Therapeutic Applications of Quadruplex Nucleic Acids

Stephen Neidle

• Publisher: Academic Press
• Year: 2011
• Print ISBN: 9780123751386
• eBook ISBN: 9780123751393
• Topic: Medicine
• Subtopic: Pharmaceutical, Biotechnology & Healthcare Industry

The study of G-quadruplexes has emerged in recent years as an important focus of research in nucleic acids. This is now a rapidly growing area, not least because of its potential as a novel approach to cancer therapeutics, and there is much current activity on the design of quadruplex-selective small-molecule ligands and the study of their cellular effects. This timely publication gives a uniquely integrated view of quadruplex nucleic acids that will be a major resource in future drug-discovery strategies.Therapeutic Applications of Quadruplex Nucleic Acids provides a single comprehensive survey that describes and assesses recent advances in quadruplex therapeutics and targeting strategies. It also covers the underlying fundamentals of such topics as quadruplex structure, small-molecule recognition, biological roles of genomic quadruplexes, and quadruplex informatics.Written by a world leader in this field, this book is a vital resource for researchers in medicinal chemistry, chemical biology, structural biology, drug discovery, and pharmacology in cancer and other therapeutic areas, as well as for chemists and biologists working on nucleic acids, and will be useful for both active researchers and students in these areas.

1. Introduction

Quadruplexes and their Biology

The fundamental features of guanine self-aggregation into a G-quartet arrangement are discussed. The guanine-rich DNA sequences that can aggregate in this way are found in telomeres, the specialized nucleoprotein assemblies at the ends of eukaryotic chromosomes. The extreme ends of telomeres comprise single-stranded telomeric DNA sequences, which can form more complex quadruplex structures built up from repeated G-quartet cores. Telomeres in somatic cells shorten during replication, though not in cancer cells. In most instances telomeres are maintained in length by a specialized enzyme complex, telomerase, which is selectively expressed in the majority of human cancer cells but not in normal somatic cells. Its inhibition leads to selective cancer cell death and is thus a potential anti-cancer strategy. The principal approaches to telomerase inhibition are discussed, in particular the small-molecule induction of a quadruplex structure in the single-stranded overhang, which is the substrate for telomerase-mediated telomere extension. Methods for measuring telomerase activity are surveyed, together with computational methods for locating potential quadruplex-forming sequences more generally within genomes.

Keywords

guanosine gels, four-stranded helix, G-quartet: telomeres, D-loop, shelterin, telomeric proteins, telomerase, TRAP assay, quadruplex bioinformatics, quadruplex genomics

This book is organized so that the reader can progress through accounts of the fundamentals of quadruplex biology and three-dimensional structure, through to the chemistry and biology of quadruplex interactions with small molecules. The functionally and structurally distinct telomeric, genomic and RNA quadruplexes are each discussed in separate chapters. The book continues with an extended discussion of the major issues and challenges for quadruplexes as therapeutic targets. The underlying theme throughout the book is molecular structure and in particular how structural concepts can be applied to quadruplex-targeted ligand design and discovery. The concluding chapter provides background material for this, including the basics of diffraction and crystallographic techniques as applied to quadruplex nucleic acids.

Helical Arrangements of Guanosine Repeats

The observations that guanine-rich nucleic acids, and indeed guanosine itself, have unusual physical properties, are exactly 100 years old. It was first noted by Bang (1910) that these readily formed gel-like substances in aqueous solution. Analogous findings of (highly ordered) aggregation were made with the first oligonucleotides containing deoxyguanosine to have been synthesized (Ralph, Connors & Khorana, 1962). These workers also reported some of the first spectroscopic studies on these unusual nucleic acids and showed that the optical density of the tri- and tetradeoxynucleotides d(pGGG) and d(pGGGG) changed with temperature to give a sharp thermal transition point (T_m), indicative of an ordered secondary structure, although the authors did not speculate on its nature. These observations were rationalized in structural terms by the systematic X-ray fiber diffraction study of Gellert, Lipsett and Davies (1962), who studied fibers formed from gels of 3′- and 5′-guanosine monophosphate, analogous to the original gels produced some 50 years previously by Bang. The diffraction patterns showed a number of the characteristics of helical nucleic acid structural arrangements seen a decade earlier with diffraction patterns of fibrous random-sequence double-helical DNA by Franklin and Wilkins, with, in particular, a strong meridional reflection at 3.3Å indicative of stacked bases, although the dimensions of the GMP quasi-helices are distinct from those of the double helix. Gellert et al. also pointed out that the regular structure and high stability apparent in these helices could be explained by a hydrogen-bonding arrangement of four guanine bases (subsequently termed the G-quartet or G-tetrad), with two hydrogen bonds between each pair (Figure 1–1) involving four donor/acceptor atoms of each guanine base: the N1, N7, O6 and N2 atoms (Davis, 2004). The four-fold symmetrical G-quartet arrangement was based on a dimerization of a guanine–guanine base pairing earlier suggested by Donohue (1956). Subsequent fiber-diffraction studies, discussed in Chapter 2, have confirmed and extended this model.

Figure 1–1 The structure of the G-quartet, showing the hydrogen bonding arrangement between the four coplanar guanine bases.

The Rise of the Quadruplex Concept

These early observations and rationalizations of guanine aggregation were given new impetus by subsequent findings over two decades after the initial fiber-diffraction study that guanine-rich sequences in immunoglobin switch regions (Sen & Gilbert, 1988) and in telomeric regions at the ends of eukaryotic chromosomes (Henderson et al., 1987 and Sundquist and Klug, 1989) can also form this type of four-stranded structural arrangement. Such sequences have discrete runs of guanine tracts, which do not form continuous helices but instead comprise compact structured arrangements, which it was soon realized can also be formed by short-length oligonucleotides of appropriate sequence. These are termed quadruplexes (the name tetraplex is occasionally also used), and can be constructed from one, two or four strands of (ribo- or deoxy-) oligonucleotide (Figure 1–2). Quadruplexes are thus structures containing as their basis typically 3–4 G-quartets linked together, and can be either di...

Table of contents

• Cover image
• Table of Contents
• Front-matter
• Copyright
• Dedication
• Preface
• 1. Introduction
• 2. DNA and RNA Quadruplex Structures
• 3. The Structures of Human Telomeric DNA Quadruplexes
• 4. Telomeric Quadruplex Ligands I
• 5. Telomeric Quadruplex Ligands II
• 6. The Biology and Pharmacology of Telomeric Quadruplex Ligands
• 7. Genomic Quadruplexes as Therapeutic Targets
• 8. RNA Quadruplexes
• 9. Design Principles for Quadruplex-binding Small Molecules
• 10. The Determination of Quadruplex Structures
• Index