In molecular biology, G-QUADRUPLEXES (also known as G4 DNA) are
secondary structures formed in nucleic acids by sequences that are
rich in guanine . These structures are four stranded helical
structures and occur naturally in nature. They are normally located
near the ends of the chromosomes or the better known as the telomeric
regions and in transcriptional regulatory regions of multiple
oncogenes. Four guanine bases can associate through Hoogsteen
hydrogen bonding to form a square planar structure called a guanine
tetrad, and two or more guanine tetrads can stack on top of each other
to form a G-quadruplex. The placement and bonding to form
G-quadruplexes are not random and serve very unusual functional
purposes. The quadruplex structure is further stabilized by the
presence of a cation , especially potassium , which sits in a central
channel between each pair of tetrads. They can be formed of
DNA , RNA
, LNA , and PNA , and may be intramolecular , bimolecular , or
tetramolecular. Depending on the direction of the strands or parts of
a strand that form the tetrads, structures may be described as
parallel or antiparallel .
G-quadruplex structures can be
computationally predicted from
RNA sequence motifs, but their
actual structures can be quite varied within and between the motifs,
which can number over 100,000 per genome. Their activities in basic
genetic processes are an active area of research in telomere, gene
regulation, and functional genomics research (Rhodes et al., NAR
2015). (replacement figure 1) Structure of a
G-quadruplex. Left: a G-tetrad. Right: an intramolecular
3D Structure of the intramolecular human telomeric
potassium solution (PDB ID 2HY9). The backbone is represented by a
tube. The center of this structure contains three layers of G-tetrads.
The hydrogen bonds in these layers are represented by blue dashed
* 1 Quadruplex topology
* 2 Telomeric quadruplexes
* 3 Non-telomeric quadruplexes
* 4 Quadruplex function
* 5 Ligands which bind quadruplexes
* 6 Quadruplex prediction techniques
* 7 Notes
* 8 References
* 9 External links
* 9.1 Quadruplex websites
* 9.2 Tools to predict
The length of the nucleic acid sequences involved in tetrad formation
determines how the quadruplex folds. Short sequences, consisting of
only a single contiguous run of three or more guanine bases, require
four individual strands to form a quadruplex. Such a quadruplex is
described as tetramolecular, reflecting the requirement of four
separate strands. Longer sequences, which contain two contiguous runs
of three or more guanine bases, where the guanine regions are
separated by one or more bases, only require two such sequences to
provide enough guanine bases to form a quadruplex. These structures,
formed from two separate G-rich strands, are termed bimolecular
quadruplexes. Finally, sequences which contain four distinct runs of
guanine bases can form stable quadruplex structures by themselves, and
a quadruplex formed entirely from a single strand is called an
Depending on how the individual runs of guanine bases are arranged in
a bimolecular or intramolecular quadruplex, a quadruplex can adopt one
of a number of topologies with varying loop configurations. If all
DNA proceed in the same direction, the quadruplex is termed
parallel. For intramolecular quadruplexes, this means that any loop
regions present must be of the propeller type, positioned to the sides
of the quadruplex. If one or more of the runs of guanine bases has a
5’-3’ direction opposite to the other runs of guanine bases, the
quadruplex is said to have adopted an antiparallel topology. The loops
joining runs of guanine bases in intramolecular antiparallel
quadruplexes are either diagonal, joining two diagonally opposite runs
of guanine bases, or lateral (edgewise) type loops, joining two
adjacent runs of guanine base pairs.
In quadruplexes formed from double-stranded DNA, possible interstrand
topologies have also been discussed . Interstrand quadruplexes
contain guanines that originate from both strands of dsDNA.
Telomeric repeats in a variety of organisms have been shown to form
these quadruplex structures in vitro , and subsequently they have also
been shown to form in vivo . The human telomeric repeat (which is
the same for all vertebrates ) consists of many repeats of the
sequenced (GGTTAG), and the quadruplexes formed by this structure have
been well studied by
X-ray crystal structure determination.
The formation of these quadruplexes in telomeres has been shown to
decrease the activity of the enzyme telomerase , which is responsible
for maintaining length of telomeres and is involved in around 85% of
all cancers . This is an active target of drug discovery, including
Quadruplexes are present in locations other than at the telomere .
The proto-oncogene c-myc forms a quadruplex in a nuclease
hypersensitive region critical for gene activity. Other genes shown
to form G-quadruplexes in their promoter regions include the chicken
β-globin gene , human ubiquitin -ligase RFP2, and the proto-oncogenes
c-kit , bcl-2 , VEGF , H-ras and N-ras .
Genome -wide surveys based on a quadruplex folding rule have been
performed, which have identified 376,000 Putative Quadruplex Sequences
(PQS) in the human genome , although not all of these probably form in
vivo. A similar study has identified putative G-quadruplexes in
prokaryotes . There are several possible models for how quadruplexes
could influence gene activity, either by upregulation or
downregulation . One model is shown below, with
in or near a promoter blocking transcription of the gene, and hence
de-activating it. In another model, quadruplex formed at the
DNA strand helps to maintain an open conformation of the
DNA strand and enhance an expression of the respective gene.
Model for quadruplex-mediated down-regulation of gene expression
Nucleic acid quadruplexes have been described as "structures in
search of a function", as for many years there was minimal evidence
pointing towards a biological role for these structures. It has been
suggested that quadruplex formation plays a role in immunoglobulin
heavy chain switching. As cells have evolved mechanisms for resolving
(i.e., unwinding) quadruplexes that form, quadruplex formation may be
potentially damaging for a cell; the helicases WRN and Bloom syndrome
protein have a high affinity for resolving G4 DNA. More recently,
there are many studies that implicate quadruplexes in both positive
and negative transcriptional regulation, and in allowing programmed
recombination of immunologlobin heavy genes and the pilin antigenic
variation system of the pathogenic Neisseria. The roles of quadruplex
structure in translation control are not as well explored. The direct
visualization of quadruplex structures in human cells has provided
an important confirmation of their existence. The potential positive
and negative roles of quadruplexes in telomere replication and
function remains controversial. T-loops and G-quadruplexes are
described as the two tertiary
DNA structures that protect telomere
ends and regulate telomere length.
LIGANDS WHICH BIND QUADRUPLEXES
One way of inducing or stabilizing
G-quadruplex formation is to
introduce a molecule which can bind to the
G-quadruplex structure. A
number of ligands, both small molecules and proteins , which can bind
to the G-quadruplex. These ligands can be naturally occurring or
synthetic. This has become an increasingly large field of research in
genetics, biochemistry, and pharmacology.
A number of naturally occurring proteins have been identified which
selectively bind to G-quadruplexes. These include the helicases
implicated in Bloom\'s and Werner\'s syndromes and the Saccharomyces
cerevisiae protein RAP1 . An artificially derived three zinc finger
protein called Gq1 , which is specific for G-quadruplexes has also
been developed, as have specific antibodies .
Cationic porphyrins have been shown to bind intercalatively with
G-quadruplexes, as well as the molecule telomestatin .
QUADRUPLEX PREDICTION TECHNIQUES
Identifying and predicting sequences which have the capacity to form
quadruplexes is an important tool in further understanding their role.
Generally, a simple pattern match is used for searching for possible
intrastrand quadruplex forming sequences: d(G3+N1-7G3+N1-7G3+N1-7G3+),
where N is any nucleotide base (including guanine ). This rule has
been widely used in on-line algorithms .
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