HOME
The Info List - G-quadruplex


--- Advertisement ---



(i) (i) (i)

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
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
G-quadruplex
structures can be computationally predicted from DNA
DNA
or RNA
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 G-quadruplex
G-quadruplex
3D Structure of the intramolecular human telomeric G-quadruplex
G-quadruplex
in 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 lines.

CONTENTS

* 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 G-quadruplex
G-quadruplex
motifs

QUADRUPLEX TOPOLOGY

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 intramolecular quadruplex.

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 strands of DNA
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 QUADRUPLEXES

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 NMR and 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 telomestatin .

NON-TELOMERIC QUADRUPLEXES

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 G-quadruplex
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
DNA
strand helps to maintain an open conformation of the coding DNA
DNA
strand and enhance an expression of the respective gene. Model for quadruplex-mediated down-regulation of gene expression

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. 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
DNA
structures that protect telomere ends and regulate telomere length.

LIGANDS WHICH BIND QUADRUPLEXES

One way of inducing or stabilizing G-quadruplex
G-quadruplex
formation is to introduce a molecule which can bind to the G-quadruplex
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 .

NOTES

* ^ Routh, Eric (2017). "A G-quadruplex
G-quadruplex
DNA-affinity approach for purification of enzymatically active G4 Resolvase1". J. Vis. Exp. 121. doi :10.3791/55496 . * ^ Han, Haiyong (2000). " G-quadruplex
G-quadruplex
DNA: a potential target for anti-cancer drug design". TiPS. 21: 136–142. doi :10.1016/s0165-6147(00)01457-7 – via Google Scholar. * ^ Largy, Eric; Mergny, Jean-Louis; Gabelica, Valérie (2016). "Chapter 7. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability". In Astrid, Sigel; Helmut, Sigel; Roland K.O., Sigel. The Alkali Metal Ions: Their Role in Life. Metal Ions in Life Sciences. 16. Springer. pp. 203–258. doi :10.1007/978-4-319-21756-7_7 . * ^ Bochman, Matthew L.; Paeschke, Katrin; Zakian, Virginia A. (2012). DNA
DNA
secondary structures: stability and function of G-quadruplex
G-quadruplex
structures. Nature Reviews Genetics. 13. Nature Publishing Group. pp. 770–780. doi :10.1038/nrg3296 . * ^ Rhodes, Daniela; Lipps, Hans J. (2015). "G-quadruplexes and their regulatory roles in biology" . Nucleic Acids Res. 43 (18): 8627–8637. PMC 4605312  . PMID 26350216 . doi :10.1093/nar/gkv862 . * ^ A B Simonsson, T. (2001). "G-Quadruplex DNA
DNA
Structures Variations on a Theme". Biological Chemistry. 382 (4): 621–628. PMID 11405224 . doi :10.1515/BC.2001.073 . * ^ Burge, S.; Parkinson, G. N.; Hazel, P.; Todd, A. K.; Neidle, S. (2006). "Quadruplex DNA: Sequence, topology and structure" . Nucleic Acids Research. 34 (19): 5402–5415. PMC 1636468  . PMID 17012276 . doi :10.1093/nar/gkl655 . * ^ Cao, K.; Ryvkin, P.; Johnson, FB. (2012). "Computational detection and analysis of sequences with duplex-derived interstrand G-quadruplex
G-quadruplex
forming potential." . Methods. 57 (1): 3–10. PMC 3701776  . PMID 22652626 . doi :10.1016/j.ymeth.2012.05.002 . * ^ Kudlicki, A. (2016). "G-Quadruplexes Involving Both Strands of Genomic DNA
DNA
Are Highly Abundant and Colocalize with Functional Sites in the Human
Human
Genome" . PLoS ONE. 11 (1): e0146174. PMC 4699641  . PMID 26727593 . doi :10.1371/journal.pone.0146174 . * ^ Schaffitzel, C; Berger, I; Postberg, J; Hanes, J; Lipps, H. J.; Plückthun, A (2001). " In vitro generated antibodies specific for telomeric guanine-quadruplex DNA
DNA
react with Stylonychia lemnae macronuclei" . Proceedings of the National Academy of Sciences. 98 (15): 8572–7. PMC 37477  . PMID 11438689 . doi :10.1073/pnas.141229498 . * ^ Paeschke, K.; Simonsson, T.; Postberg, J.; Rhodes, D.; Lipps, H. J. (2005). " Telomere end-binding proteins control the formation of G-quadruplex
G-quadruplex
DNA
DNA
structures in vivo". Nature Structural & Molecular Biology. 12 (10): 847–854. PMID 16142245 . doi :10.1038/nsmb982 . * ^ Simonsson, T.; Pecinka, P.; Kubista, M. (1998). " DNA
DNA
tetraplex formation in the control region of c-myc" . Nucleic Acids Research. 26 (5): 1167–1172. PMC 147388  . PMID 9469822 . doi :10.1093/nar/26.5.1167 . * ^ Siddiqui-Jain, A.; Grand, C. L.; Bearss, D. J.; Hurley, L. H. (2002). "Direct evidence for a G-quadruplex
G-quadruplex
in a promoter region and its targeting with a small molecule to repress c-MYC transcription" . Proceedings of the National Academy of Sciences. 99 (18): 11593–11598. PMC 129314  . PMID 12195017 . doi :10.1073/pnas.182256799 . * ^ Huppert, Julian L.; Balasubramanian, Shankar (14 December 2006). "G-quadruplexes in promoters throughout the human genome". Nucleic Acids Research. 35 (2): 406–413. doi :10.1093/nar/gkl1057 . * ^ Dai, Jixun; et al. (5 January 2006). "An Intramolecular G-Quadruplex Structure with Mixed Parallel/Antiparallel G-Strands Formed in the Human
Human
BCL-2 Promoter Region in Solution". J. Am. Chem. Soc. 128: 1096–1098. doi :10.1021/ja055636a . CS1 maint: Explicit use of et al. (link ) * ^ Fernando, Himesh; et al. (28 May 2006). "A Conserved Quadruplex Motif Located in a Transcription Activation Site of the Human
Human
c-kit Oncogene". Biochemistry. 45: 7854–7860. doi :10.1021/bi0601510 . CS1 maint: Explicit use of et al. (link ) * ^ Huppert, J. L.; Balasubramanian, S. (2005). "Prevalence of quadruplexes in the human genome" . Nucleic Acids Research. 33 (9): 2908–2916. PMC 1140081  . PMID 15914667 . doi :10.1093/nar/gki609 . * ^ Rawal, P.; Kummarasetti, V. B.; Ravindran, J.; Kumar, N.; Halder, K.; Sharma, R.; Mukerji, M.; Das, S. K.; Chowdhury, S. (2006). "Genome-wide prediction of G4 DNA
DNA
as regulatory motifs: Role in Escherichia coli global regulation" . Genome Research. 16 (5): 644–655. PMC 1457047  . PMID 16651665 . doi :10.1101/gr.4508806 . * ^ Bugaut A, Balasubramanian S (2012). "5\'-UTR RNA G-quadruplexes: translation regulation and targeting." . Nucleic Acids Res. 40 (11): 4727–41. PMC 3367173  . PMID 22351747 . doi :10.1093/nar/gks068 . * ^ Sen, D.; Gilbert, W. (1988). "Formation of parallel four-stranded complexes by guanine-rich motifs in DNA
DNA
and its implications for meiosis". Nature. 334 (6180): 364–366. PMID 3393228 . doi :10.1038/334364a0 . * ^ Kamath-Loeb, A.; Loeb, L. A.; Fry, M. (2012). Cotterill, Sue, ed. "The Werner Syndrome Protein
Protein
is Distinguished from the Bloom Syndrome Protein
Protein
by Its Capacity to Tightly Bind Diverse DNA Structures" . PLoS ONE. 7 (1): e30189. PMC 3260238  . PMID 22272300 . doi :10.1371/journal.pone.0030189 . * ^ Maizels, N.; Gray, L. T. (2013). Rosenberg, Susan M, ed. "The G4 Genome" . PLoS Genetics. 9 (4): e1003468. PMC 3630100  . PMID 23637633 . doi :10.1371/journal.pgen.1003468 . * ^ Biffi, G.; Tannahill, D.; McCafferty, J.; Balasubramanian, S. (2013). "Quantitative visualization of DNA
DNA
G-quadruplex
G-quadruplex
structures in human cells" . Nature Chemistry. 5 (3): 182–186. PMC 3622242  . PMID 23422559 . doi :10.1038/nchem.1548 . * ^ Rice C, Skordalakes E (2016). "Structure and function of the telomeric CST complex" . Computational and Structural Biotechnology Journal . 14: 161–167. PMC 4872678  . PMID 27239262 . doi :10.1016/j.csbj.2016.04.002 . * ^ Todd, A. K.; Johnston, M.; Neidle, S. (2005). "Highly prevalent putative quadruplex sequence motifs in human DNA" . Nucleic Acids Research. 33 (9): 2901–2907. PMC 1140077  . PMID 15914666 . doi :10.1093/nar/gki553 .

REFERENCES

* Jiangtao Ren; Jiahai Wang*; Lei Han; Erkang Wang*; Jin Wang* (2011). "Kinetically grafting G-qaudruplex onto DNA
DNA
nanostructure as structure and function encoding via DNA
DNA
machine". Chem. Commun. 47 (38): 10563–10565. doi :10.1039/c1cc13973h . * Johnson JE, Smith JS, Kozak ML, Johnson FB (2008). "In vivo veritas: using yeast to probe the biological functions of G-quadruplexes". Biochimie. 90 (8): 1250–1263. PMC 2585026  . PMID 18331848 . doi :10.1016/j.biochi.2008.02.013 . * Huppert JL, Balasubramanian S (2005). "Prevalence of quadruplexes in the human genome". Nucleic Acids Research. 33 (9): 2908–2916. PMC 1140081  . PMID 15914667 . doi :10.1093/nar/gki609 . * Todd AK, Johnston M, Neidle S (2005). "Highly prevalent putative quadruplex sequence motifs in human DNA". Nucleic Acids Research. 33 (9): 2901–2907. PMC 1140077  . PMID 15914666 . doi :10.1093/nar/gki553 . * Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S (2006). "Quadruplex DNA: sequence, topology and structure". Nucleic Acids Research. 34 (19): 5402–5415. PMC 1636468  . PMID 17012276 . doi :10.1093/nar/gkl655 . * Siddiqui-Jain A, Grand CL, Bearss DJ, Hurley LH (2002). "Direct evidence for a G-quadruplex
G-quadruplex
in a promoter region and its targeting with a small molecule to repress c-MYC transcription". PNAS. 99 (18): 11593–8. PMC 129314  . PMID 12195017 . doi :10.1073/pnas.182256799 . * Rawal P, Kummarasetti VB, Ravindran J, Kumar N, Halder K, Sharma R, Mukerji M, Das SK, Chowdhury S (2006). "Genome-wide prediction of G4 DNA
DNA
as regulatory motifs: Role in Escherichia coli global regulation". Genome Res. 16 (5): 644–55. PMC 1457047  . PMID 16651665 . doi :10.1101/gr.4508806 . * Xu Hou; Wei Guo; Fan Xia; Fu-Qiang Nie; Hua Dong; Ye Tian; Liping Wen; Lin Wang; Liuxuan Cao; Yang Yang; Jianming Xue; Yanlin Song; Yugang Wang; Dongsheng Liu; Lei Jiang (2009). "A biomimetic potassium responsive nanochannel: G-quadruplex
G-quadruplex
DNA
DNA
conformational switching in a synthetic nanopore". J. Am. Chem. Soc. 131 (22): 7800–7805. PMID 19435350 . doi :10.1021/ja901574c . * Neidle & Balasubramanian, ed. (2006). Quadruplex Nucleic Acids. ISBN 0-85404-374-8 . * Rowland, Gerald B.; Barnett, Kerry; DuPont, Jesse I.; Akurathi, Gopalakrishna; Le, Vu H.; Lewis, Edwin A (1 December 2013). "The effect of pyridyl substit