(72)90029-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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34
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Epinatjeff C, Pongs O. Ribonuclease T 1. Spectrophotometric investigations of the interaction of the enzyme with substrate analogues. EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 26:434-41. [PMID: 5036976 DOI: 10.1111/j.1432-1033.1972.tb01784.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Fritzsche H, Tresselt D, Zimmer C. The nucleoside-copper (II) interaction and the tautomeric forms of the nucleosides. EXPERIENTIA 1971; 27:1253-5. [PMID: 4332431 DOI: 10.1007/bf02136669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Chantot JF, Sarocchi MT, Guschlbauer W. Physico-chemical properties of nucleosides. 4. Gel formation by quanosine and its analogues. Biochimie 1971; 53:347-54. [PMID: 5564224 DOI: 10.1016/s0300-9084(71)80101-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Wagner R, von Philipsborn W. [Protonization of purine, adenine, and guanine. NMR spectra and structure of mono, di, and tri cations]. Helv Chim Acta 1971; 54:1543-58. [PMID: 5131788 DOI: 10.1002/hlca.19710540604] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Pullman B, Pullman A. Electronic Aspects of Purine Tautomerism. ADVANCES IN HETEROCYCLIC CHEMISTRY 1971. [DOI: 10.1016/s0065-2725(08)60349-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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Christensen JJ, Rytting JH, Izatt RM. Thermodynamic pK, delta H-o, delta S-o, and delta Cp-o values for proton dissociation from several purines and their nucleosides in aqueous solution. Biochemistry 1970; 9:4907-13. [PMID: 5480155 DOI: 10.1021/bi00827a012] [Citation(s) in RCA: 124] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Zimmer C, Venner H. Influence of copper 2+ ions on the denaturation and spectral properties of DNA and methylated DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1970; 15:40-7. [PMID: 5489837 DOI: 10.1111/j.1432-1033.1970.tb00973.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Ts'o PO, Schweizer MP, Hollis DP. Contribution of nuclear magnetic resonance to the study of the structure and electronic aspects of nucleic acids. Ann N Y Acad Sci 1969; 158:256-97. [PMID: 5256963 DOI: 10.1111/j.1749-6632.1969.tb56226.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Howard FB, Frazier J, Miles HT. Interaction of Poly-5-bromocytidylic Acid with Polyinosinic Acid. J Biol Chem 1969. [DOI: 10.1016/s0021-9258(18)91842-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Courtois Y, Fromageot P, Guschlbauer W. Protonated polynucleotide structures. 3. An optical rotatory dispersion study of the protonation of DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1968; 6:493-501. [PMID: 5701966 DOI: 10.1111/j.1432-1033.1968.tb00472.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Courtois Y, Guschlbauer W, Fromageot P. [Interaction between pigments and nucleic acids. 6. Study of the interaction of actinomycin with DNA by optical rotatory dispersion]. EUROPEAN JOURNAL OF BIOCHEMISTRY 1968; 6:106-13. [PMID: 5749684 DOI: 10.1111/j.1432-1033.1968.tb00426.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Abstract
Optical rotatory dispersion and circular dichroism have been used to investigate the protonation of guanosine and some of its analogues. An inversion of the principal Cotton effect and the dichroic band is observed below the acid pK. It is suggested that a conformational change from the anti form above the pK to the syn form below the pK occurs. The reasons why this change should occur only in guanosine and not in adenosine are discussed.
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Affiliation(s)
- W Guschlbauer
- Service de Biochimie, Département de Biologie, Centre d'Etudes Nucléaires de Saclay, B.P. No. 2, F-91, Gif-sur-Yvette, France
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The isolation, analysis and chemical reactions of deoxyribonucleic acid [DNA]—III. The chemical reactions of DNA. Eur Polym J 1968. [DOI: 10.1016/0014-3057(68)90006-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Shapiro R. Chemistry of guanine and its biologically significant derivatives. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1968; 8:73-112. [PMID: 4875811 DOI: 10.1016/s0079-6603(08)60544-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Fritzsche H. Infrared studies of deoxyribonucleic acids, their consituents and analogues. II. Deoxyribonucleic acids with different base composition. Biopolymers 1967; 5:863-70. [PMID: 6063542 DOI: 10.1002/bip.1967.360050908] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Price TD, Ashman DF, Melicow MM. Organophosphates of urine, including adenosine 3',5'-monophosphate and guanosine 3',5'-monophosphate. BIOCHIMICA ET BIOPHYSICA ACTA 1967; 138:452-65. [PMID: 5341200 DOI: 10.1016/0005-2787(67)90542-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Venner H, Zimmer C. Studies on nucleic acids. VIII. Changes in the stability of DNA secondary structure by interaction with divalent metal ions. Biopolymers 1966. [DOI: 10.1002/bip.1966.360040306] [Citation(s) in RCA: 54] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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