Hydration is Required in DNA G‐Quadruplex–Protein Binding

Nagatoishi, Satoru; Isono, Noburu; Tsumoto, Kouhei; Sugimoto, Naoki

doi:10.1002/cbic.201100264

Cited by 16 publications

(26 citation statements)

References 48 publications

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“…As for ligand binding, information regarding hydration changes upon protein binding can be obtained by studying the interaction in the presence of cosolutes. For example, Nagatoishi et al determined the number of water molecules bound upon binding of quadruplex-forming aptamer TBA to thrombin (about 68 water molecules) [46].…”

Section: Studying G-quadruplex Binding Propertiesmentioning

confidence: 99%

“…ITC is a useful tool to study the energetic aspects of G-quadruplexes interaction with ligands and other biomolecules [16], both in the absence and presence of molecular crowding conditions [46]. A typical ITC experiment is carried out by the stepwise addition of one of the component of the complex (e.g.…”

Section: Studying G-quadruplex Binding Propertiesmentioning

confidence: 99%

“…Molecular crowding has a remarkable impact on the structural and biophysical properties of G-quadruplexes and can affect rates, equilibria, and mechanisms of their interaction with proteins or small ligands [11,[45][46][47]. Given the profound influence on the Gquadruplexes, it would be important to know the effect of molecular crowding on quadruplex-ligand interaction, which should not be neglected when developing an efficient drug targeting G-quadruplex structures.…”

Section: Studying G-quadruplex Binding Propertiesmentioning

confidence: 99%

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Studying the effect of crowding and dehydration on DNA G-quadruplexes

Petraccone

Pagano

Giancola

2012

Methods

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Section: Studying G-quadruplex Binding Propertiesmentioning

confidence: 99%

Section: Studying G-quadruplex Binding Propertiesmentioning

confidence: 99%

Section: Studying G-quadruplex Binding Propertiesmentioning

confidence: 99%

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Studying the effect of crowding and dehydration on DNA G-quadruplexes

Petraccone

Pagano

Giancola

2012

Methods

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“…Water plays a dominant role in guiding the conformational preferences of nucleic acids, as well as in modulating and mediating nucleic acid recognition by small molecules and RNA‐ and DNA‐binding proteins . With respect to G‐quadruplexes, water has been shown to participate in and modulate the thermodynamic stability of G‐quadruplex formation, G‐quadruplex polymorphism, and protein‐G‐quadruplex recognition . Hence, an understanding of the interplay between various molecular forces that govern the polymorphism of G‐quadruplex conformations requires a combination of structural, thermodynamic, and hydration characterizations.…”

Section: Introductionmentioning

confidence: 99%

Folding thermodynamics of the hybrid‐1 type intramolecular human telomeric G‐quadruplex

et al. 2013

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Guanine-rich DNA sequences that may form G-quadruplexes are located in strategic DNA loci with the ability to regulate biological events. G-quadruplexes have been under intensive scrutiny owing to their potential to serve as novel drug targets in emerging anticancer strategies. Thermodynamic characterization of G-quadruplexes is an important and necessary step in developing predictive algorithms for evaluating the conformational preferences of G-rich sequences in the presence or the absence of their complementary C-rich strands. We use a combination of spectroscopic, calorimetric, and volumetric techniques to characterize the folding/unfolding transitions of the 26-meric human telomeric sequence d[A3G3(T2AG3)3A2]. In the presence of K+ ions, the latter adopts the hybrid-1 G-quadruplex conformation, a tightly packed structure with an unusually small number of solvent-exposed atomic groups. The K+-induced folding of the G-quadruplex at room temperature is a slow process that involves significant accumulation of an intermediate at the early stages of the transition. The G-quadruplex state of the oligomeric sequence is characterized by a larger volume and compressibility and a smaller expansibility than the coil state. These results are in qualitative agreement with each other all suggesting significant dehydration to accompany the G-quadruplex formation. Based on our volume data, 432±19 water molecules become released to the bulk upon the G-quadruplex formation. This large number is consistent with a picture in which DNA dehydration is not limited to water molecules in direct contact with the regions that become buried but involves a general decrease in solute-solvent interactions all over the surface of the folded structure.

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“…Naoki Sugimoto (Konan University, Japan) demonstrated that thrombin and potassium use different mechanisms to stabilize G4 formation distinguished by specific binding between thrombin and thymine bases within quadruplex loops. Furthermore, water –which may be of limited availability under crowded macromolecular conditions – is required for the binding of thrombin to TBA [14]. Interestingly, water may be more available in the relatively dilute environment of the bloodstream, where thrombin principally functions, consistent with the biological relevance of these findings.…”

Section: Discussionmentioning

confidence: 82%

G-ruption: The third international meeting on G-quadruplex and G-assembly

2012

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A three and a half day conference focusing on nucleic acid structures called G-quadruplexes (G4s) and other guanine-based assemblies was held in Sorrento, Italy (June 28–July 1, 2011) and featured 35 invited talks and over 89 posters. The G-quadruplex field continues to expand at an explosive rate with the emergence of new connections to biology, chemistry, physics, and nanotechnology. Following the trend established by the previous two international G4 meetings, the conference touched upon all these areas and facilitated productive exchanges of ideas between researchers from all over the world.

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Hydration is Required in DNA G‐Quadruplex–Protein Binding

Cited by 16 publications

References 48 publications

Studying the effect of crowding and dehydration on DNA G-quadruplexes

Studying the effect of crowding and dehydration on DNA G-quadruplexes

Folding thermodynamics of the hybrid‐1 type intramolecular human telomeric G‐quadruplex

G-ruption: The third international meeting on G-quadruplex and G-assembly

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