**2. Basic structures of DNA G-quad**

DNA is often described as a double helix structure based on the typical Watson-Crick base pairing, where hydrogen bonds are formed between guanine and cytosine or adenine with thymine [8]. However, it was later discovered that a different bonding interaction based on hydrogen bonding could contribute to base paring, called the Hoogsteen bonding. The basic structure of G-quad involves four G bases forming a square planar array called the G-quartet that is stabilized by eight Hoogsteen and Watson-Crick hydrogen bonds. G-quad are formed by stacking up square planar arrays that is joined by the phosphodiester backbone and stabilized by the π–π stacking interactions of the stacked G-quartets and specific cations such as K+ , Na+ , Li+ , NH4 + , Pb2+and Sr2+ that gives rise to the strong electrostatic interaction between G and the cations [9-10].

NMR and crystallography studies have shown G-quad structures to be highly polymorphic [11]. They can form many different structures depending on the length of the DNA, orientation of the chains, positions of the loops and nature of the cations. G-quad can be found in many different forms ranging from one, two or four separate chains that give rise to unimolecular, bimolecular and tetramolecular structures [12]. There are also a variety of topologies of G-quad due to different possible combinations of the stretches of G-rich sequences, loop formation and also sequences [13-14]. Generally, the stretches of G can fold into different forms that include the parallel, basket, hairpin and chair conformation. Four strands of G can fold to form a parallel four-stranded structure while two chains of G will fold into dimeric structures by dimerization of a pair of hairpin that results in a bimolecular G-quad with two loops [15]. Two structures of different loop orientations can be formed which are 'edgewise' loops that connect adjacent anti-parallel chains and the 'diagonal' loops that connect cross-over anti-parallel chains. As reported, the use of different cations in these two structures will form different loop conformations. The NMR solution of these two structures showed that with K+ ions, the Gquad structure gave 'edgewise' loops, and, on the other hand, the G-quad structure in Na+ ions produced 'diagonal' loops [16, 17]. A single-stranded G-rich sequence with four G repeats will form a unimolecular G-quad structure. This single stretch of G will fold and form an intramo‐ lecular G-quad with three loops in the presence of cations. Due to the steric hindrance and electrostatic repulsion caused by the loops, the orientation of the three loops is not entirely anti-parallel [13].

[3]. Besides, G-quad structure is found to be polymorphic as it forms many different structural arrangements depending on the variation in DNA composition and environment. Different formation of G-quad structure has different yet specific functions in nature. Thus, the study of G-quad has driven the structure into many applications, especially in the field of medicine,

The biological functions of the G-quad structure are well documented and the principles of it can be exploited for use as biosensors and therapeutics. One of the functions of the structure is the formation of DNA enzyme or catalytic enzymes, in short, DNAzyme, that can exhibit catalytic capabilities such as exhibiting peroxidase-like activity. G-quad can also serve as internal fluorescent probes in which its nucleobases are modified or attached with fluorescent dyes for sensing. In addition, G-quad can be combined with some electrochemical methods to produce signal readout. The discovery of such remarkable advantages of G-quad have given rise to the development of assays exploiting the G-quad structure such as DNA detection assay,

Taken together, the advantages and flexibilities accorded to DNA G-quad have made G-quad very useful for the development of a variety of reporter systems for sensing applications. Consequently, DNA-based assay has now become a potential alternative to the conventional diagnostic platforms that use enzymes. In this chapter, the focus of our discussion would be on the structural features and application of DNA G-quad structures for the development of

DNA is often described as a double helix structure based on the typical Watson-Crick base pairing, where hydrogen bonds are formed between guanine and cytosine or adenine with thymine [8]. However, it was later discovered that a different bonding interaction based on hydrogen bonding could contribute to base paring, called the Hoogsteen bonding. The basic structure of G-quad involves four G bases forming a square planar array called the G-quartet that is stabilized by eight Hoogsteen and Watson-Crick hydrogen bonds. G-quad are formed by stacking up square planar arrays that is joined by the phosphodiester backbone and stabilized by the π–π stacking interactions of the stacked G-quartets and specific cations such

NMR and crystallography studies have shown G-quad structures to be highly polymorphic [11]. They can form many different structures depending on the length of the DNA, orientation of the chains, positions of the loops and nature of the cations. G-quad can be found in many different forms ranging from one, two or four separate chains that give rise to unimolecular, bimolecular and tetramolecular structures [12]. There are also a variety of topologies of G-quad due to different possible combinations of the stretches of G-rich sequences, loop formation and also sequences [13-14]. Generally, the stretches of G can fold into different forms that include the parallel, basket, hairpin and chair conformation. Four strands of G can fold to form a

, Pb2+and Sr2+ that gives rise to the strong electrostatic interaction between

protein detection assay and even the detection of molecules and ions [4-7].

biology and material sciences.

122 Nucleic Acids - From Basic Aspects to Laboratory Tools

various sensing platforms.

as K+

, Na+ , Li+ , NH4 +

G and the cations [9-10].

**2. Basic structures of DNA G-quad**

The polymorphism in the G-quad is the result of a balance between several stabilizing factors. The G-quad structures are mainly determined by monovalent cations as these structures are cation-dependent and require it for stability. Besides, other factors such as hydrogen bonding, base-stacking forces and hydrophobic effects also affect the formation of different topologies of the G-quad structures. However, this remarkable polymorphism has driven the increasing influence of G-quad in various functions and applications, especially in the field of medicine, biology and material sciences [18]. The main attractive application of G-quad revolves around the potential diagnostic application of G-quad as a reporter system where signal readouts are easily amplified by standard DNA amplification processes to yield a sensitive sensing system.
