Journal articles: 'DNA Deprotonation'

1

Smiatek, Jens, and Andreas Heuer. "Deprotonation mechanism of a single-stranded DNA i-motif." RSC Adv. 4, no. 33 (2014): 17110–13. http://dx.doi.org/10.1039/c4ra01420k.

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Ganguly, Sonali, and Kiron K. Kundu. "Protonation/deprotonation energetics of uracil, thymine, and cytosine in water from e.m.f./spectrophotometric measurements." Canadian Journal of Chemistry 72, no. 4 (April 1, 1994): 1120–26. http://dx.doi.org/10.1139/v94-143.

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The protonation/deprotonation constants for uracil (U) (pK1 and pK2), thymine (T) (pK1) and cytosine (C) (pK1 and pK2) in water have been determined from emf measurements of Harned–Ehler type cells comprising H2 and Ag–AgI electrodes at five equidistant temperatures ranging from 15–35 °C. The pKa values were fitted in the temperature equation pKa = AT−1 + B + CT by the method of least squares and the standard free energies (ΔG0), entropies (ΔS0), and enthalpies (ΔH0) of protonation/deprotonation processes in water were evaluated using the values of the coefficients A, B, and C of the respective acids. The second step deprotonation constant for T was determined using precise spectrophotometric method. The results have been duly compared with the existing literature data and are also shown to derive important reflections on the sites of protonation/deprotonation in the light of pK values of some acids and bases of comparable functional groups and especially the entropies of protonation/deprotonation of the key DNA–RNA base molecules.

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Wu, Lidan, Kunhui Liu, Jialong Jie, Di Song, and Hongmei Su. "Direct Observation of Guanine Radical Cation Deprotonation in G-Quadruplex DNA." Journal of the American Chemical Society 137, no. 1 (December 30, 2014): 259–66. http://dx.doi.org/10.1021/ja510285t.

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4

Jie, Jia-long, Chen Wang, Hong-mei Zhao, Di Song, and Hong-mei Su. "Experimental and Theoretical Study of Deprotonation of DNA Adenine Cation Radical." Chinese Journal of Chemical Physics 30, no. 6 (December 27, 2017): 664–70. http://dx.doi.org/10.1063/1674-0068/30/cjcp1710198.

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Gregory, Mark T., Yang Gao, Qiang Cui, and Wei Yang. "Multiple deprotonation paths of the nucleophile 3′-OH in the DNA synthesis reaction." Proceedings of the National Academy of Sciences 118, no. 23 (June 4, 2021): e2103990118. http://dx.doi.org/10.1073/pnas.2103990118.

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DNA synthesis by polymerases is essential for life. Deprotonation of the nucleophile 3′-OH is thought to be the obligatory first step in the DNA synthesis reaction. We have examined each entity surrounding the nucleophile 3′-OH in the reaction catalyzed by human DNA polymerase (Pol) η and delineated the deprotonation process by combining mutagenesis with steady-state kinetics, high-resolution structures of in crystallo reactions, and molecular dynamics simulations. The conserved S113 residue, which forms a hydrogen bond with the primer 3′-OH in the ground state, stabilizes the primer end in the active site. Mutation of S113 to alanine destabilizes primer binding and reduces the catalytic efficiency. Displacement of a water molecule that is hydrogen bonded to the 3′-OH using the 2′-OH of a ribonucleotide or 2′-F has little effect on catalysis. Moreover, combining the S113A mutation with 2′-F replacement, which removes two potential hydrogen acceptors of the 3′-OH, does not reduce the catalytic efficiency. We conclude that the proton can leave the O3′ via alternative paths, supporting the hypothesis that binding of the third Mg2+ initiates the reaction by breaking the α–β phosphodiester bond of an incoming deoxyribonucleoside triphosphate (dNTP).

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Lin, Chien-Chu, Yi-Ping Chen, Wei-Zen Yang, James C. K. Shen, and Hanna S. Yuan. "Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B." Nucleic Acids Research 48, no. 7 (February 21, 2020): 3949–61. http://dx.doi.org/10.1093/nar/gkaa111.

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Abstract DNA methyltransferases are primary enzymes for cytosine methylation at CpG sites of epigenetic gene regulation in mammals. De novo methyltransferases DNMT3A and DNMT3B create DNA methylation patterns during development, but how they differentially implement genomic DNA methylation patterns is poorly understood. Here, we report crystal structures of the catalytic domain of human DNMT3B–3L complex, noncovalently bound with and without DNA of different sequences. Human DNMT3B uses two flexible loops to enclose DNA and employs its catalytic loop to flip out the cytosine base. As opposed to DNMT3A, DNMT3B specifically recognizes DNA with CpGpG sites via residues Asn779 and Lys777 in its more stable and well-ordered target recognition domain loop to facilitate processive methylation of tandemly repeated CpG sites. We also identify a proton wire water channel for the final deprotonation step, revealing the complete working mechanism for cytosine methylation by DNMT3B and providing the structural basis for DNMT3B mutation-induced hypomethylation in immunodeficiency, centromere instability and facial anomalies syndrome.

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Kobayashi, Kazuo, Ryuhei Yamagami, and Seiichi Tagawa. "Effect of Base Sequence and Deprotonation of Guanine Cation Radical in DNA." Journal of Physical Chemistry B 112, no. 34 (August 2008): 10752–57. http://dx.doi.org/10.1021/jp804005t.

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8

Kobayashi, Kazuo, and Seiichi Tagawa. "Direct Observation of Guanine Radical Cation Deprotonation in Duplex DNA Using Pulse Radiolysis." Journal of the American Chemical Society 125, no. 34 (August 2003): 10213–18. http://dx.doi.org/10.1021/ja036211w.

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9

Adhikary, Amitava, Anil Kumar, Brian J. Palmer, Andrew D. Todd, Alicia N. Heizer, and Michael D. Sevilla. "Reactions of 5-methylcytosine cation radicals in DNA and model systems: Thermal deprotonation from the 5-methyl group vs. excited state deprotonation from sugar." International Journal of Radiation Biology 90, no. 6 (February 10, 2014): 433–45. http://dx.doi.org/10.3109/09553002.2014.884293.

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10

Wang, Yinghui, Hongmei Zhao, Qian Zhou, Xiaojuan Dai, Kunhui Liu, Di Song, and Hongmei Su. "Monitoring the Structure-Dependent Reaction Pathways of Guanine Radical Cations in Triplex DNA: Deprotonation Versus Hydration." Journal of Physical Chemistry B 123, no. 13 (March 5, 2019): 2853–63. http://dx.doi.org/10.1021/acs.jpcb.9b00608.

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11

Adhikary, Amitava, Anil Kumar, Shawn A. Munafo, Deepti Khanduri, and Michael D. Sevilla. "Prototropic equilibria in DNA containing one-electron oxidized GC: intra-duplex vs. duplex to solvent deprotonation." Physical Chemistry Chemical Physics 12, no. 20 (2010): 5353. http://dx.doi.org/10.1039/b925496j.

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12

Müller, Pavel, Elisabeth Ignatz, Stephan Kiontke, Klaus Brettel, and Lars-Oliver Essen. "Sub-nanosecond tryptophan radical deprotonation mediated by a protein-bound water cluster in class II DNA photolyases." Chemical Science 9, no. 5 (2018): 1200–1212. http://dx.doi.org/10.1039/c7sc03969g.

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13

Xie, Jia-qing, Shu-lan Cai, and Fa-mei Feng. "Transition Metal Complexes of a Diaza-Crown Ether with two Carbamoylmethyl Substituents: Synthesis and Assessment as a Functional Nuclease." Progress in Reaction Kinetics and Mechanism 42, no. 2 (May 2017): 136–44. http://dx.doi.org/10.3184/146867817x14806858832144.

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We report the synthesis, catalytic function and catalytic mechanism of two transition metal complexes (CuL, ZnL) of a diaza-crown ether with two acetylamino side arms [L = 2,2′-(1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl)diacetamide] in the hydrolysis of DNA. Their nuclease functions on pUC19 DNA cleavage were investigated. The results indicated that the active species might be formed by the deprotonation of the water-coordinated molecules in the complex and the optimum pH is 8.0 for both CuL and ZnL. The catalytic activity of CuL is higher than that of ZnL in DNA hydrolytic cleavage due to the difference in the Lewis acidity of the central metal ions, which is contrary to the result with the Cu and Zn complexes of the parent ligand L0 (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane) as artificial nuclease. Comparison studies of DNA cleavage in the presence and absence of several oxygen scavengers showed that these complexes can promote DNA cleavage by a hydrolytic pathway. Our proposed mechanism suggests that the negative charge on the phosphorus oxygen atom of the substrate molecule is dispersed and the intermediate is formed and stabilised by hydrogen bonding between the DNA molecule and the acetylamino group of the complex.

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14

Vonderach, Matthias, Oli T. Ehrler, Katerina Matheis, Patrick Weis, and Manfred M. Kappes. "Isomer-Selected Photoelectron Spectroscopy of Isolated DNA Oligonucleotides: Phosphate and Nucleobase Deprotonation at High Negative Charge States." Journal of the American Chemical Society 134, no. 18 (May 2012): 7830–41. http://dx.doi.org/10.1021/ja300619j.

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15

Ren, Hang, Cameron G. Cheyne, Aaron M. Fleming, Cynthia J. Burrows, and Henry S. White. "Single-Molecule Titration in a Protein Nanoreactor Reveals the Protonation/Deprotonation Mechanism of a C:C Mismatch in DNA." Journal of the American Chemical Society 140, no. 15 (March 21, 2018): 5153–60. http://dx.doi.org/10.1021/jacs.8b00593.

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16

Roston, Daniel, Darren Demapan, and Qiang Cui. "Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase." Proceedings of the National Academy of Sciences 116, no. 50 (November 22, 2019): 25048–56. http://dx.doi.org/10.1073/pnas.1914613116.

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Transphosphorylation of nucleotide triphosphates is the central reaction in DNA replication by DNA polymerase as well as many other biological processes. Despite its importance, the microscopic chemical mechanism of transphosphorylation of nucleotide triphosphates is, in most cases, unknown. Here we use extensive simulations of DNA polymerase η to test mechanistic hypotheses. We systematically survey the reactive space by calculating 2D free-energy surfaces for 10 different plausible mechanisms that have been proposed. We supplement these free-energy surfaces with calculations of pKa for a number of potentially acidic protons in different states relevant to the catalytic cycle. We find that among all of the conditions that we test, the smallest activation barrier occurs for a reaction where a Mg2+-coordinated water deprotonates the nucleophilic 3′-OH, and this deprotonation is concerted with the phosphoryl transfer. The presence of a third Mg2+ in the active site lowers the activation barrier for the water-as-base mechanism, as does protonation of the pyrophosphate leaving group, which is consistent with general acid catalysis. The results demonstrate the value of simulations, when used in conjunction with experimental data, to help establish a microscopic chemical mechanism in a complex environment.

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17

Balanikas, Evangelos, Akos Banyasz, Gérard Baldacchino, and Dimitra Markovitsi. "Populations and Dynamics of Guanine Radicals in DNA strands—Direct versus Indirect Generation." Molecules 24, no. 13 (June 26, 2019): 2347. http://dx.doi.org/10.3390/molecules24132347.

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Guanine radicals, known to be involved in the damage of the genetic code and aging, are studied by nanosecond transient absorption spectroscopy. They are generated in single, double and four-stranded structures (G-quadruplexes) by one and two-photon ionization at 266 nm, corresponding to a photon energy lower than the ionization potential of nucleobases. The quantum yield of the one-photon process determined for telomeric G-quadruplexes (TEL25/Na+) is (5.2 ± 0.3) × 10−3, significantly higher than that found for duplexes containing in their structure GGG and GG sequences, (2.1 ± 0.4) × 10−3. The radical population is quantified in respect of the ejected electrons. Deprotonation of radical cations gives rise to (G-H1)• and (G-H2)• radicals for duplexes and G-quadruplexes, respectively. The lifetimes of deprotonated radicals determined for a given secondary structure strongly depend on the base sequence. The multiscale non-exponential dynamics of these radicals are discussed in terms of inhomogeneity of the reaction space and continuous conformational motions. The deviation from classical kinetic models developed for homogeneous reaction conditions could also be one reason for discrepancies between the results obtained by photoionization and indirect oxidation, involving a bi-molecular reaction between an oxidant and the nucleic acid.

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18

RUNGROTMONGKOL, THANYADA, SUPA HANNONGBUA, and ADRIAN MULHOLLAND. "MECHANISTIC STUDY OF HIV-1 REVERSE TRANSCRIPTASE AT THE ACTIVE SITE BASED ON QM/MM METHOD." Journal of Theoretical and Computational Chemistry 03, no. 04 (December 2004): 491–500. http://dx.doi.org/10.1142/s0219633604001252.

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HIV-1 RT catalyses the reverse transcription of viral genetic material (RNA) into double-stranded DNA, and is an important target of antiviral therapy in the treatment of AIDS. Better understanding of the structure, mechanism and functional role of residues involved in the resistance of HIV-1 RT against nucleoside-analog drugs may assist in the development of improved inhibitors, and also in understanding the effects of genetic variation on RT specificity and activity. In this study, firstly, molecular dynamics simulations (with CHARMM27) have been used to investigate binding interactions at the active site and the conformational behavior of the enzyme, then, mechanisms of deprotonation and DNA polymerization reactions have been modelled by the QM/MM method. A combined quantum mechanical and molecular mechanical (QM/MM) method (AM1/CHARMM) has been used to study the triphosphate substrate and the active site of HIV-1 reverse transcriptase complex structure, a virally-encoded enzyme. Free energy profiles for the reaction are also calculated. The obtained results provide important insight into the mechanistic activity of HIV-1 RT.

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19

TEHRANI, ZAHRA ALIAKBAR, MARJAN JEBELI JAVAN, ALIREZA FATTAHI, and MOHAMMAD MAHMOODI HASHEMI. "EFFECT OF CATION RADICAL FORMATION ON REACTIVITY AND ACIDITY ENHANCEMENT OF CYTOSINE NUCLEOBASE: NATURAL BOND ORBITAL AND ATOM IN MOLECULE ANALYSIS." Journal of Theoretical and Computational Chemistry 11, no. 02 (April 2012): 313–27. http://dx.doi.org/10.1142/s0219633612500228.

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The radical cations of DNA constituents generated by the ionizing radiation initiate an alteration of the bases, which is one of the main types of cytotoxic DNA lesions. These cation radical spices are known for their role in producing nucleic acid strand break. In this study, the gas-phase intrinsic chemical properties of the gaseous radical cations of cytosine and its base pair with guanine were examined by employing density functional theory (B3LYP) with the 6-311++G(d,p) basis set. Structures, geometries, adiabatic ionization energies, adiabatic electron affinities, charge distributions, molecular orbital analysis and proton-transfer process of these molecules were investigated. The influence of cation radical formation on acidities of multiple sites in cytosine molecule was investigated. Results of calculations revealed that cytosine radicals formed by deprotonation of cytosine cation radicals can exothermically abstract hydrogen atoms from thiol groups, phenol, and α-positions of amino acid. Furthermore, comparison of acidity value of N–H sites of cytosine cation radical with the known proton affinities (PA) of organic and biological molecules implied that cytosine cation radical can exothermically transfer onto basic sites of amino acids and peptides.

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20

Sahasrabudhe, S. R., X. Luo, and M. Z. Humayun. "Specificity of base substitutions induced by the acridine mutagen ICR-191: mispairing by guanine N7 adducts as a mutagenic mechanism." Genetics 129, no. 4 (December 1, 1991): 981–89. http://dx.doi.org/10.1093/genetics/129.4.981.

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Abstract As the most nucleophilic site in DNA, the guanine N7 atom is a major site of adduction by a large number of alkylating mutagens and carcinogens. Aflatoxin B1, a powerful mutagen, is believed to act through its reaction with this DNA site. On the basis of the specificity of base substitutions induced by various adduct forms of aflatoxin, we have proposed that bulky guanine N7 adducts elicit base substitutions by two mechanisms. The first mechanism is similar to that observed for a number of bulky noninstructive lesions, whereas the second mechanism invokes mispairing between N7-adducted guanine and thymine. A prediction of the mispairing hypothesis is that diverse bulky guanine N7 adducts (regardless of structural similarities with the aflatoxins) should induce predominantly G-to-A transitions. Accordingly, we have recently observed that base substitutions induced by the acridine half-mustard ICR-191 in the M13 double-stranded DNA transfection system are predominantly G:C-to-A:T transitions. Here, by transfecting ICR-191-treated M13 AB28 single-stranded DNA into Escherichia coli, we show that base substitutions are predominantly targeted to guanines. Since the N7-adducted-guanine:thymine mispairing is proposed to require N1 deprotonation promoted by the primary N7 lesion, guanine imidazole ring-opening should abolish this mispairing property, and thereby alter the specificity of mutagenesis. Here, we show that the incubation of ICR-191-treated RF DNA at pH 10.5 results in a significant reversal of the specificity of G:C-targeted substitutions such that G-to-T transversions predominated over G-to-A transitions.(ABSTRACT TRUNCATED AT 250 WORDS)

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21

Balanikas, Evangelos, Akos Banyasz, Gérard Baldacchino, and Dimitra Markovitsi. "Guanine Radicals Generated in Telomeric G-Quadruplexes by Direct Absorption of Low-Energy UV Photons: Effect of Potassium Ions." Molecules 25, no. 9 (April 30, 2020): 2094. http://dx.doi.org/10.3390/molecules25092094.

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The study deals with the primary species, ejected electrons, and guanine radicals, leading to oxidative damage, that is generated in four-stranded DNA structures (guanine quadruplexes) following photo-ionization by low-energy UV radiation. Performed by nanosecond transient absorption spectroscopy with 266 nm excitation, it focusses on quadruplexes formed by folding of GGG(TTAGGG)3 single strands in the presence of K+ ions, TEL21/K+. The quantum yield for one-photon ionization (9.4 × 10−3) was found to be twice as high as that reported previously for TEL21/Na+. The overall population of guanine radicals decayed faster, their half times being, respectively, 1.4 and 6.7 ms. Deprotonation of radical cations extended over four orders of magnitude of time; the faster step, concerning 40% of their population, was completed within 500 ns. A reaction intermediate, issued from radicals, whose absorption spectrum peaked around 390 nm, was detected.

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22

Chatgilialoglu, Chryssostomos. "The Two Faces of the Guanyl Radical: Molecular Context and Behavior." Molecules 26, no. 12 (June 9, 2021): 3511. http://dx.doi.org/10.3390/molecules26123511.

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The guanyl radical or neutral guanine radical G(-H)• results from the loss of a hydrogen atom (H•) or an electron/proton (e–/H+) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC•+ pair. The role of the two G(-H)• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed.

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23

Borys-Brzywczy, Ewa, Katarzyna D. Arczewska, Murat Saparbaev, Ulrike Hardeland, Primo Schär, and Jarosław T. Kuśmierek. "Mismatch dependent uracil/thymine-DNA glycosylases excise exocyclic hydroxyethano and hydroxypropano cytosine adducts." Acta Biochimica Polonica 52, no. 1 (March 31, 2005): 149–65. http://dx.doi.org/10.18388/abp.2005_3501.

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Exocyclic adducts of DNA bases, such as etheno- and hydroxyalkano- ones, are generated by a variety of bifunctional agents, including endogenously formed products of lipid peroxidation. In this work we selectively modified cytosines in the 5'-d(TTT TTT CTT TTT CTT TTT CTT TTT T)-3' oligonucleotide using: chloroacetaldehyde to obtain 3,N(4)-alpha-hydroxyethano- (HEC) and 3,N(4)-etheno- (epsilonC), acrolein to obtain 3,N(4)-alpha-hydroxypropano- (HPC) and crotonaldehyde to obtain 3,N(4)-alpha-hydroxy-gamma-methylpropano- (mHPC) adducts of cytosine. The studied adducts are alkali-labile which results in oligonucleotide strain breaks at the sites of modification upon strong base treatment. The oligonucleotides carrying adducted cytosines were studied as substrates of Escherichia coli Mug, human TDG and fission yeast Thp1p glycosylases. All the adducts studied are excised by bacterial Mug although with various efficiency: epsilonC >HEC >HPC >mHPC. The yeast enzyme excises efficiently epsilonC>HEC>HPC, whereas the human enzyme excises only epsilonC. The pH-dependence curves of excision of eC, HEC and HPC by Mug are bell shaped and the most efficient excision of adducts occurs within the pH range of 8.6-9.6. The observed increase of excision of HEC and HPC above pH 7.2 can be explained by deprotonation of these adducts, which are high pK(a) compounds and exist in a protonated form at neutrality. On the other hand, since epsilonC is in a neutral form in the pH range studied, we postulate an involvement of an additional catalytic factor. We hypothesize that the enzyme structure undergoes a pH-induced rearrangement allowing the participation of Lys68 of Mug in catalysis via a hydrogen bond interaction of its epsilon-amino group with N(4) of the cytosine exocyclic adducts.

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24

Malarvizhi, M., G. Subramanian, and PR Athappan. "Template Synthesis, Spectral and Redox Behavior of Metal Complexes of Macrocyclic Tetraaza Schiff Base and their Interaction with Herring Sperm DNA." Materials Science Forum 699 (September 2011): 205–29. http://dx.doi.org/10.4028/www.scientific.net/msf.699.205.

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This paper documents the detailed investigation of the relationship between molecular structure and biological activity of few tetraaza macrocyclic metal (II) complexes equipped by the template condensation of o-bromoaniline, ethylenediamine and salbenz in 2:1:1 ratio with metal (II) salts (1mM). All these complexes are found to be stable in air and soluble in CN3CN or DMSO, and are characterized through spectral (UV-Vis, IR, EPR) and electrochemical methods. A square planar geometry is proposed for Cu(II), Ni(II) and Co(II) complexes, while an octahedral geometry is suggested for Mn(II) and Fe(II). The IR spectra indicate that the NH groups of the amine exist as such even after complexation without deprotonation, and all the complexes show a strong band in 1580-1590 cm-1region corresponding to ν(C=N), due to coordinated azomethine group to the metal. The solution electronic spectra of these complexes show intense LMCT bands around 400 nm. Intense electronic absorption spectra as well as the four line pattern in EPR spectra with broad g⊥suggests that the copper(II) complexes have distorted square planar geometry. On titration with herring sperm DNA, CuN4,CoN4,NiN4and MnN4complexes exhibit an abrupt amend in their electronic spectrum and cyclic voltammogram. The intense intraligand π-π* transition in the region 350–420 nm is found to show hypochromicity on titration with DNA in all these complexes, due to their electrostatic interaction with DNA. All these complexes show one well–defined quasi-reversible redox couple with values ranging from ∆Ep 137 to 337 mV. Their spectral and electrochemical outcome designate that the square planar complexes Cu(II), Co(II) and Ni(II) interact much better than the axially coordinated octahedral complexes Mn(II) and Fe(II). The decrease found in the negative absorption peak, characteristic peak due to helicity of DNA, in circular dichroism studies reflects the perversion in the helical nature of B-DNA upon the addition of complex. The binding of plasmid DNA by these complexes has also been investigated by agarose gel electrophoresis, remarkably Ni(II) complex was found to cleave the DNA double helix.

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25

Hardy, L. W. "Structural aspects of the inhibition and catalytic mechanism of thymidylate synthase." Acta Biochimica Polonica 42, no. 4 (December 31, 1995): 367–80. http://dx.doi.org/10.18388/abp.1995_4891.

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Thymidylate synthase (TS) is a target for anticancer drugs, due to its unique role in the biosynthesis of an essential DNA precursor. The X-ray structures available for several bacterial enzymes have been used to design novel inhibitors of TS, to structurally analyze the binding mode of existing inhibitors, and to propose catalytic roles for amino-acid residues on the protein. The first part of this paper describes some aspects of structure-based drug design, including a recent result from the groups of Montfort and Maley emphasizing the importance of conformational changes in inhibitor binding. The second part of the paper describes the work of the author on the TS mechanism, especially the catalytic roles of active site amino acids Asn177 and Glu58 in TS from Escherichia coli. An important function for Glu58 is proposed to be preventing the excessive stabilization of a covalent intermediate. The use of isotope effects to probe the mechanistic basis for stimulation of E. coli TS by magnesium ions, and to identify differences between the E. coli and human enzymes, is described. The hypothesis that N5 of tetrahydrofolate provides the basicity for deprotonation of the nucleotide is also discussed.

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26

Wille, Uta, and Catrin Goeschen. "Oxidative Damage of Thymidines by the Atmospheric Free-Radical Oxidant NO3•." Australian Journal of Chemistry 64, no. 6 (2011): 833. http://dx.doi.org/10.1071/ch11102.

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Analysis of the products formed in the reaction of nitrate radicals, NO3 •, with the N- and O-methylated and acetylated thymidines 1a and 1b revealed, for the first time, insight regarding how this important atmospheric free-radical oxidant can cause irreversible damage to DNA building blocks. Mechanistic studies indicated that the initial reaction step likely proceeds via NO3 • induced electron transfer at the pyrimidine ring, followed by deprotonation of the methyl group at C5. The oxidation ultimately leads to formation of nitrates 2, aldehydes 4 and, in the case of high [NO3 •], also to carboxylic acids 5. In addition to this, through a very minor pathway, loss of the methyl group at C5 also occurred to give the respective 2′-deoxyuridines 6. The nitrates 2 are highly labile compounds that undergo rapid hydrolysis during work-up and purification of the reaction mixtures, which could lead to serious misinterpretation of the experimental findings and reaction mechanism. Products resulting from NO3 • addition to the C5=C6 double bond in the pyrimidine ring were not observed. Also, no reaction of NO3 • with the 2′-deoxyribose moiety was detected.

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27

Chatturgoon, Teshica, and Matthew P. Akerman. "X-ray and DFT-calculated structures of bis[N-(quinolin-8-yl)benzamidato-κ2N,N′]copper(II)." Acta Crystallographica Section C Structural Chemistry 72, no. 3 (February 25, 2016): 234–38. http://dx.doi.org/10.1107/s2053229616003120.

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The application of transition metal chelates as chemotherapeutic agents has the advantage that they can be used as a scaffold around which ligands with DNA recognition elements can be anchored. The facile substitution of these components allows for the DNA recognition and binding properties of the metal chelates to be tuned. Copper is a particularly interesting choice for the development of novel metallodrugs as it is an endogenous metal and is therefore less toxic than other transition metals. The title compound, [Cu(C16H11N2O)2], was synthesized by reactingN-(quinolin-8-yl)benzamide and the metal in a 2:1 ratio. Ligand coordination required deprotonation of the amide N—H group and the isolated complex is therefore neutral. The metal ion adopts a flattened tetrahedral coordination geometry with the ligands in a pseudo-transconfiguration. The free rotation afforded by the formal single bond between the amide group and phenyl ring allows the phenyl rings to rotate out-of-plane, thus alleviating nonbonded repulsion between the phenyl rings and the quinolyl groups within the complex. Weak C—H...O interactions stabilize a dimer in the solid state. Density functional theory (DFT) simulations at the PBE/6-311G(dp) level of theory show that the solid-state structure (C1 symmetry) is 79.33 kJ mol−1higher in energy than the lowest energy gas-phase structure (C2 symmetry). Natural bond orbital (NBO) analysis offers an explanation for the formation of the C—H...O interactions in electrostatic terms, but the stabilizing effect is insufficient to support the dimer in the gas phase.

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28

Beyere, L., P. Arboleda, V. Monga, and G. R. Loppnow. "The dependence of thymine and thymidine Raman spectra on solvent." Canadian Journal of Chemistry 82, no. 6 (June 1, 2004): 1092–101. http://dx.doi.org/10.1139/v04-052.

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Recent work has focused on developing Raman spectroscopy as a noninvasive probe of DNA interactions with solvents, intercalants, proteins, and other ligands. Here, we report the Raman spectra of thymine in eight solvents and thymidine in nine solvents obtained with visible excitation. Raman spectra under acidic, neutral, and basic conditions were also obtained of both thymine and thymidine. Changes in both the frequencies and intensities of several of the vibrational bands in the 8001800 cm1 region are observed. No evidence of deprotonation in the different solvents is observed for either thymine or thymidine. Correlations of the observed frequency shifts of specific vibrational modes with characteristic properties of the solvent for both thymine and thymidine show a significant correlation with acceptor and donor numbers, measures of the hydrogen-bonding ability of the solvent, in both thymine and thymidine. These results are interpreted in terms of hydrogen-bonding interactions between the N-H protons of the thymine base and lone pairs of electrons on the solvent molecules and between the solvent hydrogens and lone pairs on C=O sites. The solvent-dependent intensity in vibrational bands of thymine between 1500 and 1800 cm1 indicates a strong interaction between thymine and solvent at the C=O and N-H sites that leads to separation of the C=O stretches from the C=C stretch. The intensity variations with solvent were much smaller for thymidine than for thymine, perhaps as a result of replacing the N1 proton by the sugar. These results suggest that Raman spectroscopy is uniquely sensitive to specific interactions of thymine and thymidine with their environment.Key words: Raman spectroscopy, thymine, thymidine, solvent effects, hydrogen bonding.

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Alrawashdeh, Ahmad I., Mansour H. Almatarneh, and Raymond A. Poirier. "Computational study on the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O." Canadian Journal of Chemistry 91, no. 7 (July 2013): 518–26. http://dx.doi.org/10.1139/cjc-2012-0416.

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Deamination of adenine is one of several forms of premutagenic lesions occurring in DNA. In the present study, mechanisms for the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O were investigated. HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), and B3LYP/6-31+G(d) levels of theory were employed to search for and optimize all geometries. Energies were calculated at the G3MP2B3 and CBS-QB3 levels of theory. The effect of solvent (water) was computed using the polarizable continuum model (PCM). Intrinsic reaction coordinate (IRC) calculations were performed for all transition states. Five pathways were investigated for the deamination reaction of adenine with OH−/nH2O and 3H2O. The first four pathways (A–D) are initiated by deprotonation at the amino group of adenine by OH−, while pathway E is initiated by tautomerization of adenine. For all pathways the next two steps involve formation of a tetrahedral intermediate followed by dissociation to products via a 1,3-proton shift. Deamination with a single OH− has a high activation barrier (190 kJ mol−1 using the G3MP2B3 level) for the rate-determining step. The addition of one water molecule reduces this barrier by 68 kJ mol−1 at the G3MP2B3 level. Adding additional water molecules decreases the overall activation energy of the reaction, but the effect becomes smaller with each additional water molecule. The most plausible mechanism is pathway E, the deamination reaction of adenine with 3H2O, with an overall G3MP2B3 activation energy of 139 and 137 kJ mol−1 for the gas phase and PCM, respectively. This barrier is lower than that for the deamination with OH−/3H2O by 6 and 2 kJ mol−1 for the gas phase and PCM, respectively.

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Kilde, Martin Drøhse, Paloma Garcia Arroyo, Anders S. Gertsen, Kurt V. Mikkelsen, and Mogens Brøndsted Nielsen. "Molecular solar thermal systems – control of light harvesting and energy storage by protonation/deprotonation." RSC Advances 8, no. 12 (2018): 6356–64. http://dx.doi.org/10.1039/c7ra13762a.

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The optical properties of pyridyl-substituted dihydroazulene (DHA) photoswitches can be tuned by protonation/deprotonation as well as the thermal back-reaction rate and amount of heat release from the vinylheptafulvene (VHF) photoisomers.

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Priyadi, Sapto, Purnama Darmadji, Umar Santoso, and Pudji Hastuti. "DISTRIBUSI PLUMBUM, CADMIUM PADA BIJI KEDELAI, DAN DEPROTONASI GUGUS FUNGSIONAL KARBOKSIL ASAM SITRAT DALAM KHELASI (Distribution of Plumbum, Cadmium on Soybeans and Deprotonation of Carboxyl Functional Groups of Citric Acid in the Chelation)." Jurnal Agritech 34, no. 04 (February 11, 2015): 407. http://dx.doi.org/10.22146/agritech.9435.

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A study on the distribution of plumbum, cadmium on soybeans and deprotonation of carboxyl functional groups of citric acid in the chelation process. This study was deprotonation phase of carboxyl functional groups of citric acid as chelating agent, that was review chemically activity (protons number) functional group of citric acid was caused of chelation environment pH changes. Research factors were 1) ratios of citric acid with water, consists of three levels i.e. 0,1:1; 0,2:1 and 0,3:1 second factors was chelation environment pH, consists of three levels i.e. 5; 7.5 and 10. The results showed that, the plumbum (Pb) accumulation in seed coat tissue average value 0,37 ± 0,03 ppm, whereas Pb on cotyledon tissue average value 0,39 ± 0,07 ppm. Cadmium (Cd) accumulation in seed coat tissue average value was 0,02 ± 0,004 ppm while the Cd on cotyledon tissue average value 0,02 ± 0,003 ppm. The highest deprotonation offunctional groups citric acid as chelating agent 9,43cmol+kg was reached on chelation condition citric acid ratios with water 0,3:1 on chelation environment pH 10 (A3B3–1). The study result non significant difference with citric acid ratios with water 0,2:1 and 0,1:1 on chelation environment pH 10.Keywords: Soybean, plumbum, cadmium and deprotonation ABSTRAKTelah dilakukan penelitian tentang distribusi plumbum, cadmium pada biji kedelai dan deprotonasi gugus fungsional karboksil asam sitrat dalam proses khelasi. Penelitian ini merupakan tahapan deprotonasi gugus fungsional karboksil asam sitrat, yaitu tinjauan secara kimiawi keaktifan (jumlah proton) gugus fungsional asam sitrat akibat perubahan pHlingkungan khelasi. Faktor penelitian meliputi ratio asam sitrat terhadap air yang terdiri dari tiga taraf 0,1:1, 0,2:1 dan 0,3:1 dengan pH lingkungan khelasi yang terdiri dari tiga taraf 5; 7,5 dan 10. Hasil penelitian menunjukkan bahwa, akumulasi plumbum (Pb) pada jaringan kulit biji kedelai rerata 0,37 ± 0,03 ppm, sedangkan Pb pada jaringan kotiledon rerata 0,39 ± 0,07 ppm. Akumulasi cadmium (Cd) pada jaringan kulit biji kedelai rerata 0,02 ± 0,004 ppm sedangkan Cd pada jaringan kotiledon rerata 0,02 ± 0,004 ppm. Deprotonasi gugus fungsional chelating agent asam sitrat tertinggi 9,43 cmol + kg –1 dicapai pada kondisi khelasi dengan ratio asam sitrat terhadap air 0,3:1 pada lingkungan khelasi pH 10 (A). Keadaan tersebut tidak berbeda nyata dengan perlakuan ratio asam sitrat 0,2:1 dan 0,1:1 pada lingkungan khelasi pH 10.Kata kunci: Kedelai, plumbum, cadmium dan deprotonasi

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Patra, Ranjan, and Israel Goldberg. "A one-dimensional coordination polymer of 5-[(imidazol-1-yl)methyl]benzene-1,3-dicarboxylic acid with CuIIcations." Acta Crystallographica Section C Crystal Structure Communications 69, no. 4 (March 6, 2013): 344–47. http://dx.doi.org/10.1107/s0108270113005313.

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5-[(Imidazol-1-yl)methyl]benzene-1,3-dicarboxylic acid (H2L) was synthesized and the dimethylformamide- and dimethylacetamide-solvated structures of its adducts with CuII, namelycatena-poly[[copper(II)-bis[μ-3-carboxy-5-[(imidazol-1-yl)methyl]benzoato]] dimethylformamide disolvate], {[Cu(C12H9N2O4)2]·2C3H7NO}n, (I), andcatena-poly[[copper(II)-bis[μ-3-carboxy-5-[(imidazol-1-yl)methyl]benzoato]] dimethylacetamide disolvate], {[Cu(C12H9N2O4)2]·2C4H9NO}n, (II), the formation of which are associated with mono-deprotonation of H2L. The two structures are isomorphous and isometric. They consist of one-dimensional coordination polymers of the organic ligand with CuIIin a 2:1 ratio, [Cu(μ-HL)2]n, crystallizing as the dimethylformamide (DMF) or dimethylacetamide (DMA) disolvates. The CuIIcations are characterized by a coordination number of six, being located on centres of crystallographic inversion. In the polymeric chains, each CuIIcation is linked to four neighbouring HL−ligands, and the organic ligand is coordinatedviaCu—O and Cu—N bonds to two CuIIcations. In the corresponding crystal structures of (I) and (II), the coordination chains, aligned parallel to thecaxis, are further interlinked by strong hydrogen bonds between the noncoordinated carboxy groups in one array and the coordinated carboxylate groups of neighbouring chains. Molecules of DMF and DMA (disordered) are accommodated at the interface between adjacent polymeric assemblies. This report provides the first structural evidence for the formation of coordination polymers with H2Lviamultiple metal–ligand bonds through both carboxylate and imidazole groups.

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Nururrozi, Alfarisa, Soedarmanto Indarjulianto, Yanuartono Yanuartono, Hary Purnamaningsih, Sitarina Widyarini, Slamet Raharjo, and Dhasia Ramandani. "Terapi Ammonium Khlorida-Asam Askorbat untuk Menurunkan Tingkat Keasaman Urin dan Kristalisasi Struvit pada Kucing Urolithiasis (THERAPY AMMONIUM CHLORIDE-ASCORBIC ACID FOR LOWERING URINE ACIDITY AND STRUVITE CRYSTALLIZATION IN FELINE UROLITHIASIS)." Jurnal Veteriner 20, no. 1 (May 24, 2019): 8. http://dx.doi.org/10.19087/jveteriner.2019.20.1.8.

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Struvite/Magnesium ammonium phosphate (MAP) is common causes of feline urolithiasis. Prevent the formation of MAP crystallization can be treated by adjusting the pH urine in acid conditions. Urine with an acid pH will decrease struvite activity product (SAP) by preventing the phosphate deprotonation process which is the main constituent of struvite components. This study aims to determine the potential of a combination of ammonium chloride (NH4Cl) and ascorbic acid to decrease SAP by retain the urine pH under normal conditions. Twelve male cats, 2-5 years old and body weight 3.0 ± 0.8 kg were diagnosed struvite urolithiasis used for this study. Cats have a9clinical history of hematuria, dysuria, polyuria, and stranguria. Diagnosis of urolithiasis performed by clinical examination, USG, x-rays, and urinalysis. Cats that found struvite urolith, treated with 200 mg/kg NH4Cl and 100 mg/kg ascorbic acid orally twice a day. The research objects were observed included urine pH and crystaluria density. The data were analyzed using analisis of varian. The result of this study showed NH4Cl and ascorbic acid treatment can decrease the urine pH at 8 cats (89%) with an average pH 6.3 ± 0.3. Microscopic examination of the urine showed the struvite crystallization more infrequently than before therapy. The study concluded that the combination of NH4Cl and asam askorbat can lower the urine pH and reduce struvite crystal density in the urine.

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Littel, R. J., G. F. Versteeg, and W. P. M. Van Swaaij. "Kinetics of CO2 with primary and secondary amines in aqueous solutions—I. Zwitterion deprotonation kinetics for DEA and DIPA in aqueous blends of alkanolamines." Chemical Engineering Science 47, no. 8 (June 1992): 2027–35. http://dx.doi.org/10.1016/0009-2509(92)80319-8.

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Perdana, Fitra, Karna Wijaya, and Ria Armunanto. "Studi Teoritis Senyawa Turunan Kalkon Hidroksi Sebagai Sensor Kimia Berbagai Anion." Jurnal Kimia Riset 3, no. 2 (March 4, 2019): 95. http://dx.doi.org/10.20473/jkr.v3i2.10425.

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AbstrakStudi secara teoritis telah dilakukan untuk mempelajari interaksi senyawa turunan kalkon hidroksi (CH) sebagai sensor kimia dengan anion F-, Cl-, Br-, CN-, CH3COO-, dan NO3-. Penelitian ini bertujuan untuk memodelkan struktur molekul senyawa turunan kalkon hidroksi (CH) dan sifat sensornya serta model interaksinya dengan anion dengan metode DFT. Hasil optimasi geometri menunjukkan terjadinya pemanjangan ikatan O-H sebesar 0,63-0,85 Å dengan adanya anion F-, CN-, and CH3COO-. Hal ini mengindikasikan terjadinya deprotonasi sensor kalkon hidroksi (CH) oleh anion. Sedangkan interaksi sensor kalkon hidroksi (CH) dengan anion Cl-, Br-, dan NO3- hanya berupa ikatan hidrogen dengan pemanjangan ikatan O-H sebesar 0,08-0,46 Å. Sensor kalkon hidroksi (CH) yang mengalami deprotonasi memiliki energi interaksi yang lebih besar yaitu -209,37 – -424,06 kJ/mol dibandingkan sensor yang hanya membentuk ikatan hidrogen yaitu -98,60 – -125,59 kJ/mol. Sensor yang mengalami deprotonasi mengakibatkan turunnya selisih energi HOMO-LUMO dari -3,94 – -4,06 eV menjadi -2,62 – -2,75 eV.Kata kunci: sensor kimia, kalkon hidroksi, anion, DFT AbstractTheoretical study had been carried out to investigate interaction between hydroxy chalcone derivatives (CH) as chemosensors with F-, Cl-, Br-, CN-, CH3COO-, and NO3- anions. This study was aimed to design molecular structures of chemosensor hydroxy chalcone (CH) properties for the anions and their interaction models with DFT method. The result of geometry optimization showed 0,63-0,85 Å O-H bond elongation of the hydroxy chalcone was occured by F-, CN-, and CH3COO-. It was indicated deprotonation of sensor hydroxy chalcone (CH) by anions. Where as the interaction of the hydroxy chalcone (CH) with Cl-, Br-, and NO3- just formed an hydrogen bond with 0,08-0,46 Å O-H bond elongation. Deprotonized sensor hydroxy chalcone (CH) had more energy change of interaction -209,37– -424,06 kJ/mol than sensor which just formed the hydrogen bond -98,60 – -125,59 kJ/mol. Deprotonized sensor caused reduction of the difference of HOMO-LUMO energy from - 3,94 – -4,06 eV to -2,62 – -2,75 eV.Keywords: chemosensor, hydroxy chalcone, anion, DFT

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Arnò, Barbara, Andrea Coletta, Cinzia Tesauro, Laura Zuccaro, Paola Fiorani, Sara Lentini, Pierluca Galloni, Valeria Conte, Barbara Floris, and Alessandro Desideri. "A small organic compound enhances the religation reaction of human topoisomerase I and identifies crucial elements for the religation mechanism." Bioscience Reports 33, no. 2 (March 7, 2013). http://dx.doi.org/10.1042/bsr20120118.

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The different steps of the human Top1 (topoisomerase I) catalytic cycle have been analysed in the presence of a pentacyclic-diquinoid synthetic compound. The experiments indicate that it efficiently inhibits the cleavage step of the enzyme reaction, fitting well into the catalytic site. Surprisingly the compound, when incubated with the binary topoisomerase–DNA cleaved complex, helps the enzyme to remove itself from the cleaved DNA and close the DNA gap, increasing the religation rate. The compound also induces the religation of the stalled enzyme–CPT (camptothecin)–DNA ternary complex. Analysis of the molecule docked over the binary complex, together with its chemical properties, suggests that the religation enhancement is due to the presence on the compound of two oxygen atoms that act as hydrogen acceptors. This property facilitates the deprotonation of the 5′ DNA end, suggesting that this is the limiting step in the topoisomerase religation mechanism.

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Rahmawati, Atik, and Sri Juari Santoso. "STUDI ADSORPSI LOGAM Pb(II) DAN Cd(II) PADA ASAM HUMAT DALAM MEDIUM AIR." ALCHEMY, May 13, 2013. http://dx.doi.org/10.18860/al.v0i0.2296.

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It had been conducted a study on adsorption of Cd (II) and Pb (II) of humic acid isolated from peat soil from village of Sambutan, the subdistrict of Samarinda Ilir, East Kalimantan. Aspects studied covered adsorption kinetics and adsorption isotherm of Cd (II) and Pb (II) of humic acid in water medium.Adsorption process carried out by batch method. Kinetics study conducted by intracting metal adsorption of Cd (II) and Pb (II) with humic acid at various times, meanwhile studying the adsorption isotherm is done by interacting Cd (II) and Pb (II) at various concentrations with humic acid.The results showed the adsorption rate of Cd (II) and Pb (II) on humic acid followed first order with rate constants of Cd (II) and Pb (II) of 0.0012 and 0.0038 mg menit-1/10 humic acid. Carboxylic groups of humic acid as the main groups which were actively involved in the interaction of metal-humic acid and have experienced deprotonation is hard nucleophile. It made Pb (II) was more quickly and easily adsorbed than Cd (II). Adsorption isotherm of Cd (II) and Pb (II) on humic acid followed the pattern of Langmuir isotherm with adsorption capacities of Pb (II) of 1.66 x10-3 mol / g and for Cd (II) 3.83 x10-3 mol / g . The adsorption energy of both metals is relatively small that is equal to 16.1 for Cd(II) and 21.4 kJ / mol for Pb(II).

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Journal articles on the topic 'DNA Deprotonation'

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