Introduction: Nucleic Acids Structure, Function, and Why Studying Them In Vacuo
This introductory chapter sets the stage for the various methods and application that will be described in the book “Nucleic acids in the gas phase.” Using key review articles as references, nucleic acid structures are introduced, with progression from pr
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Introduction: Nucleic Acids Structure, Function, and Why Studying Them In Vacuo Vale´rie Gabelica
Abstract
This introductory chapter sets the stage for the various methods and application that will be described in the book “Nucleic acids in the gas phase.” Using key review articles as references, nucleic acid structures are introduced, with progression from primary structure to the main secondary, tertiary, and quaternary structures of DNA and RNA. Nucleic acid function is also overviewed, from the roles of natural nucleic acids in biology to those of artificial nucleic acids in the biotechnology, biomedical, or nanotechnology fields. Importantly, the question of why studying nucleic acids in the gas phase is addressed from three different points of view. First, because isolated molecules in vacuo cannot exchange energy with their surroundings, reactivity can be studied in well-defined energetic conditions. Second, isolating molecules from their solvent and environment allow to study their intrinsic properties. Finally, the rapidly expanding field of mass spectrometry, an intrinsically gas-phase analysis method, calls for better understanding of ion structure and reactivity in vacuo. Keywords
Gas phase • Mass spectrometry • Ionization • Oligonucleotide • Primary structure • Secondary structure • Double helix • Watson–Crick • Triplex • G-quadruplex • Sequencing • Conformation • DNA • RNA • Biotechnology • Nanotechnology • Solvent effect • Desolvation • Biology
V. Gabelica (*) IECB, ARNA Laboratory, Univ. Bordeaux, 33600 Pessac, France U869, ARNA Laboratory, Inserm, 33000 Bordeaux, France e-mail: [email protected] V. Gabelica (ed.), Nucleic Acids in the Gas Phase, Physical Chemistry in Action, DOI 10.1007/978-3-642-54842-0_1, # Springer-Verlag Berlin Heidelberg 2014
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Abbreviations A BIRD bp C DNA FDA G G4-DNA IR LNA miRNA mRNA MS MS/MS ncRNA NMR nt ODN PDB PNA RNA ROS rRNA SASA siRNA T TFO tRNA U UV VEGF
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Adenine Blackbody infrared radiation-induced dissociation Base pair Cytosine Deoxyribonucleic acid Food and Drug Adminstration Guanine G-quadruplex DNA Infrared Locked nucleic acid Micro RNA Messenger RNA Mass spectrometry Tandem mass spectrometry Noncoding RNA Nuclear magnetic resonance Nucleotide Oligodeoxynucleotide Protein data bank Peptide nucleic acid Ribonucleic acid Reactive oxygen species Ribosomal RNA Solvent-accessible surface area Silencing RNA Thymine Triplex forming oligonucleotide Transfer RNA Uracil Ultraviolet Vascular endothelial growth factor
Nucleic Acids Structure
This section summarizes the fundamentals and most common nomenclature for nucleic acid structure. The connections between primary, secondary, and tertiary structure are highlighted. Also, the attention of the reader is drawn to the slightly different meanings of “secondary” and “tertiary” structures in the case of nucleic acids compared to the field of proteins.
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Introduction: Nucleic Acids Structure, Function, and Why Studying Them In Vacuo
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Fig. 1.1 Chemical structure of the five natural
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