Effects of Salt on the Stability of a G-Quadruplex from the Human c-MYC Promoter

Kim, Byul

doi:10.1016/j.bpj.2015.11.2190

Cited by 2 publications

(6 citation statements)

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“…The n M+ V M+ term in Equation (14) serves to take this contribution into account. On the other hand, G-quadruplex unfolding is not accompanied by a pronounced release of externally bound (condensed) counterions [ 34 , 35 , 56 ]. In this respect, G-quadruplexes are distinct from other DNA structures, such as the double-stranded B-DNA.…”

Section: Differential Volume Of Four-stranded and Single-stranded Conformationsmentioning

confidence: 99%

“…In this respect, G-quadruplexes are distinct from other DNA structures, such as the double-stranded B-DNA. Depending on the specific G-quadruplex topology and loop and flanking sequences, the unfolding transition may lead to a very slight release, no release, or significant uptake of external counterions [ 34 , 35 , 56 ]. Thus, the uptake or release of these counterions should contribute only modestly to the observed changes in volume.…”

Section: Differential Volume Of Four-stranded and Single-stranded Conformationsmentioning

confidence: 99%

“…The thermodynamic and kinetic properties of interconversions between the duplex, tetraplex, and single-stranded conformations will necessarily constrain and define the role these structures play in vivo [ 7 , 32 , 33 ]. The stability characteristics of G-quadruplex and i -motif structures have been extensively and systematically studied by varying parameters such as temperature, pH, salt, and the concentration of cosolvent [ 4 , 5 , 7 , 31 , 32 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 ]. These studies have provided a wealth of information about the modulation of the differential free energy of the folded and unfolded conformations of the two tetrahelical DNA structures as a function of temperature, pH, salt, and the identity and concentration of cosolvents [ 32 ].…”

Section: Introductionmentioning

confidence: 99%

“…The volumetric characteristics of G-quadruplexes and i -motifs reflect their structural and hydration properties, which differ significantly from those of other nucleic acid secondary structures, such as the B-form DNA duplex. The four-stranded structures are globular in shape with a surface charge density lower than that of other DNA structures; in addition, the G-quadruplex exhibits a compressible and expandable internal cavity [ 34 , 35 , 56 , 57 ].…”

Section: Introductionmentioning

confidence: 99%

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Volumetric Properties of Four-Stranded DNA Structures

Chalikian

Macgregor

2021

Biology

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Four-stranded non-canonical DNA structures including G-quadruplexes and i-motifs have been found in the genome and are thought to be involved in regulation of biological function. These structures have been implicated in telomere biology, genomic instability, and regulation of transcription and translation events. To gain an understanding of the molecular determinants underlying the biological role of four-stranded DNA structures, their biophysical properties have been extensively studied. The limited libraries on volume, expansibility, and compressibility accumulated to date have begun to provide insights into the molecular origins of helix-to-coil and helix-to-helix conformational transitions involving four-stranded DNA structures. In this article, we review the recent progress in volumetric investigations of G-quadruplexes and i-motifs, emphasizing how such data can be used to characterize intra-and intermolecular interactions, including solvation. We describe how volumetric data can be interpreted at the molecular level to yield a better understanding of the role that solute–solvent interactions play in modulating the stability and recognition events of nucleic acids. Taken together, volumetric studies facilitate unveiling the molecular determinants of biological events involving biopolymers, including G-quadruplexes and i-motifs, by providing one more piece to the thermodynamic puzzle describing the energetics of cellular processes in vitro and, by extension, in vivo.

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Section: Differential Volume Of Four-stranded and Single-stranded Conformationsmentioning

confidence: 99%

Section: Differential Volume Of Four-stranded and Single-stranded Conformationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Volumetric Properties of Four-Stranded DNA Structures

Chalikian

Macgregor

2021

Biology

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“…It is well-established that K + has a strong stabilizing effect on G-quadruplexes (53)(54)(55). Considering the high K + content in the E.coli cytosol, up to 200 mM (56), together with previous studies indicating a role of G-quadruplexes with Table 2 in the presence of K + and Li + according to the change at 260 nm using CD spectrophotometer indicates similar melting temperatures for both structures (73 • C and 71 • C, respectively).…”

Section: Identification Of G-quadruplexes With Shorter Stem G-tract Lmentioning

confidence: 99%

G-quadruplex prediction in E.coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch

Doluca¹,

Kaplan

Berber

et al. 2015

Preprint

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Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, noncanonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns.

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Effects of Salt on the Stability of a G-Quadruplex from the Human c-MYC Promoter

Cited by 2 publications

References 0 publications

Volumetric Properties of Four-Stranded DNA Structures

Volumetric Properties of Four-Stranded DNA Structures

G-quadruplex prediction in E.coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch

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