Double stranded promoter region of BRAF undergoes to structural rearrangement in nearly physiological conditions

Greco, Maria Laura; Folini, Marco; Sissi, Claudia

doi:10.1016/j.febslet.2015.06.025

Cited by 11 publications

(6 citation statements)

References 43 publications

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“…A small stabilization is also observed for the i-motif structure formed by the complementary SMC03 sequence, which hardly melts at these conditions in pure aqueous media. Overall, this tendency agrees with previous reported works where it was shown that Hoogsteen base pairs are stabilized in the presence of PEG200 32,36 . On the contrary, the thermal stability of the Watson-Crick duplex formed by the mixture of the two sequences was reduced, a fact that also agreed with previous reports 37 .…”

Section: Resultssupporting

confidence: 93%

A pH-dependent bolt involving cytosine bases located in the lateral loops of antiparallel G-quadruplex structures within the SMARCA4 gene promotor

Benabou

Mazzini

Aviñó

et al. 2019

Sci Rep

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Some lung and ovarian tumors are connected to the loss of expression of SMARCA4 gene. In its promoter region, a 44-nucleotides long guanine sequence prone to form G-quadruplex structures has been studied by means of spectroscopic techniques (circular dichroism, molecular absorption and nuclear magnetic resonance), size exclusion chromatography and multivariate analysis. The results have shown that the central 21-nucleotides long sequence comprising four guanine tracts of disparate length is able to fold into a pH-dependent ensemble of G-quadruplex structures. Based on acid-base titrations and melting experiments of wild and mutated sequences, the formation of a c•c + base pair between cytosine bases present at the two lateral loops is shown to promote a reduction in conformational heterogeneity, as well as an increase in thermal stability. The formation of this base pair is characterized by a pK a value of 7.1 ± 0.2 at 20 °C and 150 mM KCl. This value, higher than those usually found in i-motif structures, is related to the additional stability provided by guanine tetrads in the G-quadruplex. To our knowledge, this is the first thermodynamic description of this base pair in loops of antiparallel G-quadruplex structures. Nucleic acids can adopt structures other than the Watson-Crick double helix, such as the i-motif or G-quadruplex structures with biologically relevant roles. The i-motif is formed within cytosine-rich (C-rich) sequences, being its building block the C•C + base pair. As the protonation of some cytosine bases is needed for its formation, the overall stability of the i-motif structure is strongly dependent on pH 1,2. Because of this fact, the potential role in vivo of i-motif structures is still under investigation 3,4. On the other hand, G-quadruplexes are formed by DNA or RNA sequences that are particularly rich in guanine bases. The building block of these structures is the G-quartet (or G-tetrad), which consist on four guanine bases held together by Hoogsteen-type hydrogen bonds in a planar arrangement (Fig. 1a). G-quadruplex structures are mainly stabilized by intramolecular or intermolecular stacking of these G-quartets, as well as by electrostatic interactions with cations (such as K + or Na +) placed within the structure. G-quadruplex structure variability depends strongly on the length of the guanine tracks, the loops connecting the stacked G-quartets, the syn/anti preference of the purine bases, and the presence of ligands or modifiers. Hence, G-quadruplexes may be classified into 'antiparallel' , 'parallel' or even 'hybrid' arrangements (Fig. 1b) 5. The in vitro formation of such structures in DNA sequences corresponding to the end of telomeres and to the promoter regions of several oncogenes has previously been shown, as well as their in vivo presence 6,7. Hence, the role of G-quadruplex structures in biological processes like cancer or aging seems to be clear 8-12. Accordingly, research is being made to identify ligands that could selectively bind to G-quadruplex structures to modulate g...

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Section: Resultssupporting

confidence: 93%

A pH-dependent bolt involving cytosine bases located in the lateral loops of antiparallel G-quadruplex structures within the SMARCA4 gene promotor

Benabou

Mazzini

Aviñó

et al. 2019

Sci Rep

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“…There are two main G- and C-rich segments in the promoter region of this gene. One called B-raf is located downstream of the transcription start site and other called B-raf-176 found upstream of the start site at −176 position …”

Section: Resultsmentioning

confidence: 99%

Environment-Sensitive Nucleoside Probe Unravels the Complex Structural Dynamics of i-Motif DNAs

Khatik

Srivatsan

2022

Bioconjugate Chem.

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Although evidence for the existence and biological role of i-motif (iM) DNA structures in cells is emerging, probing their structural polymorphism and identifying physiologically active conformations using currently available tools remain a major challenge. Here, we describe the development of an innovative device to investigate the conformation equilibrium of different iMs formed by C-rich telomeric repeat and oncogenic Braf promoter sequences using a new conformation-sensitive dualpurpose nucleoside probe. The nucleoside is composed of a trifluoromethyl-benzofuran-2-yl moiety at the C5 position of 2′deoxyuridine, which functions as a responsive fluorescent and 19 F NMR probe. While the fluorescent component is useful in monitoring and estimating the folding process, the 19 F label provides spectral signatures for various iMs, thereby enabling a systematic analysis of their complex population equilibrium under different conditions (e.g., pH, temperature, metal ions, and cell lysate). Distinct 19 F signals exhibited by the iMs formed by the human telomeric repeat helped in calculating their relative population. A battery of fluorescence and 19 F NMR studies using native and mutated B-raf oligonucleotides gave valuable insights into the iM structure landscape and its dependence on environmental conditions and also helped in predicting the structure of the major iM conformation. Overall, our findings indicate that the probe is highly suitable for studying complex nucleic acid systems.

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“…In a number of instances the sequences are within established nuclease hypersensitive/transcriptional activation sites within or upstream of promoter regions. Well-studied examples of genes containing such quadruplex sites for which quadruplex formation in vitro has been demonstrated include c- MYC , BCL -2, , h- RAS , k- RAS , c- KIT , , HIF , , b- RAF , , the androgen receptor, RET , , HSP90 , MET , and VEGF, whereas promoter quadruplexes appear to under-represented in genes associated with normal cellular processes. Many validated and putative promoter quadruplexes tend to be within 1 kb, more commonly immediately upstream and close to the transcription start site in these genes.…”

Section: Promoter Quadruplexesmentioning

confidence: 99%

Quadruplex Nucleic Acids as Novel Therapeutic Targets

2016

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Quadruplex-forming sequences are widely prevalent in human and other genomes, including bacterial ones. These sequences are over-represented in eukaryotic telomeres, promoters, and 5' untranslated regions. They can form quadruplex structures, which may be transient in many situations in normal cells since they can be effectively resolved by helicase action. Mutated helicases in cancer cells are unable to unwind quadruplexes, which are impediments to transcription, translation, or replication, depending on their location within a particular gene. Small molecules that can stabilize quadruplex structures augment these effects and produce cell and proliferation growth inhibition. This article surveys the chemical biology of quadruplexes. It critically examines the major classes of quadruplex-binding small molecules that have been developed to date and the various approaches to discovering selective agents. The challenges of requiring (and achieving) small-molecule targeted selectivity for a particular quadruplex are discussed in relation to the potential of these small molecules as clinically useful therapeutic agents.

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Double stranded promoter region of BRAF undergoes to structural rearrangement in nearly physiological conditions

Cited by 11 publications

References 43 publications

A pH-dependent bolt involving cytosine bases located in the lateral loops of antiparallel G-quadruplex structures within the SMARCA4 gene promotor

A pH-dependent bolt involving cytosine bases located in the lateral loops of antiparallel G-quadruplex structures within the SMARCA4 gene promotor

Environment-Sensitive Nucleoside Probe Unravels the Complex Structural Dynamics of i-Motif DNAs

Quadruplex Nucleic Acids as Novel Therapeutic Targets

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