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Enzymatic and Chemical Synthesis of Nucleic Acid Derivatives


Enzymatic and Chemical Synthesis of Nucleic Acid Derivatives


1. Aufl.

von: Jesús Fernández Lucas, María-José Camarasa Rius

133,99 €

Verlag: Wiley-VCH
Format: PDF
Veröffentl.: 25.10.2018
ISBN/EAN: 9783527812073
Sprache: englisch
Anzahl Seiten: 352

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Beschreibungen

A review of innovative tools for creative nucleic acid chemists that open the door to novel probes and therapeutic agents <br> <br> Nucleic acids continue to gain importance as novel diagnostic and therapeutic agents. With contributions from noted scientists and scholars, Enzymatic and Chemical Synthesis of Nucleic Acid Derivatives is a practical reference that includes a wide range of approaches for the synthesis of designer nucleic acids and their derivatives. <br> <br> The book covers enzymatic (including chemo-enzymatic) methods, with a focus on the synthesis and incorporation of modified nucleosides. The authors also offer a review of innovative approaches for the non-enzymatic chemical synthesis of nucleic acids and their analogs and derivatives, highlighting especially challenging species. The book offers a concise review of the methods that prepare novel and heavily modified polynucleotides in sufficient amount and purity for most clinical and research applications. This important book: <br> <br> -Presents a timely and topical guide to the synthesis of designer nucleic acids and their derivatives <br> -Addresses the growing market for nucleotide-derived pharmaceuticals used as anti-infectives and chemotherapeutic agents, as well as fungicides and other agrochemicals. <br> -Covers novel methods and the most recent trends in the field <br> -Contains contributions from an international panel of noted scientistics <br> <br> Written for biochemists, medicinal chemists, natural products chemists, organic chemists, and biotechnologists, Enzymatic and Chemical Synthesis of Nucleic Acid Derivatives is a practice-oriented guide that reviews innovative methods for the enzymatic as well as non-enzymatic synthesis of nucleic acid species. <br>
<p>Preface xi</p> <p><b>1 Enzymatic Synthesis of Nucleoside Analogues by Nucleoside Phosphorylases </b><b>1<br /></b><i>Sarah Kamel, Heba Yehia, Peter Neubauer, and AnkeWagner</i></p> <p>1.1 Introduction 1</p> <p>1.1.1 Nucleosides and Nucleoside Analogues 1</p> <p>1.1.2 Enzymes Involved in the Enzymatic Synthesis of Nucleoside Analogues 3</p> <p>1.2 Nucleoside Phosphorylases 3</p> <p>1.2.1 Classification and Substrate Spectra of Nucleoside Phosphorylases 3</p> <p>1.2.1.1 Nucleoside Phosphorylase-I Family 4</p> <p>1.2.1.2 Nucleoside Phosphorylase-II Family 6</p> <p>1.2.2 Limitations in the Current Classification 7</p> <p>1.2.3 Reaction Mechanism 8</p> <p>1.2.4 Domain Structure and Active Site Residues of Nucleoside Phosphorylases 9</p> <p>1.2.4.1 NP-I Family Members 9</p> <p>1.2.4.2 NP-II FamilyMembers 10</p> <p>1.3 Enzymatic Approaches to Produce Nucleoside Analogues Using Nucleoside Phosphorylases 11</p> <p>1.3.1 One-pot Two-Step Transglycosylation Reaction 11</p> <p>1.3.2 Pentofuranose-1-phosphate as Universal Glycosylating Substrate for Nucleoside Phosphorylase (NP) 12</p> <p>1.3.2.1 Nucleoside Synthesis from Chemically Synthesized Pentose-1P 12</p> <p>1.3.2.2 Nucleosides Synthesis from d-Glyceraldehyde-3-phosphate 13</p> <p>1.3.2.3 Nucleoside Synthesis from d-Pentose 13</p> <p>1.3.2.4 Nucleoside Synthesis from Enzymatically Produced Pentose-1P 13</p> <p>1.4 Approaches to Produce Nucleoside Analogues 14</p> <p>1.4.1 Whole Cell Catalysis 14</p> <p>1.4.2 Crude Enzyme Extract 15</p> <p>1.4.3 Application of Purified Enzymes 15</p> <p>1.4.3.1 Immobilized Enzymes 16</p> <p>1.4.3.2 Enzyme Reactors 17</p> <p>1.5 Upscaling Approaches for the Production of Nucleoside Analogues 18</p> <p>1.6 Production of Pharmaceutically Active Compounds by Nucleoside Phosphorylases 18</p> <p>1.7 Outlook for the Application of Nucleoside Phosphorylase in the Production of Nucleoside Analogues 19</p> <p>References 20</p> <p><b>2 Enzymatic Phosphorylation of Nucleosides</b> <b>29</b><br /><i>Daniela Ubiali and Giovanna Speranza</i></p> <p>2.1 Introduction 29</p> <p>2.2 Nonspecific Acid Phosphatases (NSAPs) 30</p> <p>2.3 Deoxyribonucleoside Kinases (dNKs) 33</p> <p>2.4 Conclusion 37</p> <p>References 37</p> <p><b>3 Enzymatic Synthesis of Nucleic Acid Derivatives UsingWhole Cells </b><b>43<br /></b><i>Elizabeth S. Lewkowicz and AdolfoM. Iribarren</i></p> <p>3.1 Introduction 43</p> <p>3.2 Nucleoside Synthesis Mediated by Microbial Nucleoside Phosphorylases 45</p> <p>3.3 Nucleoside Analogues Synthesis by the Combined Action of Microbial Nucleoside Phosphorylases and Other Enzymes 48</p> <p>3.3.1 Nucleoside Phosphorylases Coupled to Deaminases 48</p> <p>3.3.2 Nucleoside Phosphorylases Coupled to Phosphopentomutase 48</p> <p>3.3.3 Nucleoside Phosphorylases Coupled to Phosphopentomutase and Other Enzymes 49</p> <p>3.3.4 Nucleoside Phosphorylases Coupled to Other Enzymes 51</p> <p>3.4 Chemoenzymatic Preparation of Nonconventional Nucleoside Analogues Involving Whole Cell Biocatalyzed Key Steps 51</p> <p>3.4.1 l-Nucleosides 52</p> <p>3.4.2 Carbocyclic Nucleosides 55</p> <p>3.4.3 C-Nucleosides 56</p> <p>3.5 Nucleoside Prodrugs Preparation by Whole Cell Systems 57</p> <p>3.5.1 Acylnucleosides 57</p> <p>3.5.2 Nucleoside Phosphates 59</p> <p>3.6 Other Nucleoside Derivatives 61</p> <p>3.6.1 NDP 61</p> <p>3.6.2 NDP-sugar 61</p> <p>3.7 Perspectives 65</p> <p>References 65</p> <p><b>4 Enzymatic Synthesis of Nucleic Acid Derivatives by Immobilized Cells </b><b>79<br /></b><i>Jorge A. Trelles, CintiaW. Rivero, Claudia N. Britos, and María J. Lapponi</i></p> <p>4.1 Introduction 79</p> <p>4.2 Nucleic Acid Derivatives 81</p> <p>4.3 Whole Cell Immobilization: Generalities 85</p> <p>4.4 Synthesis of Nucleosides by Immobilized Cells 86</p> <p>4.4.1 Natural Nucleoside Synthesis 87</p> <p>4.4.2 Nucleoside Analogues Synthesis 88</p> <p>4.4.3 Nucleoside Analogues Derivatives Synthesis 92</p> <p>4.5 Conclusion 98</p> <p>References 98</p> <p><b>5 Enzymatic Synthesis of Nucleic Acid Derivatives by Immobilized Enzymes </b><b>107<br /></b><i>Jesús Fernández-Lucas andMiguel Arroyo</i></p> <p>5.1 Introduction 107</p> <p>5.2 Immobilized Glycosyltransferases 108</p> <p>5.2.1 Immobilized Nucleoside Phosphorylases 108</p> <p>5.2.1.1 Stabilization of Nucleoside Phosphorylases by Immobilization 108</p> <p>5.2.1.2 Synthesis of Nucleosides Catalyzed by Immobilized Nucleoside Phosphorylases 109</p> <p>5.2.2 Immobilized Nucleoside 2′-Deoxyribosyltransferases 111</p> <p>5.2.2.1 Stabilization of Nucleoside 2′-Deoxyribosyltransferases by Immobilization 113</p> <p>5.2.2.2 Synthesis of Nucleosides Catalyzed by Immobilized</p> <p>2′-Deoxyribosyltransferases 114</p> <p>5.2.3 Immobilized Nucleobase Phosphoribosyltransferases 116</p> <p>5.3 Immobilized Nucleoside Oxidase 117</p> <p>5.4 Immobilized Hydrolases 118</p> <p>5.4.1 Immobilized Lipases 118</p> <p>5.4.2 Immobilized Proteases 120</p> <p>5.4.3 Immobilized Esterases 121</p> <p>5.4.4 Immobilized Deaminases 121</p> <p>5.4.5 Immobilized S-Adenosylhomocysteine Hydrolases 122</p> <p>5.5 Immobilized Phosphopentomutases 122</p> <p>5.6 Immobilized Deoxyribonucleoside Kinases 123</p> <p>References 124</p> <p><b>6 Synthesis of Nucleic Acid Derivatives by Multi-Enzymatic Systems </b><b>129<br /></b><i>Qingbao Ding</i></p> <p>6.1 Multi-Enzymatic Systems in Biosynthesis 129</p> <p>6.2 General Overview of Multi-Enzymatic Synthesis of Nucleic Acid</p> <p>Derivatives 131</p> <p>6.3 Multi-Enzymatic Synthesis of Nucleosides and Their Derivatives 132</p> <p>6.3.1 Multi-Enzymatic Synthesis of Nucleosides and Their Analogues by</p> <p>Nucleoside Phosphorylase 132</p> <p>6.3.2 Transglycosylation Coupled with Xanthine Oxidase 134</p> <p>6.3.3 Transglycosylation Reactions Coupled with Deamination 135</p> <p>6.3.4 ADase in Combination with Lipase 136</p> <p>6.3.5 Esterification of Nucleosides 138</p> <p>6.3.6 Multi-Enzymatic Synthesis of Fluorine Nucleosides 140</p> <p>6.3.7 Multi-Enzymatic Synthesis of Nucleosides via R5P 142</p> <p>6.3.8 Other Reactions 144</p> <p>6.4 Multi-Enzymatic Synthesis of Nucleotides and Their Derivatives 145</p> <p>6.4.1 Multi-Enzymatic Synthesis of NMPs and dNMPs 146</p> <p>6.4.2 Multi-Enzymatic Synthesis of NTPs and dNTPs 147</p> <p>6.4.3 Multi-Enzymatic Synthesis of NDP-Sugars and Other NDP</p> <p>Derivatives 148</p> <p>6.5 Conclusion 150</p> <p>References 151</p> <p><b>7 Enzymatic Synthesis Using Polymerases of Modified Nucleic Acids and Genes </b>159<br /><i>Elena Eremeeva and Piet Herdewijn</i></p> <p>7.1 Introduction 159</p> <p>7.2 Types of XNA Biomolecules 161</p> <p>7.3 Enzymatic Synthesis of XNA and DNA Polymerases 161</p> <p>7.4 Base-Modified XNAs (Base-XNAs) 167</p> <p>7.4.1 Nucleobase Analogues 167</p> <p>7.4.1.1 Non-Canonical Nucleotides 167</p> <p>7.4.1.2 Amino-acid-Like Groups 174</p> <p>7.4.1.3 Functional Tags 176</p> <p>7.4.2 Unnatural Base Pairs 177</p> <p>7.4.2.1 Hydrogen-Bonding Base Pairs 177</p> <p>7.4.2.2 Hydrophobic Base Pairs 179</p> <p>7.5 Sugar-Modified XNAs (Sugar-XNAs) 180</p> <p>7.5.1 Pentose-XNA 180</p> <p>7.5.2 2′-Ribose-XNA 182</p> <p>7.6 Phosphodiester Backbone-XNA 183</p> <p>7.7 A Mirror-Image l-DNA 184</p> <p>7.8 Conclusions 184</p> <p>References 185</p> <p><b>8 Synthetic Approaches to the Fleximer Class of Nucleosides – A Historic Perspective </b>195<br /><i>Therese C. Ku and Katherine Seley-Radtke</i></p> <p>8.1 Distal Fleximers 198</p> <p>8.1.1 Ribose Distal Fleximers 198</p> <p>8.1.2 2′-Deoxyribose Distal Fleximers 201</p> <p>8.1.3 2′-Modified Distal Fleximers 209</p> <p>8.2 Proximal Fleximers 209</p> <p>8.2.1 Ribose Proximal Fleximers 209</p> <p>8.2.2 2′-Deoxyribose Proximal Fleximers 215</p> <p>8.2.3 Carbocyclic Proximal Fleximers 216</p> <p>8.2.4 Proximal Fleximers from Other Groups 218</p> <p>8.3 “Reverse” Fleximers 222</p> <p>8.4 Acyclic Fleximers 226</p> <p>8.5 Conclusion 228</p> <p>References 229</p> <p><b>9 Synthesis of Oligonucleotides Carrying Nucleic Acid Derivatives of Biomedical and Structural Interest </b>237<br /><i>Ramon Eritja, Anna Aviñó, Carme Fàbrega, Adele Alagia, Andreia F. Jorge, and</i></p> <p>Santiago Grijalvo</p> <p>9.1 Introduction 237</p> <p>9.2 Oligonucleotides Carrying the DNA Lesion O6-Alkylguanine 238</p> <p>9.3 The Effect of Chemical Modifications in Non-Canonical DNA</p> <p>Structures 240</p> <p>9.3.1 Triplex-Forming Oligonucleotides 241</p> <p>9.3.2 G-quadruplex-Forming Oligonucleotides 243</p> <p>9.3.3 Oligonucleotides Forming i-Motif Structures 245</p> <p>9.4 Modified siRNAs for Gene Silencing 246</p> <p>9.4.1 Modifications of the 3′-Overhangs 246</p> <p>9.4.2 Modifications of the 5′-End 249</p> <p>References 251</p> <p><b>10 Synthesis of Carbohydrate–Oligonucleotide Conjugates and Their Applications </b>259<br /><i>Juan C. Morales</i></p> <p>10.1 Introduction 259</p> <p>10.2 Synthesis of COCs 260</p> <p>10.2.1 On-Support Synthesis 260</p> <p>10.2.1.1 Phosphoramidite Chemistry 261</p> <p>10.2.1.2 Derivatization of Nucleoside Base Residues 261</p> <p>10.2.1.3 Oximation Chemistry 263</p> <p>10.2.1.4 Amide Chemistry 263</p> <p>10.2.1.5 Urea Chemistry 264</p> <p>10.2.1.6 CuAAC Chemistry 264</p> <p>10.2.2 Solution-Phase Conjugation 265</p> <p>10.2.2.1 Disulfide Formation 265</p> <p>10.2.2.2 Nucleophilic Addition on Unsaturated Carbon 265</p> <p>10.2.2.3 Carbonyl Addition–Elimination Reaction 267</p> <p>10.2.2.4 CuAAC Chemistry 267</p> <p>10.2.2.5 Diazocoupling Reaction 267</p> <p>10.2.2.6 Amide Bond Formation 267</p> <p>10.2.2.7 Enzymatic Incorporation of Saccharides or Nucleotides 268</p> <p>10.3 Synthesis of Glycocluster Oligonucleotides 268</p> <p>10.3.1 dsDNA Scaffolds 269</p> <p>10.3.2 Non-Canonical DNA Scaffolds (G4 and three-Way Junction) 269</p> <p>10.3.3 Organic Spacer Scaffolds 270</p> <p>10.3.4 Biomolecules as Scaffolds 271</p> <p>10.4 Applications of COCs 273</p> <p>10.4.1 Improving Cellular Uptake 273</p> <p>10.4.2 Molecular Interactions Probes 279</p> <p>10.4.3 Lectin Binding and Glycoarrays 280</p> <p>10.5 Outlook 281</p> <p>References 281</p> <p><b>11 Advances in Light-Directed Synthesis of High-Density Microarrays and Extension to RNA and 2</b><b>′</b><b>F-ANA Chemistries </b><b>291<br /></b><i>Jory Lietard,Masad J. Damha, andMarkM. Somoza</i></p> <p>11.1 Introduction 291</p> <p>11.2 Phosphoramidite Chemistry Applied to the Photolithographic</p> <p>Synthesis of Microarrays 293</p> <p>11.3 Recent Improvements in the Synthesis of DNA Microarrays 295</p> <p>11.4 Synthesis of RNA Microarrays 300</p> <p>11.5 Enzymatic Approaches to RNA Array Synthesis 305</p> <p>11.6 Synthesis of 2′F-ANA Microarrays 306</p> <p>11.7 Conclusion and Outlook 309</p> <p>References 310</p> <p><b>12 SAMHD1-Mediated Negative Regulation of Cellular dNTP Levels: HIV-1, Innate Immunity, and Cancers </b><b>313<br /></b><i>TatsuyaMaehigashi, Dong-Hyun Kim, Raymond F. Schinazi, and Baek Kim</i></p> <p>12.1 Cellular dNTP Concentrations 313</p> <p>12.2 SAMHD1 and Negative Regulation of Cellular dNTPs 314</p> <p>12.3 SAMHD1 Substrates, Activators, and Inhibitors 316</p> <p>12.4 SAMHD1 and HIV-1 Reverse Transcription 318</p> <p>12.5 SAMHD1 Mutations and Innate Immunity 318</p> <p>12.6 SAMHD1 and Cancers 321</p> <p>12.7 Summary 321</p> <p>Acknowledgment 322</p> <p>References 322</p> <p>Index 327</p>
<p><b><i>Jesús Fernández-Lucas, PhD,</i></b><i> is a tenured professor at the European University of Madrid, where he leads the Applied Biotechnology research group. His research is focused on the design and application of novel biocatalysts for the enzymatic synthesis of nucleosides.</i> <p><b><i>María José Camarasa Rius, PhD,</i></b><i> is Full Professor at the Medicinal Chemistry Institute of the Spanish National Research Council (IQM-CSIC) in Madrid, working on the design of novel enzymatic inhibitors with potential anticancer, antifungal and antiviral activity.</i>
<p><b>A review of innovative tools for creative nucleic acid chemists that open the door to novel probes and therapeutic agents</b> <p><b>N</b>ucleic acids continue to gain importance as novel diagnostic and therapeutic agents. With contributions from noted scientists and scholars, <i>Enzymatic and Chemical Synthesis of Nucleic Acid Derivatives</i> is a practical reference that includes a wide range of approaches for the synthesis of designer nucleic acids and their derivatives. <p>The book covers enzymatic (including chemo-enzymatic) methods, with a focus on the synthesis and incorporation of modified nucleosides. The authors also offer a review of innovative approaches for the non-enzymatic chemical synthesis of nucleic acids and their analogs and derivatives, highlighting especially challenging species. The book offers a concise review of the methods that prepare novel and heavily modified polynucleotides in sufficient amount and purity for most clinical and research applications. This important book: <ul> <li>Presents a timely and topical guide to the synthesis of designer nucleic acids and their derivatives</li> <li>Addresses the growing market for nucleotide-derived pharmaceuticals used as anti-infectives and chemotherapeutic agents, as well as fungicides and other agrochemicals.</li> <li>Covers novel methods and the most recent trends in the field</li> <li>Contains contributions from an international panel of noted scientistics</li> </ul> <p>Written for biochemists, medicinal chemists, natural products chemists, organic chemists, and biotechnologists,<i> Enzymatic and Chemical Synthesis of Nucleic Acid Derivatives</i> is a practice-oriented guide that reviews innovative methods for the enzymatic as well as non-enzymatic synthesis of nucleic acid species.

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