G-quadruplex
Encyclopedia
In molecular biology, G-quadruplexes (also known as G-tetrads or G4-DNA) are nucleic acid sequences that are rich in guanine
and are capable of forming a four-stranded structure. Four guanine bases can associate through Hoogsteen
hydrogen bond
ing 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 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 (geometry)
or antiparallel
.
repeats in a variety of organisms have been shown to form these structures in vitro, and they have also been shown to form in vivo in some cases. The human
telomeric
repeat (which is the same for all vertebrate
s) consists of many repeats of the sequence d(GGTTAG), and the quadruplexes formed by this structure have been well studied by NMR
and X-ray
crystal structure
determination. The formation of these quadruplexes in telomere
s 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 cancer
s. This is an active target of drug discovery.
. This was given a large boost by the work by Simonsson and Hurley on the proto-oncogene c-myc, which was shown to form a quadruplex in a nuclease
hypersensitive region critical for gene activity. Since then, many other genes have been shown to have G-quadruplexes in their promoter regions, including the chicken
β-globin
gene
, human ubiquitin
-ligase RFP2 and the proto-oncogenes c-kit, bcl-2
, VEGF
, H-ras and N-ras. This list is ever-increasing.
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 control gene activity, either by upregulation or downregulation. One model is shown below, with G-quadruplex formation in or near a promoter blocking transcription
of the gene, and hence de-activating it. In another model, quadruplex formed at the non-coding DNA strand helps to maintain an open conformation of the coding DNA strand and enhance an expression of the respective gene.
s, have been developed which can do so. This has become an increasingly large field of research.
A number of naturally occurring proteins have been identified which selectively bind to G-quadruplexes. These include the helicase
s 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 porphyrin
s have been shown to bind intercalatively with G-quadruplexes, as well as the molecule telomestatin
.
d(G3+N1-7G3+N1-7G3+N1-7G3+), where N is any base
(including guanine
).
This rule has been widely used in on-line algorithm
s.
Guanine
Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine . In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with...
and are capable of forming a four-stranded structure. Four guanine bases can associate through Hoogsteen
Hoogsteen base pair
A Hoogsteen base pair is a variation of base-pairing in nucleic acids such as the A•T pair. In this manner, two nucleobases on each strand can be held together by hydrogen bonds in the major groove...
hydrogen bond
Hydrogen bond
A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
ing 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 quadruplex structure is further stabilized by the presence of a cation, especially potassium
Potassium
Potassium is the chemical element with the symbol K and atomic number 19. Elemental potassium is a soft silvery-white alkali metal that oxidizes rapidly in air and is very reactive with water, generating sufficient heat to ignite the hydrogen emitted in the reaction.Potassium and sodium are...
, which sits in a central channel between each pair of tetrads. They can be formed of DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
, RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
, LNA
Locked nucleic acid
A locked nucleic acid , often referred to as inaccessible RNA, is a modified RNA nucleotide. The ribose moiety of an LNA nucleotide is modified with an extra bridge connecting the 2' oxygen and 4' carbon. The bridge "locks" the ribose in the 3'-endo conformation, which is often found in the A-form...
, and PNA, and may be intramolecular
Intramolecular
Intramolecular in chemistry describes a process or characteristic limited within the structure of a single molecule, a property or phenomenon limited to the extent of a single molecule.- Examples :...
, 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 (geometry)
Parallel (geometry)
Parallelism is a term in geometry and in everyday life that refers to a property in Euclidean space of two or more lines or planes, or a combination of these. The assumed existence and properties of parallel lines are the basis of Euclid's parallel postulate. Two lines in a plane that do not...
or antiparallel
Antiparallel (biochemistry)
In biochemistry, two molecules are antiparallel if they run side-by-side in opposite directions or when both strands are complimentary to each other....
.
Quadruplex topology
Depending on how the individual runs of guanine bases are arranged, a quadruplex can adopt one of a number of topologies with varying loop configurations. If the 5' - 3’ direction of all the strands is the same,the quadruplex is termed parallel; that is, all the strands of DNA are proceeding in the same direction. For intramolecular quadruplexes, this means that any loop regions present must be of the edge, or propellor, type, which are 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 edge type loops, which join two adjacent runs of guanines.Telomeric quadruplexes
TelomericTelomere
A telomere is a region of repetitive DNA sequences at the end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos "end" and merοs "part"...
repeats in a variety of organisms have been shown to form these structures in vitro, and they have also been shown to form in vivo in some cases. The human
Human
Humans are the only living species in the Homo genus...
telomeric
Telomere
A telomere is a region of repetitive DNA sequences at the end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos "end" and merοs "part"...
repeat (which is the same for all vertebrate
Vertebrate
Vertebrates are animals that are members of the subphylum Vertebrata . Vertebrates are the largest group of chordates, with currently about 58,000 species described. Vertebrates include the jawless fishes, bony fishes, sharks and rays, amphibians, reptiles, mammals, and birds...
s) consists of many repeats of the sequence d(GGTTAG), and the quadruplexes formed by this structure have been well studied by NMR
NMR
NMR may refer to:Applications of Nuclear Magnetic Resonance:* Nuclear magnetic resonance* NMR spectroscopy* Solid-state nuclear magnetic resonance* Protein nuclear magnetic resonance spectroscopy* Proton NMR* Carbon-13 NMR...
and X-ray
X-ray
X-radiation is a form of electromagnetic radiation. X-rays have a wavelength in the range of 0.01 to 10 nanometers, corresponding to frequencies in the range 30 petahertz to 30 exahertz and energies in the range 120 eV to 120 keV. They are shorter in wavelength than UV rays and longer than gamma...
crystal structure
Crystal structure
In mineralogy and crystallography, crystal structure is a unique arrangement of atoms or molecules in a crystalline liquid or solid. A crystal structure is composed of a pattern, a set of atoms arranged in a particular way, and a lattice exhibiting long-range order and symmetry...
determination. The formation of these quadruplexes in telomere
Telomere
A telomere is a region of repetitive DNA sequences at the end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos "end" and merοs "part"...
s has been shown to decrease the activity of the enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
telomerase
Telomerase
Telomerase is an enzyme that adds DNA sequence repeats to the 3' end of DNA strands in the telomere regions, which are found at the ends of eukaryotic chromosomes. This region of repeated nucleotide called telomeres contains non-coding DNA material and prevents constant loss of important DNA from...
, which is responsible for maintaining length of telomeres and is involved in around 85% of all cancer
Cancer
Cancer , known medically as a malignant neoplasm, is a large group of different diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invade nearby parts of the body. The cancer may also spread to more distant parts of the...
s. This is an active target of drug discovery.
Non-telomeric quadruplexes
Recently, there has been increasing interest in quadruplexes in locations other than at the telomereTelomere
A telomere is a region of repetitive DNA sequences at the end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos "end" and merοs "part"...
. This was given a large boost by the work by Simonsson and Hurley on the proto-oncogene c-myc, which was shown to form a quadruplex in a nuclease
Nuclease
A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids. Older publications may use terms such as "polynucleotidase" or "nucleodepolymerase"....
hypersensitive region critical for gene activity. Since then, many other genes have been shown to have G-quadruplexes in their promoter regions, including the chicken
Chicken
The chicken is a domesticated fowl, a subspecies of the Red Junglefowl. As one of the most common and widespread domestic animals, and with a population of more than 24 billion in 2003, there are more chickens in the world than any other species of bird...
β-globin
Beta globulins
Beta globulins are a group of globular proteins in plasma thatare more mobile in alkaline or electrically charged solutions than gamma globulins, but less mobile than alpha globulins. Beta globin is on chromosome 11.Examples of beta globulins include:...
gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
, human ubiquitin
Ubiquitin
Ubiquitin is a small regulatory protein that has been found in almost all tissues of eukaryotic organisms. Among other functions, it directs protein recycling.Ubiquitin can be attached to proteins and label them for destruction...
-ligase RFP2 and the proto-oncogenes c-kit, bcl-2
Bcl-2
Bcl-2 is the founding member of the Bcl-2 family of apoptosis regulator proteins encoded by the BCL2 gene. Bcl-2 derives its name from B-cell lymphoma 2, as it is the second member of a range of proteins initially described in chromosomal translocations involving chromosomes 14 and 18 in...
, VEGF
Vascular endothelial growth factor
Vascular endothelial growth factor is a signal protein produced by cells that stimulates vasculogenesis and angiogenesis. It is part of the system that restores the oxygen supply to tissues when blood circulation is inadequate....
, H-ras and N-ras. This list is ever-increasing.
Genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
-wide surveys based on a quadruplex folding rule have been performed, which have identified 376,000 Putative Quadruplex Sequences (PQS) in the human
Human
Humans are the only living species in the Homo genus...
genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
, 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 control gene activity, either by upregulation or downregulation. One model is shown below, with G-quadruplex formation in or near a promoter blocking transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
of the gene, and hence de-activating it. In another model, quadruplex formed at the non-coding DNA strand helps to maintain an open conformation of the coding DNA strand and enhance an expression of the respective gene.
Quadruplex function
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.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, and a number of ligands, both small molecules and proteinProtein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s, have been developed which can do so. This has become an increasingly large field of research.
A number of naturally occurring proteins have been identified which selectively bind to G-quadruplexes. These include the helicase
Helicase
Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis.-Function:Many cellular processes Helicases are a...
s implicated in Bloom's
Bloom syndrome
Bloom's syndrome , also known as Bloom–Torre–Machacek syndrome, is a rare autosomal recessive chromosomal disorder characterized by a high frequency of breaks and rearrangements in an affected person's chromosomes. The condition was discovered and first described by dermatologist Dr...
and Werner's syndromes and the Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes...
protein RAP1. An artificially derived three zinc finger
Zinc finger
Zinc fingers are small protein structural motifs that can coordinate one or more zinc ions to help stabilize their folds. They can be classified into several different structural families and typically function as interaction modules that bind DNA, RNA, proteins, or small molecules...
protein called Gq1, which is specific for G-quadruplexes has also been developed, as have specific antibodies
Antibody
An antibody, also known as an immunoglobulin, is a large Y-shaped protein used by the immune system to identify and neutralize foreign objects such as bacteria and viruses. The antibody recognizes a unique part of the foreign target, termed an antigen...
.
Cationic porphyrin
Porphyrin
Porphyrins are a group of organic compounds, many naturally occurring. One of the best-known porphyrins is heme, the pigment in red blood cells; heme is a cofactor of the protein hemoglobin. Porphyrins are heterocyclic macrocycles composed of four modified pyrrole subunits interconnected at...
s have been shown to bind intercalatively with G-quadruplexes, as well as the molecule telomestatin
Telomestatin
Telomestatin is a macrocyclic chemical compound that acts by inhibiting the telomerase activity of the cancer cells. It was first isolated from the bacteria Streptomyces anulatus. Telomestatin induces the formation of basket-type G-quadruplex structures from hybrid-type G-quadruplexes in the...
.
Quadruplex prediction techniques
Identifying and predicting sequences which have the capacity to form quadruplexes is an important tool in further understanding of their role. A rule for predicting the formation has been proposed, where sequences are predicted to fold based on the patternd(G3+N1-7G3+N1-7G3+N1-7G3+), where N is any base
Nucleobase
Nucleobases are a group of nitrogen-based molecules that are required to form nucleotides, the basic building blocks of DNA and RNA. Nucleobases provide the molecular structure necessary for the hydrogen bonding of complementary DNA and RNA strands, and are key components in the formation of stable...
(including guanine
Guanine
Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine . In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with...
).
This rule has been widely used in on-line algorithm
Algorithm
In mathematics and computer science, an algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function. Algorithms are used for calculation, data processing, and automated reasoning...
s.
Quadruplex websites
- COST MP0802 Quadruplex Network - the European network of G-quadruplex community: From first principles to applications
- Quadruplex.org - a website to serve the quadruplex community
- Quadbase - downloadable data on predicted G-quadruplexes
- Greglist - a database listing potential G-quadruplex regulated genes
- Database on Quadruplex information: QuadBase from IGIB
- GRSDB- a database of G-quadruplexes near RNA processing sites.
- GRS_UTRdb- a database of G-quadruplexes in the UTRs.
- G-quadruplex Resource Site
- non-B Motif Search Tool at non-B DB- a web server to predict G-quadruplex forming motifs and other non-B DNA forming motifs from users' DNA sequences.
Tools to predict G-quadruplex motifs
- Quadparser: Downloadable program for finding putative quadruplex-forming sequences
- QGRS Mapper: a web-based application for predicting G-quadruplexes in nucleotide sequences and NCBI genes
- Quadfinder: Tool for Prediction and Analysis of G Quadruplex Motifs in DNA/RNA Sequences from IGIB, Delhi, India