Preface

Chapter 8 **Small-molecule Nucleic-acid-based Gene-silencing**

Chapter 9 **Temperature-Dependent Regulation of Bacterial Gene Expression by RNA Thermometers 157**

Chapter 10 **A Review on the Thermodynamics of Denaturation Transition of DNA Duplex Oligomers in the Context of**

**Strategies 137**

**VI** Contents

João C. O. Guerra

Zhijie Xu and Lifang Yang

Yahan Wei and Erin R. Murphy

**Nearest-Neighbor Models 183**

Nucleic acids, the most common of which are DNA and RNA, have a wide variety of func‐ tions in the main system of life, expression, maintenance, and so on. In the postgenomic era, when the primary structure of our genome has been fully determined, though not yet fully understood, a significant challenge for investigation is to determine not only the role of sev‐ eral small molecules of nucleic acids with promising functions but also the modification and employment of novel nucleoside analogues developed for biological research and medical applications. Nucleic acids are commonly used as laboratory tools for modulating gene ex‐ pression and have the potential to be widely used in the fields of medicine and therapeutics. They can recognize and exhibit a much stronger affinity with their corresponding counter‐ parts, such as DNA or RNA, to form a thermodynamically stable variable molecular struc‐ ture and thus can be used in gene therapy to silence genes.

This volume contains a series of chapters that highlight the development and status of the various aspects of the nucleic acids related to DNA chemistry and biology and the molecu‐ lar application of these small DNA molecules and related synthetic analogues within biolog‐ ical systems.

This book, *Nucleic Acids*, is organized into 11 chapters containing methods in DNA extrac‐ tion, molecular diagnosis, gene-silencing therapeutics, and bacterial gene regulation by RNA thermometer. The first chapter is a review presentation describing physical properties of DNA to propose a new model for allowing different DNA nucleation strategies. The sec‐ ond chapter describes the fundamental principles of different methods for nucleic acid sam‐ ple preparation and extraction, such as column-based methods using silica membranes and traditional ones without a column purification procedure; a comparative analysis of the use of these methods in DNA and RNA extraction from various biological and clinical samples; and the application of nucleic acids in molecular diagnosis. The third chapter describes the factors affecting the formalin-fixed and paraffin-embedded tissue nucleic acid extraction process, compares the available protocols, and describes the modifications of some proto‐ cols. The fourth chapter provides a summary of the application of the molecular methods for the detection of two important foodborne viruses. The fifth chapter is a an overview of the contribution of the nucleic acid discovery to the diagnosis and molecular epidemiology of pathogenic microorganisms and its relevance for veterinary and human health, principal‐ ly after the introduction of polymerase chain reaction (PCR) and post-PCR techniques em‐ ployed in infectious diseases. The sixth chapter of this book provides a description of the use of nucleic acids in molecular diagnostics, focusing on the impact of molecular testing for the management of infectious diseases, emphasizing personalized healthcare and medical needs in the developing market for molecular testing. The seventh chapter provides a review of nucleic acid aptamers for viral detection and inhibition, focusing on the most successful an‐

tiviral aptamers reported and including a description of some of the novel methods devel‐ oped for their use as diagnostic and therapeutic tools. The eighth chapter highlights the current advantages and flexibilities of the DNA G-quadruplex and its potentiality in con‐ ventional diagnostic platforms that use protein enzymes. The ninth chapter includes advan‐ ces in medical aspects related to gene-silencing therapeutics, focusing mainly on DNAzymes and siRNA and their integral role in future antigene therapies. Finally, the two last chapters summarize the current state of knowledge on bacterial RNA thermometers, including sever‐ al aspects and techniques applied to identifying different families of RNA thermometers and a review on the thermodynamics of the denaturation transition of DNA duplex oligom‐ ers in the context of nearest neighbor models.

It is our sincere hope that this book on some widely used methods for studying the several types of nucleic acids and their related molecules will inspire future translational studies focusing on targeting nucleic acid regulatory mechanisms as a strategy in several therapies in a variety of illness and diseases.

This book will serve as a textbook for the research community, academia, and the industry and provides up-to-date state-of-the-art information presented by recognized international experts in the field of the molecular biology. They have contributed to the publication of this book of high importance to researchers, scientists, engineers, and graduate students who make use of these different investigations to understand the hazardous implications in the use of nucleic acids. The provision of the publishing Web platform by the publisher InTech is gratefully acknowledged.

#### **Prof. Dr. Marcelo Larramendy**

Principal Researcher CONICET School of Natural Sciences and Museum National University of La Plata La Plata, Argentina

**Dr. Sonia Soloneski** School of Natural Sciences and Museum National University of La Plata Argentina
