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Relevant bibliographies by topics / DNA Deprotonation

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Academic literature on the topic 'DNA Deprotonation'

Author: Grafiati

Published: 25 June 2021

Last updated: 17 February 2022

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Journal articles on the topic "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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2

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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3

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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5

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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6

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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7

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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Dissertations / Theses on the topic "DNA Deprotonation"

1

DiLillo, Ana M. ""Noncovalent Complexation of Single-Wall Carbon Nanotubes with Biopolymers: Dispersion, Purification, and Protein Interactions"." Cleveland State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=csu1624461866858216.

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