Triple Helix Forming Oligonucleotides

Sequence-specific DNA binding ligands, amongst which triple helix forming oligonucleotides are the most efficient as yet, represent promising tools in a number of fields. One of their most promising applications is as antiviral tools: they can specifically target a viral gene, even if it is integrated into the host genome, and be used to specifically inactivate the viral gene or even destroy the cells harboring this gene. However, from science fiction to science there remains a gap; and we are at the moment on the threshold of this fascinating field. Triple Helix Forming Oligonucleotides considers the different aspects of the design and improvement, current or future, of these molecules and their structural analysis, as well as their applications, with special emphasis on the attempts to obtain biological effects of these potentially important tools. What emerges is that the current state of the research is encouraging, and that these molecules are already useful in some biotechnology applications.

The ability of DNA to exist in configurations other than its classical double-stranded form has been known for many years. There has been a spectacular recent surge of interest in these forms, notably in the three-stranded or triple-helical form. Triplex-like nucleic acids are now known to exist in vivo, and may well participate in significant biological processes. Interest in triple-helical nucleic acids has been greatly stimulated by their potential exploitation to control gene expression, serve as tools in genome mapping strategies, etc. The authors have written an encyclopedic introduction to nucleic acid triplexes based on many years of familiarity with the topic. The book includes information on chemistry, conformation, physical properties, applications, and hypotheses about the biological role of triplexes. It pays particular attention to the different methods for investigating these molecules, a feature which will be welcomed by those new to the field.

A collection of powerful new techniques for oligonucleotide synthesis and for the use of modified oligonucleotides in biotechnology. Among the protocol highlights are a novel two-step process that yields a high purity, less costly, DNA, the synthesis of phosphorothioates using new sulfur transfer agents, the synthesis of LNA, peptide conjugation methods to improve cellular delivery and cell-specific targeting, and triple helix formation. The applications include using molecular beacons to monitor the PCR amplification process, nuclease footprinting to study the sequence-selective binding of small molecules of DNA, nucleic acid libraries, and the use of small interference RNA (siRNA) as an inhibitor of gene expression.

The use of oligonucleotides as therapeutic agents rests upon their ability to interfere, in a sequence-specific manner, with the fundamental machinery of protein synthesis either by binding to the mRNAs transcribed from a gene or by binding directly to a target gene. This approach can be used not only for inhibition of the synthesis of host proteins but also of those required by invading pathogens. Potential therapeutic applications are enormous, ranging over hypertension, cardiovascular disease, autoimmune disease, vital and other parasitic infections (especially HIV), and cancer. This book discusses the chemistry and pharmacokinetics of oligonucleotides and their analogues, and surveys the results of structure-activity studies and current clinical trials. It also critically reviews the problems with antisense therapy, such as the enzymatic destruction of oligonucleotides, the doses required for a therapeutic response, the difficulty in directing oligonucleotides to particular target tissues and cells, the need for parenteral administration, and doubts concerning the mechanism of action (especially problems associated with non-specific binding to proteins) and long-term effects.

Antisense Research and Applications is a comprehensive review of oligonucleotide research covering molecular biological advances in this field, the current status of antisense drug research, and strategies for future research and therapeutic applications. In bringing together the latest research from an array of authoritative scientists, Antisense Research and Applications provides an integrated conceptual basis for considering oligonucleotide therapeutics. Topics covered in the 32 chapters of this book include nucleic acid structure and function, antisense RNA, medicinal chemistry of oligonucleotides, analogs, pharmacokinetics and toxicology, and activities of current antisense drugs. This volume addresses advances in a broad range of disciplines and is an excellent resource for basic researchers and applied investigators in pharmaceutical laboratories and in such fields as biochemistry and molecular biology.

With contributions from leading experts, this book is the first to focus solely on addressing the problems and reviewing the strategies currently being used to improve the delivery of antisense nucleic acids. Important delivery issues, such as improving biological stability, improving cell-specific targeting and cellular uptake, manipulating subcellular distribution and producing liposomal delivery systems for antisense agents are comprehensively covered in this volume. This book links review-type articles with contributions that contain exciting never-before-published data on the cellular delivery of oligonucleotides. It stimulates reading for both established researchers and newcomers to the antisense field.

There have been remarkable advances towards discovering agents that exhibit selectivity and sequence-specificity for DNA, as well as understanding the interactions that underlie its propensity to bind molecules. This progress has important applications in many areas of biotechnology and medicine, notably in cancer treatment as well as in future gene targeting therapies. The editor and contributing authors are leaders in their fields and provide useful perspectives from diverse and interdisciplinary backgrounds on the current status of this broad area. The role played by chemistry is a unifying theme. Early chapters cover methodologies to evaluate DNA-interactive agents and then the book provides examples of DNA-interactive molecules and technologies in development as therapeutic agents. DNA-binding metal complexes, peptide and polyamide–DNA interactions, and gene targeting tools are some of the most compelling topics treated in depth. This book will be a valuable resource for postgraduate students and researchers in chemical biology, biochemistry, structural biology and medicinal fields. It will also be of interest to supramolecular chemists and biophysicists.