Structural transition from antiparallel to parallel G-quadruplex of d(G4T4G4) induced by Ca2+

Miyoshi, Daisuke; Nakao, Atsushi; Sugimoto, Naoki

doi:10.1093/nar/gkg211

Cited by 169 publications

(124 citation statements)

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“…Under our conditions, transitions were observed by ESI-MS only for the strands d(G 3 G 3 ) and d(G 4 G 3 ), but not for d(G 4 G 4 ) and d(G 3 G 4 ), even when the latter were incubated in the NH 4 ϩ solution for more than 10 days. Miura et al found that the antiparallel bimolecular quadruplex formed by the strand d(G 4 G 4 ) was generated at low concentrations of Na ϩ and K ϩ , and that the bimolecular species was converted to the parallel four-stranded quadruplex when the concentrations of both alkali ions were increased in a range of 65-225 mM, the K ϩ being more 4 and finally to a G-wire, and the transitions were induced by the presence of Ca 2ϩ [32].°Sen°and°Gilbert°proposed°that°the°foldback°bimo-lecular quarduplexes were overstabilized intermediates and expected all of the quadruplexes formed by single, double, or four strands to be finally converted into four-stranded°parallel°quadruplexes° [30].°In°this°case, the transitions of the bimolecular species to the tetramolecular one are probably facilitated by specific structural and stability characteristics of the bimolecular quadruplexes. If 2 contains two dangling guanine residues residing at the same end of the quadruplex.…”

Section: Detections Of Trimolecular and Tetramolecular Speciesmentioning

confidence: 99%

“…As an intermediate, the bimolecular structure can°vary°from°one°form°to°another° [30] 2 and unfold the structure; the strands then rearrange alignment in the denatured state and pair with other strands to form more stable parallel structures° [32].°Xu°et°al.°indicate°a°possible°shift°be-tween the mixed-parallel/antiparallel and the chairtype quadruplexes formed by the human telomere sequence°in°K ϩ°i on°solution° [36].°In°the°present°work, we show that two of the four bimolecular quadruplexes are not terminal products and are converted to more stable structures. The transition rates probably depend on the stabilities and specific structures of the bimolecular quadruplexes, as well as on the solution conditions.…”

Section: Spectra Of the Bimolecular And Higher-order Speciesmentioning

confidence: 99%

“…Miura et al, using Raman spectroscopy, detected the transition of the antiparallel bimolecular [d(G 4 G 4 )] 2 to the parallel four-stranded structure in the solution containing Na ϩ and K ϩ by changing the K ϩ /Na ϩ ratio [31]. Miyoshi [32].…”

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confidence: 99%

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Bimolecular quadruplexes and their transitions to higher-order molecular structures detected by ESI-FTICR-MS

Guo

Liu

2007

J. Am. Soc. Mass Spectrom.

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Four individual quadruplexes, which are self-assembled in ammonium acetate solution from telomeric sequences of closely related DNA strands-d(G 4 T 4 G 4 ), d(G 3 T 4 G 4 ), d(G 3 T 4 G 3 ), and d(G 4 T 4 G 3 )-have been detected in the gas phase using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The bimolecular quadruplexes associate with the same number of NH 4 ϩ in the gas phase as NMR shows that they do in solution. The quadruplex structures formed in solution are maintained in the gas phase. Furthermore, the mass spectra show that the bimolecular quadruplexes generated by the strands d( Of particular interest is a telomeric DNA that consists of repeating sequences, such as TTAGGG in vertebrates and TTTTGGGG in Oxytricha. These sequences have been proven to fold into quadruplexes in vitro and potentially have the function of inhibiting telomerase activities. The telomerase, a reverse enzyme expressed in more than 80% of tumor cells, responds for the replication of the telomeric DNA and has been considered as a target for anticancer drug design [4,5]. Guanine-rich oligonucleotides can also self-associate into higher-order structures, such as supermolecular G-wires [6], which serve as artificial ion channels and ion receptors and which have a wide range of applications in medicine, materials science, and nanotechnology [2,7,8].DNA quadruplex structures can be formed from one, two, or four oligonucleotide strands and are stabilized by coordinated monovalent cations acting between adjacent G-quartets [1, 9 -11]. The strands with single repeating guanine sequences usually arrange themselves from the 5= to the 3= end in parallel four-stranded quadruplexes, whereas the strands with more than two tracks of repeating guanine units can form a number of quadruplexes that are distinguished by their strand number, strand orientation, and loop types. The structural topologies of DNA quadruplexes also drastically change with slight changes of the DNA sequences, with the nature of the cationic species and with their concentrations in solution. As a result, the structures of DNA quadruplexes are far from being fully recognized and have been of concern to researchers because of their potential implications in biological and structural applications.Development in electrospray ionization mass spectrometry (ESI-MS) has been shown to be superior in the analysis of DNA noncovalent complexes in terms of speed, sensitivity, stoichiometry, and specificity compared to other analytical techniques [12]. Previous work by ourselves and others have shown that some specific DNA conformations, such as hairpins, triplexes, and quadruplexes formed in solution, can survive in the gas phase [13][14][15][16][17][18][19][20]. This prompted us to explore the structural properties of DNA quadruplexes with ESI-MS so as to add new information concerning them.

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Section: Detections Of Trimolecular and Tetramolecular Speciesmentioning

confidence: 99%

Section: Spectra Of the Bimolecular And Higher-order Speciesmentioning

confidence: 99%

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Bimolecular quadruplexes and their transitions to higher-order molecular structures detected by ESI-FTICR-MS

Guo

Liu

2007

J. Am. Soc. Mass Spectrom.

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“…For parallel G quadruplex structure formation, a positive band at ∼265 nm and a negative band at ∼240 nm have been observed, whereas the signatures of an antiparallel G quadruplex structure are a negative band at ∼260 nm and a positive band at ∼295 nm (Miyoshi et al 2003;Paramasivan et al 2007;Kypr et al 2009;Vorlícǩová et al 2012;Randazzo et al 2013). Both PSD-95 Q1 and Q2 exhibit the signature of a parallel G quadruplex structure, even in the absence of K + ions (Fig.…”

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confidence: 93%

G quadruplex RNA structures in PSD-95 mRNA: potential regulators of miR-125a seed binding site accessibility

Stefanovic

Bassell

Mihailescu

2014

RNA

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Fragile X syndrome (FXS) is the most common inherited form of intellectual disability caused by the CGG trinucleotide expansion in the 3 ′ -untranslated region of the FMR1 gene on the X chromosome, that silences the expression of the Fragile X mental retardation protein (FMRP). FMRP has been shown to bind to a G-rich region within the PSD-95 mRNA which encodes for the postsynaptic density protein 95 (PSD-95), and together with the microRNA miR-125a, to play an important role in the reversible inhibition of the PSD-95 mRNA translation in neurons. The loss of FMRP in Fmr1 KO mice disables this translation control in the production of the PSD-95 protein. Interestingly, the miR-125a binding site on PSD-95 mRNA is embedded in the G-rich region bound by FMRP and postulated to adopt one or more G quadruplex structures. In this study, we have used different biophysical techniques to validate and characterize the formation of parallel G quadruplex structures and binding of miR-125a to its complementary sequence located within the 3 ′ UTR of PSD-95 mRNA. Our results indicate that the PSD-95 mRNA G-rich region folds into alternate G quadruplex conformations that coexist in equilibrium. miR-125a forms a stable complex with PSD-95 mRNA, as evident by characteristic Watson-Crick base-pairing that coexists with one of the G quadruplex forms, suggesting a novel mechanism for G quadruplex structures to regulate the access of miR-125a to its binding site.

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“…It was found that Ca 2+ and molecular crowding induced G-wire formation of d(G 4 T 4 G 4 ). 40,41 We further demonstrated that a single G to A substitution in the loops leads to a drastically different structure under molecular crowding conditions. Under crowding conditions, d(T 2 (G 3 T 2 G) 3 G) folds into very long G-wires, whereas d((G 3 T 2 A) 3 G 3 ) folds into antiparallel G-quadruplexes.…”

Section: Dna Logic Gates Based On Structural Polymorphismsmentioning

confidence: 76%

Designable DNA Functions toward New Nanobiotechnology

Sugimoto¹

2009

Bulletin of the Chemical Society of Japan

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DNA has many properties that cannot be attained with other molecules. The ability of DNA to form base pairing and its structural polymorphism allow the formation of distinct secondary and tertiary structures and may have further catalytic or aptamer function. It is also of great advantage that the base pairing of a short oligonucleotide sequence can be well predicted and designed with the thermodynamic parameters of WatsonÍCrick base pairs, mismatch pairs, and noncanonical base pairs based on the nearest-neighbor model. We have investigated the thermodynamics of various types of oligonucleotide structures, and obtained the nearest-neighbor parameters for WatsonÍCrick base pair formations and fundamental information regarding the nucleotide interactions. The data of the DNA interaction energy were also applied for molecular design of a DNA logic gate and DNA nanowire. I will further discuss the importance of quantitative data of DNA interaction energy toward the rational design of artificial DNAs carried out by our laboratory, such as base pairmimic nucleosides and DNA containing bipyridine units, useful as nanobiodevices and nanobiomaterial.1. Extraction of "Quantity" from the Quality of DNA 1.1 DNA toward the Nanobio-Research Field. DNA has excellent properties applied to technology uses, such as the recognition of target sequences, self-assembly into defined structures, and catalytic or aptamer functions. Oligonucleotides have been examined for constructing functional molecules, because they can be synthesized by an automated synthesizer and are available commercially at a relatively low cost. Association of oligonucleotides further constructs large-sized complexes and their noncovalent interaction has an advantage of reversible assembly. Moreover, conjugation of a DNA strand with other functional materials including other biomolecules, fluorescent dyes, and metal plate surfaces or nanoparticles allows an expansion of the DNA function. Therefore, DNA is one of the most promising nanobiomaterials suitable as nanoscale materials, nano-sized devices, and medicinal and therapeutic uses. In fact, development of nanobiomaterials that apply the properties of DNA to nanotechnology have become of broader interest over the past several years. 1Í4The most important property of DNA is the ability to form base pairing mediated by interbase hydrogen bonds. The major structure of DNA is the double helical structure of WatsonÍ Crick base pairs. Figure 1 shows the famous WatsonÍCrick base pairs, of which the purine (A or G) and pyrimidine (C, T, or U) nucleotides associate with each other in accordance to the geometry of hydrogen donors and acceptors on the bases. All the nucleotide bases adopt an anti configuration at the glycosidic bond in a right-handed antiparallel-stranded duplex, and the structural isomorphism among A/T, A/U, and G/C base pairs ensures the distance between glycosidic bonds of approximately 1 nm. The base stacking interaction is important for the integrity of the duplex. The stacking interaction does not ...

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Structural transition from antiparallel to parallel G-quadruplex of d(G4T4G4) induced by Ca2+

Cited by 169 publications

References 38 publications

Bimolecular quadruplexes and their transitions to higher-order molecular structures detected by ESI-FTICR-MS

Bimolecular quadruplexes and their transitions to higher-order molecular structures detected by ESI-FTICR-MS

G quadruplex RNA structures in PSD-95 mRNA: potential regulators of miR-125a seed binding site accessibility

Designable DNA Functions toward New Nanobiotechnology

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