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Through recent research into this specific gene pathway, the polypurine and polypyrimidine region allows for the transcription of this specific gene and the formation of an intramolecular G-quadruplex structure. However, more research is necessary to determine whether the formation of G-quadruplex regulates the expression of this gene in a positive or negative manner. The c-kit oncogene deals with a pathway that encodes an RTK, which was shown to have elevated expression levels in certain types of cancer.

The rich guanine sequence of this promoter region has shown the ability to form a variety of quadruplexes. Current research on this pathway is focusing on discovering the biological function of this specific quadruplex formation on the c-kit pathway, while this quadruplex sequence has been noticed in various species. The RET oncogene functions in the transcription of kinase which has been abundant in certain types of cancer.

The guanine rich sequence in the promoter region for this pathway exudes a necessity for baseline transcription of this receptor tyrosine kinase. In certain types of cancers, the RET protein has shown increased expression levels. The research on this pathway suggested the formation of a G-quadruplex in the promoter region and an applicable target for therapeutic treatments.

Another oncogene pathway involving PDGF-A, platelet-derived growth factor, involves the process of wound healing and function as mitogenic growth factors for cells. High levels of expression of PDGF have been associated with increased cell growth and cancer. The presence of a guanine-rich sequence in the promoter region of PDGF-A has exhibited the ability to form intramolecular parallel G-quadruplex structures and remains suggested to play a role in transcriptional regulation of PDGF-A.

However, research has also identified the presence of G-quadruplex structures within this region due to the interaction of TMPyP4 with this promoter sequence. Telomeres are generally made up of G-quadruplexes and remain important targets for therapeutic research and discoveries.

These complexes have a high affinity for porphyrin rings which makes them effective anticancer agents. Ligand design and development remains an important field of research into therapeutic reagents due to the abundance of G-quadruplexes and their multiple conformational differences. One type of ligand involving a Quindoline derivative, SYUIQ, utilizes the stabilization of G-quadruplexes in promoter regions to inhibit the production of both the c-Myc protein product and the human telomerase reverse transcriptase hTERT.

This main pathway of targeting this region results in the lack of telomerase elongation, leading to arrested cell development. Further research remains necessary for the discovery of a single gene target to minimize unwanted reactivity with more efficient antitumor activity.

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 , which can be both small molecules and proteins , 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. Cationic porphyrins have been shown to bind intercalatively with G-quadruplexes, as well as the molecule telomestatin.

The binding of ligands to G-quadruplexes is vital for anti-cancer pursuits because G-quadruplexes are found typically at translocation hot spots. MM41, a ligand that binds selectively for a quadruplex on the BCL-2 promoter, is shaped with a central core and 4 side chains branching sterically out.

The shape of the ligand is vital because it closely matches the quadruplex which has stacked quartets and the loops of nucleic acids holding it together. What makes this binding strong is the fluidity in the position of the loops to better associate with the ligand side chains. When designing ligands to be bound to G-quadruplexes, the ligands have a higher affinity for parallel folded G-quadruplexes. It has been found that ligands with smaller side chains bind better to the quadruplex because smaller ligands have more concentrated electron density.

Furthermore, the hydrogen bonds of ligands with smaller side chains are shorter and therefore stronger. Ligands with mobile side chains, ones that are able to rotate around its center chromophore, associate more strongly to G-quadruplexes because conformation of the G4 loops and the ligand side chains can align.

Identifying and predicting sequences which have the capacity to form quadruplexes is an important tool in further understanding their role. Although the rule effectively identifies sites of G-quadruplex formation, it also identifies a subset of the imperfect homopurine mirror repeats capable of triplex formation [78] and C-strand i-motif formation. In one study, [81] it was found that the observed number per base pair i. This suggests that the sequences may be under positive selection enabled by the evolution of systems capable of suppressing non-B structure formation.

A number of experimental methods have been developed to support the computational prediction of G-quadruplexes. These methods can be broadly defined into two classes: biophysical and biochemical methods. Biochemical techniques were employed to interrogate G-quadruplex formation in a longer sequence context. In the DNA polymerase stop assay, the formation of a G-quadruplex in a DNA template can act as a roadblock and cause polymerase stalling, which halts the primer extension.

The topology of the G-quadruplex structure can be determined by monitoring the positive or negative circular dichroism CD signals at specific wavelengths. Likewise, the thermostability of the G-quadruplex structure can be identified by observing the UV signal at nm. Another approach for detection of G-quadruplexes includes nanopore -based methods. Firstly, it was shown that biological nanopores can detect G-quadruplexes based on size exclusion and specific interaction of G-quadruplex and protein nanocavity.

G-quadruplexes have been implicated in neurological disorders through two main mechanisms. The first is through expansions of G-repeats within genes that lead to the formation of G-quadruplex structures that directly cause disease, as is the case with the C9orf72 gene and amyotrophic lateral sclerosis ALS or frontotemporal dementia FTD. The second mechanism is through mutations that affect the expression of G-quadruplex binding proteins, as seen in the fragile X mental retardation gene 1 FMR1 gene and Fragile X Syndrome.

The C9orf72 gene codes for the protein C9orf72 which is found throughout the brain in neuronal cytoplasm and at presynaptic terminals. Nucleolin is involved in the synthesis and maturation of ribosomes within the nucleus, and separation of nucleolin by the mutated RNA transcripts impairs nucleolar function and ribosomal RNA synthesis. Fragile X mental retardation protein FMRP is a widely expressed protein coded by the FMR1 gene that binds to G-quadruplex secondary structures in neurons and is involved in synaptic plasticity.

This repeat expansion promotes DNA methylation and other epigenetic heterochromatin modifications of FMR1 that prevent the transcription of the gene, leading to pathological low levels of FMRP. Antisense-mediated interventions and small-molecule ligands are common strategies used to target neurological diseases linked to G-quadruplex expansion repeats.

Therefore, these techniques are especially advantageous for targeting neurological diseases that have a gain-of-function mechanism, which is when the altered gene product has a new function or new expression of a gene; this has been detected in the C9orf72 chromosome 9 open reading frame Antisense therapy is the process by which synthesized strands of nucleic acids are used to bind directly and specifically to the mRNA produced by a certain gene, which will inactivate it.

Another commonly used technique is the utilization of small-molecule ligands. These can be used to target G-quadruplex regions that cause neurological disorders. Approximately 1, various G-quadruplex ligands exist in which they are able to interact via their aromatic rings ; this allows the small-molecule ligands to stack on the planar terminal tetrads within the G-quadruplex regions. A disadvantage of using small-molecule ligands as a therapeutic technique is that specificity is difficult to manage due to the variability of G-quadruplexes in their primary sequences, orientation, thermodynamic stability, and nucleic acid strand stoichiometry.

As of now, [ when? This provides evidence that small-molecule ligands are an effective and efficient process to target GGGGCC regions, and that specificity for small-molecule ligand binding is a feasible goal for the scientific community. Metal complexes have a number of features that make them particularly suitable as G4 DNA binders and therefore as potential drugs.

While the metal plays largely a structural role in most G4 binders, there are also examples where it interacts directly with G4s by electrostatic interactions or direct coordination with nucleobases. From Wikipedia, the free encyclopedia.

Structure in molecular biology. 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. PMC PMID Journal of Visualized Experiments. Metal Ions in Life Sciences. Bibcode : Natur. S2CID Genome Research.

Chemical and Engineering News. Journal of Medicinal Chemistry. Trends in Pharmacological Sciences. Nature Reviews. Nucleic Acids Research. Bibcode : PNAS Biological Chemistry. Bibcode : PLoSO.. Journal of the American Chemical Society. Analytical Chemistry. Journal of Biological Chemistry. ISSN International Journal of Molecular Sciences. Cotterill S ed. Bibcode : PLoSO The Journal of Biological Chemistry. Rosenberg SM ed. PLOS Genetics. Nature Chemistry. Bibcode : NatCh Computational and Structural Biotechnology Journal.

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