Table Of ContentQuadruplex Nucleic Acids
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Quadruplex Nucleic Acids
Edited by
Stephen Neidle
The School of Pharmacy, University of London, London, UK
Shankar Balasubramanian
Department of Chemistry, University of Cambridge, Cambridge,
UK
ISBN-10:0-85404-374-8
ISBN-13:978-0-85404-374-3
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Preface
The knowledge that guanine-rich DNA can form unusual structures has its
origininfindingsthatprecedethedouble-helixstructureby50years.However,
the nature of the guanine aggregation, at the polynucleotide helix level, was
only revealed in the 1960s by fibre diffraction and other biophysical studies.
These showed that guanine polynucleotides form four-stranded helices held
together, not by the Watson–Crick base-pair motif, but by four guanines
hydrogen-bondedin-planeG-quartets.Thistypeofstructureappearedinitially
tohavelittlebiologicalrelevanceuntilitwasdemonstratedthatnaturalG-rich
sequences in telomeric DNA at the ends of chromosomes could form such
structures, at least in vitro. The study of quadruplex biophysical chemistry
made steady progress in the 1990s, with NMR and to some extent X-ray
crystallography defining some structural detail. The biology of quadruplexes
remained a relatively unexplored area until it was demonstrated that small-
molecule stabilisation of the single-stranded ends of telomeric DNA into
quadruplexes, is an effective way of inhibiting telomerase activity, and could
therefore lead to anti-telomerase anticancer therapy. Furthermore, a growing
numberofquadruplex-specificproteinsarebeingdiscovered.Thereisnowthe
increasing realisation that non-telomeric sequences in human and other gen-
omes can form (or perhaps can be induced to form) quadruplexes, and that
these quadruplexes play a role in the regulation of gene expression. The
diversity in quadruplex architecture is also of increasing interest, even though
muchremainstobeestablished,andrulesrelatingsequencetofold cannotyet
be defined.
We believe that it is now timely to review many of these themes, and so
clarify where the quadruplex area is going. We have been fortunate in being
abletobringtogethermanyoftheleadingexpertsinthisexcitingfield,andare
grateful to them for having delivered their manuscripts so promptly.
Shankar Balasubramanian, Cambridge
Stephen Neidle, London
v
Contents
Chapter 1 Fundamentals of Quadruplex Structures 1
Gary Nigel Parkinson
1.1 Background and Introduction to Quadruplexes 1
1.2 Fundamental Components of DNA and RNA 3
1.2.1 Building Blocks 3
1.2.2 DNA/RNA as a Helical Structure 7
1.2.3 Stabilizing Factors in Quadruplexes 9
1.3 Folding and Topology of Quadruplexes 15
1.3.1 Loop Length, Sequence, and Stability 19
1.3.2 Polymorphism in Sequence and in Topology 21
1.3.3 Other Quadruplex Forming Sequences 23
1.4 Experimental Methods Used in Quadruplex
Characterization 25
1.4.1 UV Melting Experiments 25
1.4.2 Circular Dichroism Spectroscopy 26
1.4.3 Polyacrylamide Gels Electrophoresis 26
1.4.4 Fluorescence Resonance Energy Transfer
(FRET) 26
1.4.5 Sedimentation Velocity Analysis and
Sedimentation Equilibrium 27
1.4.6 Cross-Linking DNA and Topology 27
References 27
Chapter 2 Energetics, Kinetics and Dynamics of Quadruplex Folding 31
Jean-Louis Mergny, Julien Gros, Anne De Cian,
Anne Bourdoncle, Fre´de´ric Rosu, Barbara Sacca`,
Lionel Guittat, Samir Amrane, Martin Mills, Patrizia
Alberti, Masashi Takasugi and Laurent Lacroix
vii
viii Contents
2.1 Introduction 31
2.2 Thermodynamics 32
2.2.1 Enthalpy and Entropy of Formation 32
2.2.2 Loop Contribution to Folding and Dynamics 34
2.2.3 Stability under Physiological Conditions 35
2.2.4 Which Quadruplexes are the Most Stable:
Intra-, Bi- or Tetramolecular? Parallel or
Antiparallel? 36
2.2.5 Competition with Duplexes 37
2.3 Cations Play a Central Role! 38
2.3.1 Modes of Interaction 38
2.3.2 Location of Ions 39
2.3.3 Dynamics of Ions 41
2.3.4 Proton Exchange, Transient Opening of the
Quartet 41
2.4 Multiple Quadruplex Conformations 42
2.4.1 Initial Observations 42
2.4.2 Telomeric Repeats 42
2.4.3 Consequences of Polymorphism 44
2.5 Kinetic Analysis: Technical Considerations 44
2.5.1 Elementary Precautions 44
2.5.2 General Considerations 44
2.5.3 Limitations of the Current Methods 45
2.6 Kinetics of Intramolecular Quadruplexes 46
2.6.1 Presentation 46
2.6.2 Kinetic Analysis 46
2.6.3 Quadruplex Interconversion 48
2.7 Kinetics of Bimolecular Quadruplexes 49
2.7.1 Presentation 49
2.7.2 Kinetic Analysis 49
2.7.3 Quadruplex Interconversion 51
2.8 Kinetics of Tetramolecular Quadruplexes 52
2.8.1 Presentation 52
2.8.2 Thermal Stability 52
2.8.3 Association Process 54
2.9 Higher Order Structures 57
2.9.1 Quadruplex Dimers 57
2.9.2 G-Wires 59
2.10 Effect of Chemical Modifications 60
2.10.1 RNA and 20-Sugar Modified Analogues 60
2.10.2 Further Backbone Modifications 61
2.10.3 Base Substitutions 63
Contents ix
2.11 Effect of Quadruplex Ligands 64
2.11.1 Small Ligands and Bimolecular
Quadruplexes 64
2.11.2 Small Ligands and Intramolecular
Quadruplexes 65
2.11.3 Small Ligands and Tetramolecular
Quadruplexes 65
2.11.4 Effects of Proteins 65
2.12 Implications for the Folding Pathway 67
2.12.1 Tetramolecular Quadruplexes 67
2.12.2 Are G-G Hairpins Plausible Intermediates for
Bimolecular Quadruplexes? 68
2.12.3 Molecular Modelling of Intermediate
States 68
2.13 Conclusion 70
Acknowledgements 72
References 72
Chapter 3 Structural Diversity of G-Quadruplex Scaffolds 81
Anh Tuaˆn Phan, Vitaly Kuryavyi, Kim Ngoc Luu and
Dinshaw J. Patel
3.1 Introduction 81
3.2 Core and Loops in G-Quadruplexes 82
3.2.1 G-Tetrad Core 82
3.2.2 Loops 82
3.3 G-Quadruplexes with Different Structural
Elements 84
3.3.1 Triad-Containing Edgewise Loops 84
3.3.2 Triad-Containing Diagonal Loops 85
3.3.3 V-Shaped Loop 85
3.3.4 Interlocked G-Quadruplexes 86
3.3.5 Pentads, Hexads, Heptads, and Octads 87
3.3.6 Mixed Tetrads 87
3.3.7 Four-Repeat Human Telomeric Sequence 88
3.3.8 (3+1) G-Tetrad Core Topology 89
3.3.9 Fold-Back G-Quadruplex 90
3.3.10 Bulged and Interrupted G-Tetrad Core 91
3.3.11 Intercalation of Tetrads 94
3.4 Conclusion 94
References 95
