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Chemistry and biology of non-canonical nucleic acids / / Naoki Sugimoto
Chemistry and biology of non-canonical nucleic acids / / Naoki Sugimoto
Autore Sugimoto N (Naoki)
Pubbl/distr/stampa Weinheim, Germany : , : Wiley-VCH, , [2021]
Descrizione fisica 1 online resource (xii, 276 pages) : illustrations
Disciplina 574.87328
Soggetto topico Nucleic acids
Soggetto genere / forma Electronic books.
ISBN 3-527-81786-7
3-527-81788-3
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto Cover -- Title Page -- Copyright -- Contents -- Preface -- Chapter 1 History for Canonical and Non‐canonical Structures of Nucleic Acids -- 1.1 Introduction -- 1.2 History of Duplex -- 1.3 Non‐Watson-Crick Base Pair -- 1.4 Nucleic Acid Structures Including Non‐Watson-Crick Base Pairs -- 1.5 Perspective of the Research for Non‐canonical Nucleic Acid Structures -- 1.6 Conclusion and Perspective -- References -- Chapter 2 Structures of Nucleic Acids Now -- 2.1 Introduction -- 2.2 Unusual Base Pairs in a Duplex -- 2.2.1 Hoogsteen Base Pair -- 2.2.2 Purine-Pyrimidine Mismatches -- 2.2.3 Purine-Purine Mismatches -- 2.2.4 Pyrimidine-Pyrimidine Mismatches -- 2.3 Non‐canonical Backbone Shapes in DNA Duplex -- 2.4 Branched DNA with Junction -- 2.5 Multi‐stranded DNA Helices -- 2.6 Structures in RNA -- 2.6.1 Basic Structure Distinctions of RNA -- 2.6.2 Elements in RNA Secondary Structures -- 2.6.2.1 Hairpin Loop -- 2.6.2.2 Bulge Loop -- 2.6.2.3 Internal Loop -- 2.6.3 Elements in Tertiary Interactions of RNA -- 2.6.3.1 A‐Minor Interactions -- 2.6.3.2 Ribose Zipper -- 2.6.3.3 T‐Loop Motif -- 2.6.3.4 Kissing‐Loop Interaction -- 2.6.3.5 GNRA Tetraloop Receptor Interaction -- 2.6.3.6 Pseudoknot Crosslinking Distant Stem Regions -- 2.7 Conclusion -- References -- Chapter 3 Stability of Non‐canonical Nucleic Acids -- 3.1 Introduction -- 3.2 Factors Influencing Stabilities of the Canonical Duplexes -- 3.2.1 Hydrogen Bond Formations -- 3.2.2 Stacking Interactions -- 3.2.3 Conformational Entropy -- 3.3 Thermodynamic Analysis for the Formation of Duplex -- 3.4 Factors Influencing Stabilities of the Non‐canonical Nucleic Acids -- 3.4.1 Factors Influencing Stability of Triplexes -- 3.4.2 Factors Influencing Stability of Quadruplex -- 3.4.2.1 G‐Quadruplexes -- 3.4.2.2 i‐Motif -- 3.5 Thermodynamic Analysis for the Non‐canonical Nucleic Acids.
3.5.1 Thermodynamic Analysis for the Intramolecular Triplex and Tetraplex -- 3.5.2 Thermodynamic Analysis for the Intermolecular Triplex -- 3.5.3 Thermodynamic Analysis for the Tetraplex -- 3.6 Conclusion -- References -- Chapter 4 Physicochemical Properties of Non‐canonical Nucleic Acids -- 4.1 Introduction -- 4.2 Spectroscopic Properties of Non‐canonical Nucleic Acids -- 4.2.1 Effect of Non‐canonical Structure on UV Absorption -- 4.2.2 Circular Dichroism of Non‐canonical Nucleic Acids -- 4.2.3 NMR Spectroscopy -- 4.2.4 Other Spectroscopic Characteristics of Non‐canonical Nucleic Acids -- 4.3 Chemical Interactions on Non‐canonical Nucleic Acids -- 4.3.1 Hydration -- 4.3.2 Cation Binding -- 4.3.3 pH Effect -- 4.3.4 Chemical Modification -- 4.4 Chemical Platform on the Non‐canonical Structures -- 4.4.1 Specificity of a Ligand to Non‐canonical Structures -- 4.4.2 Fluorescence Platform of Non‐canonical Structures -- 4.4.3 Interface Between Proteins and Nucleic Acids -- 4.5 Physicochemical Property of Non‐canonical Nucleic Acids in Cell -- 4.5.1 Molecular Crowding Condition that Reflects Cellular Environments -- 4.5.2 Effects of Crowding Reagents on Non‐canonical Nucleic Acid Structures -- 4.5.3 Quantification of Physical Properties of Non‐canonical Structures in Crowding Condition -- 4.5.4 Non‐canonical Structures Under Mimicking Organelle Environment -- 4.5.5 Insight for the Formation of Non‐canonical Nucleic Acids in Cells -- 4.6 Conclusion -- References -- Chapter 5 Telomere -- 5.1 Introduction -- 5.2 Structural Properties of Telomere -- 5.2.1 Structures of Telomere -- 5.2.2 Structural Properties of Human Telomeric G4s -- 5.2.3 Structure of Repeats of Human Telomeric G4s -- 5.3 Biological Relevance of Telomere G4 -- 5.3.1 Telomerase Activity -- 5.3.2 Telomerase Repeated Amplification Protocol (TRAP) Assay.
5.3.3 Alternative Lengthening of Telomere (ALT) Mechanism -- 5.4 Other Non‐canonical Structures Related to Telomere Region -- 5.4.1 Telomere i‐Motif -- 5.4.2 Telomere RNA -- 5.5 Conclusion -- References -- Chapter 6 Transcription -- 6.1 Introduction -- 6.2 Transcription Process -- 6.2.1 Transcription Initiation -- 6.2.2 Transcription Elongation -- 6.2.3 Transcription Termination -- 6.3 Transcription Process Perturbed by Certain Sequences of DNA and RNA -- 6.4 Transcription Process Perturbed by Non‐canonical Structures of DNA and RNA -- 6.5 Conclusion -- References -- Chapter 7 Translation -- 7.1 Introduction -- 7.2 RNAs Involved in Translation Machinery -- 7.3 General Process of Translation -- 7.3.1 Translation Initiation -- 7.3.2 Translation Elongation -- 7.3.3 Translation Termination -- 7.4 RNA Structures Affecting Translation Reaction -- 7.4.1 Modulation of Translation Initiation in Prokaryotes -- 7.4.2 Modulation of Translation Initiation in Eukaryotes -- 7.4.3 RNA Structures Affecting Translation Elongation -- 7.4.4 RNA Structures Affecting Translation Termination -- 7.5 Conclusion -- References -- Chapter 8 Replication -- 8.1 Introduction -- 8.2 Replication Machineries -- 8.3 Replication Initiation -- 8.3.1 Mechanism of Activation of Replication Origins -- 8.3.2 Activation Control of Origins by G4s -- 8.3.3 Control of Timing of Replication Initiation by G4s -- 8.4 DNA Strand Elongation -- 8.4.1 Mechanism of DNA Strand Elongation -- 8.4.2 Impact of G4 and i‐Motif Formations on DNA Strand Synthesis -- 8.4.3 Relationship Between G4 and Epigenetic Modification -- 8.4.4 Expansion and Contraction of Replicating Strand Induced by Hairpin Structures -- 8.5 Termination of Replication -- 8.6 Chemistry of the Replication and Its Regulation -- 8.6.1 Cellular Environments -- 8.6.2 Control of Replication by Chemical Compounds -- 8.7 Conclusion -- References.
Chapter 9 Helicase -- 9.1 Introduction -- 9.2 Function and Structure of Helicases -- 9.3 Unwinding of Non‐canonical DNA Structures by Helicases -- 9.4 G4 Helicases in Gene Expressions -- 9.5 G4 Helicases in Replication -- 9.6 G4 Helicases in Telomere Maintenance -- 9.7 Relation to Diseases by Loss of G4 Helicases -- 9.8 Insight into Specific Properties of Activities of G4 Helicase Under Cellular Conditions -- 9.9 Conclusion -- References -- Chapter 10 Dynamic Regulation of Biosystems by Nucleic Acids with Non‐canonical Structures -- 10.1 Introduction -- 10.2 Time Scale of Biological Reactions -- 10.2.1 Cell Cycle -- 10.2.2 Central Dogma -- 10.2.3 Dynamic Structures of Nucleic Acids -- 10.3 Processes in the Central Dogma Affected by Dynamics of Nucleic Acid Structures -- 10.3.1 Epigenetic Regulation Caused by Chemical Modification of DNA -- 10.3.2 Co‐transcriptional Formation of Metastable RNA Structures -- 10.3.3 Co‐transcriptional Translation and Transcription Attenuation -- 10.3.4 Co‐transcriptional Ligand Binding and Gene Regulation -- 10.3.5 Translation Elongation and Co‐translational Protein Folding -- 10.4 Conclusion -- References -- Chapter 11 Cancer and Nucleic Acid Structures -- 11.1 Introduction -- 11.2 Detail Mechanism of Cancer -- 11.2.1 Cancer Incidence -- 11.2.2 The Relationship Between Genes and Cancer -- 11.3 Non‐canonical Structures of Nucleic Acids in Cancer Cells -- 11.3.1 Structural Characteristics of Nucleic Acids in Cancer Cells -- 11.3.2 Non‐canonical Structures Perturb Gene Expression of Cancer‐Related Genes -- 11.4 Roles of Non‐canonical Structures of Nucleic Acids in Cancer Cells -- 11.4.1 Monitoring of Non‐canonical Structures in Cancer Cells -- 11.4.2 Regulation of Gene Expressions by the Non‐canonical Structures in Cancer Cells -- 11.5 Conclusion -- References.
Chapter 12 Neurodegenerative Diseases and Nucleic Acid Structures -- 12.1 Introduction -- 12.2 Protein Aggregation‐Induced Neurodegenerative Diseases -- 12.3 DNA Shows Key Role for Neurodegenerative Diseases -- 12.4 RNA Toxic Plays a Key Role for Neurological Diseases -- 12.5 Conclusion -- References -- Chapter 13 Therapeutic Applications -- 13.1 Introduction -- 13.2 Oligonucleotide Therapeutics -- 13.2.1 Antisense Oligonucleotide -- 13.2.2 Functions of Antisense Oligonucleotide Therapeutics -- 13.2.3 Chemical Modifications in Therapeutic Oligonucleotides -- 13.2.3.1 Backbone Modified Oligonucleotides -- 13.2.3.2 Ribose Modified Oligonucleotides -- 13.2.3.3 Oligonucleotides with Unnatural Backbone -- 13.2.4 Oligonucleotide Therapeutics Other Than Antisense Oligonucleotide -- 13.2.4.1 Oligonucleotide Therapeutics Functioning Through RNA Interference -- 13.2.4.2 Oligonucleotide Therapeutics Functioning Through Binding to Protein -- 13.3 Non‐canonical Nucleic Acid Structures as Therapeutic Targets -- 13.3.1 Traditional Antibiotics Targeting Structured Region of RNAs -- 13.3.2 Strategies for Constructing Therapeutic Materials Targeting Structured Nucleic Acids -- 13.4 Non‐canonical Nucleic Acid Materials for Inducing Non‐canonical Structures -- 13.5 Conclusion -- References -- Chapter 14 Materials Science and Nanotechnology of Nucleic Acids -- 14.1 Introduction -- 14.2 Non‐canonical Structure‐Based Nanomaterials Resembling Protein Functions -- 14.2.1 Aptamer -- 14.2.2 DNAzyme -- 14.2.3 Ion Channel -- 14.3 Protein Engineering Using G4‐Binding Protein -- 14.4 Regulation of Gene Expression by G4‐Inducing Materials -- 14.5 Environmental Sensing -- 14.5.1 Sensing Temperature in Cells -- 14.5.2 Sensing pH in Cells -- 14.5.3 Sensing K+ Ion in Cells -- 14.5.4 Sensing Crowding Condition in Cells -- 14.6 Conclusion -- References.
Chapter 15 Future Outlook for Chemistry and Biology of Non‐canonical Nucleic Acids.
Record Nr. UNINA-9910555058803321
Sugimoto N (Naoki)  
Weinheim, Germany : , : Wiley-VCH, , [2021]
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui
Chemistry and biology of non-canonical nucleic acids / / Naoki Sugimoto
Chemistry and biology of non-canonical nucleic acids / / Naoki Sugimoto
Autore Sugimoto N (Naoki)
Pubbl/distr/stampa Weinheim, Germany : , : Wiley-VCH, , [2021]
Descrizione fisica 1 online resource (xii, 276 pages) : illustrations
Disciplina 574.87328
Soggetto topico Nucleic acids
ISBN 3-527-81786-7
3-527-81788-3
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto Cover -- Title Page -- Copyright -- Contents -- Preface -- Chapter 1 History for Canonical and Non‐canonical Structures of Nucleic Acids -- 1.1 Introduction -- 1.2 History of Duplex -- 1.3 Non‐Watson-Crick Base Pair -- 1.4 Nucleic Acid Structures Including Non‐Watson-Crick Base Pairs -- 1.5 Perspective of the Research for Non‐canonical Nucleic Acid Structures -- 1.6 Conclusion and Perspective -- References -- Chapter 2 Structures of Nucleic Acids Now -- 2.1 Introduction -- 2.2 Unusual Base Pairs in a Duplex -- 2.2.1 Hoogsteen Base Pair -- 2.2.2 Purine-Pyrimidine Mismatches -- 2.2.3 Purine-Purine Mismatches -- 2.2.4 Pyrimidine-Pyrimidine Mismatches -- 2.3 Non‐canonical Backbone Shapes in DNA Duplex -- 2.4 Branched DNA with Junction -- 2.5 Multi‐stranded DNA Helices -- 2.6 Structures in RNA -- 2.6.1 Basic Structure Distinctions of RNA -- 2.6.2 Elements in RNA Secondary Structures -- 2.6.2.1 Hairpin Loop -- 2.6.2.2 Bulge Loop -- 2.6.2.3 Internal Loop -- 2.6.3 Elements in Tertiary Interactions of RNA -- 2.6.3.1 A‐Minor Interactions -- 2.6.3.2 Ribose Zipper -- 2.6.3.3 T‐Loop Motif -- 2.6.3.4 Kissing‐Loop Interaction -- 2.6.3.5 GNRA Tetraloop Receptor Interaction -- 2.6.3.6 Pseudoknot Crosslinking Distant Stem Regions -- 2.7 Conclusion -- References -- Chapter 3 Stability of Non‐canonical Nucleic Acids -- 3.1 Introduction -- 3.2 Factors Influencing Stabilities of the Canonical Duplexes -- 3.2.1 Hydrogen Bond Formations -- 3.2.2 Stacking Interactions -- 3.2.3 Conformational Entropy -- 3.3 Thermodynamic Analysis for the Formation of Duplex -- 3.4 Factors Influencing Stabilities of the Non‐canonical Nucleic Acids -- 3.4.1 Factors Influencing Stability of Triplexes -- 3.4.2 Factors Influencing Stability of Quadruplex -- 3.4.2.1 G‐Quadruplexes -- 3.4.2.2 i‐Motif -- 3.5 Thermodynamic Analysis for the Non‐canonical Nucleic Acids.
3.5.1 Thermodynamic Analysis for the Intramolecular Triplex and Tetraplex -- 3.5.2 Thermodynamic Analysis for the Intermolecular Triplex -- 3.5.3 Thermodynamic Analysis for the Tetraplex -- 3.6 Conclusion -- References -- Chapter 4 Physicochemical Properties of Non‐canonical Nucleic Acids -- 4.1 Introduction -- 4.2 Spectroscopic Properties of Non‐canonical Nucleic Acids -- 4.2.1 Effect of Non‐canonical Structure on UV Absorption -- 4.2.2 Circular Dichroism of Non‐canonical Nucleic Acids -- 4.2.3 NMR Spectroscopy -- 4.2.4 Other Spectroscopic Characteristics of Non‐canonical Nucleic Acids -- 4.3 Chemical Interactions on Non‐canonical Nucleic Acids -- 4.3.1 Hydration -- 4.3.2 Cation Binding -- 4.3.3 pH Effect -- 4.3.4 Chemical Modification -- 4.4 Chemical Platform on the Non‐canonical Structures -- 4.4.1 Specificity of a Ligand to Non‐canonical Structures -- 4.4.2 Fluorescence Platform of Non‐canonical Structures -- 4.4.3 Interface Between Proteins and Nucleic Acids -- 4.5 Physicochemical Property of Non‐canonical Nucleic Acids in Cell -- 4.5.1 Molecular Crowding Condition that Reflects Cellular Environments -- 4.5.2 Effects of Crowding Reagents on Non‐canonical Nucleic Acid Structures -- 4.5.3 Quantification of Physical Properties of Non‐canonical Structures in Crowding Condition -- 4.5.4 Non‐canonical Structures Under Mimicking Organelle Environment -- 4.5.5 Insight for the Formation of Non‐canonical Nucleic Acids in Cells -- 4.6 Conclusion -- References -- Chapter 5 Telomere -- 5.1 Introduction -- 5.2 Structural Properties of Telomere -- 5.2.1 Structures of Telomere -- 5.2.2 Structural Properties of Human Telomeric G4s -- 5.2.3 Structure of Repeats of Human Telomeric G4s -- 5.3 Biological Relevance of Telomere G4 -- 5.3.1 Telomerase Activity -- 5.3.2 Telomerase Repeated Amplification Protocol (TRAP) Assay.
5.3.3 Alternative Lengthening of Telomere (ALT) Mechanism -- 5.4 Other Non‐canonical Structures Related to Telomere Region -- 5.4.1 Telomere i‐Motif -- 5.4.2 Telomere RNA -- 5.5 Conclusion -- References -- Chapter 6 Transcription -- 6.1 Introduction -- 6.2 Transcription Process -- 6.2.1 Transcription Initiation -- 6.2.2 Transcription Elongation -- 6.2.3 Transcription Termination -- 6.3 Transcription Process Perturbed by Certain Sequences of DNA and RNA -- 6.4 Transcription Process Perturbed by Non‐canonical Structures of DNA and RNA -- 6.5 Conclusion -- References -- Chapter 7 Translation -- 7.1 Introduction -- 7.2 RNAs Involved in Translation Machinery -- 7.3 General Process of Translation -- 7.3.1 Translation Initiation -- 7.3.2 Translation Elongation -- 7.3.3 Translation Termination -- 7.4 RNA Structures Affecting Translation Reaction -- 7.4.1 Modulation of Translation Initiation in Prokaryotes -- 7.4.2 Modulation of Translation Initiation in Eukaryotes -- 7.4.3 RNA Structures Affecting Translation Elongation -- 7.4.4 RNA Structures Affecting Translation Termination -- 7.5 Conclusion -- References -- Chapter 8 Replication -- 8.1 Introduction -- 8.2 Replication Machineries -- 8.3 Replication Initiation -- 8.3.1 Mechanism of Activation of Replication Origins -- 8.3.2 Activation Control of Origins by G4s -- 8.3.3 Control of Timing of Replication Initiation by G4s -- 8.4 DNA Strand Elongation -- 8.4.1 Mechanism of DNA Strand Elongation -- 8.4.2 Impact of G4 and i‐Motif Formations on DNA Strand Synthesis -- 8.4.3 Relationship Between G4 and Epigenetic Modification -- 8.4.4 Expansion and Contraction of Replicating Strand Induced by Hairpin Structures -- 8.5 Termination of Replication -- 8.6 Chemistry of the Replication and Its Regulation -- 8.6.1 Cellular Environments -- 8.6.2 Control of Replication by Chemical Compounds -- 8.7 Conclusion -- References.
Chapter 9 Helicase -- 9.1 Introduction -- 9.2 Function and Structure of Helicases -- 9.3 Unwinding of Non‐canonical DNA Structures by Helicases -- 9.4 G4 Helicases in Gene Expressions -- 9.5 G4 Helicases in Replication -- 9.6 G4 Helicases in Telomere Maintenance -- 9.7 Relation to Diseases by Loss of G4 Helicases -- 9.8 Insight into Specific Properties of Activities of G4 Helicase Under Cellular Conditions -- 9.9 Conclusion -- References -- Chapter 10 Dynamic Regulation of Biosystems by Nucleic Acids with Non‐canonical Structures -- 10.1 Introduction -- 10.2 Time Scale of Biological Reactions -- 10.2.1 Cell Cycle -- 10.2.2 Central Dogma -- 10.2.3 Dynamic Structures of Nucleic Acids -- 10.3 Processes in the Central Dogma Affected by Dynamics of Nucleic Acid Structures -- 10.3.1 Epigenetic Regulation Caused by Chemical Modification of DNA -- 10.3.2 Co‐transcriptional Formation of Metastable RNA Structures -- 10.3.3 Co‐transcriptional Translation and Transcription Attenuation -- 10.3.4 Co‐transcriptional Ligand Binding and Gene Regulation -- 10.3.5 Translation Elongation and Co‐translational Protein Folding -- 10.4 Conclusion -- References -- Chapter 11 Cancer and Nucleic Acid Structures -- 11.1 Introduction -- 11.2 Detail Mechanism of Cancer -- 11.2.1 Cancer Incidence -- 11.2.2 The Relationship Between Genes and Cancer -- 11.3 Non‐canonical Structures of Nucleic Acids in Cancer Cells -- 11.3.1 Structural Characteristics of Nucleic Acids in Cancer Cells -- 11.3.2 Non‐canonical Structures Perturb Gene Expression of Cancer‐Related Genes -- 11.4 Roles of Non‐canonical Structures of Nucleic Acids in Cancer Cells -- 11.4.1 Monitoring of Non‐canonical Structures in Cancer Cells -- 11.4.2 Regulation of Gene Expressions by the Non‐canonical Structures in Cancer Cells -- 11.5 Conclusion -- References.
Chapter 12 Neurodegenerative Diseases and Nucleic Acid Structures -- 12.1 Introduction -- 12.2 Protein Aggregation‐Induced Neurodegenerative Diseases -- 12.3 DNA Shows Key Role for Neurodegenerative Diseases -- 12.4 RNA Toxic Plays a Key Role for Neurological Diseases -- 12.5 Conclusion -- References -- Chapter 13 Therapeutic Applications -- 13.1 Introduction -- 13.2 Oligonucleotide Therapeutics -- 13.2.1 Antisense Oligonucleotide -- 13.2.2 Functions of Antisense Oligonucleotide Therapeutics -- 13.2.3 Chemical Modifications in Therapeutic Oligonucleotides -- 13.2.3.1 Backbone Modified Oligonucleotides -- 13.2.3.2 Ribose Modified Oligonucleotides -- 13.2.3.3 Oligonucleotides with Unnatural Backbone -- 13.2.4 Oligonucleotide Therapeutics Other Than Antisense Oligonucleotide -- 13.2.4.1 Oligonucleotide Therapeutics Functioning Through RNA Interference -- 13.2.4.2 Oligonucleotide Therapeutics Functioning Through Binding to Protein -- 13.3 Non‐canonical Nucleic Acid Structures as Therapeutic Targets -- 13.3.1 Traditional Antibiotics Targeting Structured Region of RNAs -- 13.3.2 Strategies for Constructing Therapeutic Materials Targeting Structured Nucleic Acids -- 13.4 Non‐canonical Nucleic Acid Materials for Inducing Non‐canonical Structures -- 13.5 Conclusion -- References -- Chapter 14 Materials Science and Nanotechnology of Nucleic Acids -- 14.1 Introduction -- 14.2 Non‐canonical Structure‐Based Nanomaterials Resembling Protein Functions -- 14.2.1 Aptamer -- 14.2.2 DNAzyme -- 14.2.3 Ion Channel -- 14.3 Protein Engineering Using G4‐Binding Protein -- 14.4 Regulation of Gene Expression by G4‐Inducing Materials -- 14.5 Environmental Sensing -- 14.5.1 Sensing Temperature in Cells -- 14.5.2 Sensing pH in Cells -- 14.5.3 Sensing K+ Ion in Cells -- 14.5.4 Sensing Crowding Condition in Cells -- 14.6 Conclusion -- References.
Chapter 15 Future Outlook for Chemistry and Biology of Non‐canonical Nucleic Acids.
Record Nr. UNINA-9910830012203321
Sugimoto N (Naoki)  
Weinheim, Germany : , : Wiley-VCH, , [2021]
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui