Nucleic Acids: From Basic Aspects to Laboratory Tools

219 Pages·2016·12.09 MB·English

by  Larramendy M.L.

Nucleic Acids
From Basic Aspects to Laboratory Tools
Edited by Marcelo L. Larramendy and Sonia Soloneski
Nucleic Acids: From Basic Aspects to Laboratory Tools
Edited by Marcelo L. Larramendy and Sonia Soloneski
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C ontents
Preface
Chapter 1 Nucleic Acid Isolation and Downstream Applications
by Ivo Nikolaev Sirakov
Chapter 2 Nucleic Acids Extraction from Formalin-Fixed and Paraffin-
Embedded Tissues
by Gisele R. Gouveia, Suzete C. Ferreira, Sheila A. C. Siqueira and
Juliana Pereira
Chapter 3 Nucleic Acid Detection of Major Foodborne Viral Pathogens
Human: Noroviruses and Hepatitis A Virus
by Haifeng Chen
Chapter 4 Nucleic Acid-based Diagnosis and Epidemiology of Infectious
Diseases
by Márcia Aparecida Sperança, Rodrigo Buzinaro Suzuki, Aline
Diniz Cabral and Andreia Moreira dos Santos Carmo
Chapter 5 Nucleic Acids — The Use of Nucleic Acid Testing in Molecular
Diagnostics
by Gabrielle Heilek
Chapter 6 Application of Nucleic Acid Aptamers to Viral Detection and
Inhibition
by Ana Gabriela Leija-Montoya, María Luisa Benítez-Hess and Luis
Marat Alvarez-Salas
Chapter 7 DNA G-Quadruplex as a Reporter System for Sensor
Development
by Qiuting Loh and Theam Soon Lim
VI Contents
Chapter 8 Small-molecule Nucleic-acid-based Gene-silencing Strategies
by Zhijie Xu and Lifang Yang
Chapter 9 Temperature-Dependent Regulation of Bacterial Gene Expression
by RNA Thermometers
by Yahan Wei and Erin R. Murphy
Chapter 10 A Review on the Thermodynamics of Denaturation Transition of
DNA Duplex Oligomers in the Context of Nearest-Neighbor Models
by João C. O. Guerra

Preface
This edited book, "Nucleic Acids - From Basic Aspects to
Laboratory Tools", 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 molecular application
of these small DNA molecules and related synthetic analogues
within biological systems.
Furthermore, it is hoped that the information in the present book will
be of value to those directly engaged in the handling and use of
nucleic acids, and that this book will continue to meet the
expectations and needs of all who are interested in the different
fascinating aspects of molecular biology.

Chapter 1
Nucleic Acid Isolation and Downstream Applications
Ivo Nikolaev Sirakov
Additional information is available at the end of the chapter
http://dx.doi.org/10.5772/61833
Abstract
Nucleic acids are not only a source of life but also a means of observing, understanding,
and regulating it. Nucleic acids, DNA and RNA, and their characteristics are discussed in
other chapters of the book. This chapter describes the fundamental principles of different
methods for nucleic acid sample preparation / nucleic acid extraction, such as column-
based methods using silica membranes and traditional ones without a column purifica‐
tion procedure (commercially available or homemade). Other topics discussed here
include comparative analysis of the use of these methods in DNA and RNA extraction
from a variety of biological and clinical samples, as well as the relationship between the
type of sample, the method used and the quality and amount of extracted DNA or RNA.
Finally, the chapter outlines the application of nucleic acids in the diagnosis of various
diseases, in scientific research, and bird sex determination by downstream applications
such as restriction enzyme analysis, polymerase chain reactions (PCR, reverse transcrip‐
tion-PCR, real-time PCR), and different sequencing methods (Sanger, cycling sequencing,
and next-generation sequencing).
Keywords: DNA extraction, RNA extraction, PCR methods, next-generation sequencing
1. Introduction
1.1. Nucleic acid isolation and downstream applications
The specific properties of nucleic acids have been widely employed in the development of
different molecular methods and mathematical models for their analysis. These methods are
applied to identify microorganisms and genetic predispositions, to detect different mutations
and determine their role in antibiotic resistance, to study phylogenetic relationships, and so
on. What all these methods share in common is their starting point: obtaining a purified nucleic
acid sample.