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Stability and kinetics of G-quadruplex structures.

Lane AN, Chaires JB, Gray RD, Trent JO - Nucleic Acids Res. (2008)

Bottom Line: Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes.Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium.The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology Program, JG Brown Cancer Center, University of Louisville, KY 40202, USA. anlane01@gwise.louisville.edu

ABSTRACT
In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.

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Thermal unfolding curves for the human intramolecular quadruplex. Transition curves for the denaturation of the Na+ form of the human telomere quadruplex sequence 5′AGGG(TTAGGG)3 in phosphate buffer (pH 7.0) containing 200 mM NaCl. (A) Absorbance at 295 nm versus temperature. The lines were calculated to fit the pre- and post-transition baselines. (B) Fraction of unfolded molecules (α) versus temperature after correction of the data in panel (A) for the sloping baselines and normalization. The straight line indicates the slope at the transition midpoint. (C) First derivative of the data in panel (B).
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Figure 6: Thermal unfolding curves for the human intramolecular quadruplex. Transition curves for the denaturation of the Na+ form of the human telomere quadruplex sequence 5′AGGG(TTAGGG)3 in phosphate buffer (pH 7.0) containing 200 mM NaCl. (A) Absorbance at 295 nm versus temperature. The lines were calculated to fit the pre- and post-transition baselines. (B) Fraction of unfolded molecules (α) versus temperature after correction of the data in panel (A) for the sloping baselines and normalization. The straight line indicates the slope at the transition midpoint. (C) First derivative of the data in panel (B).

Mentions: Monitoring any of these spectroscopic signals as a function of temperature provides a denaturation transition curve (‘melting curve’), which contains thermodynamic information. Figure 6 shows examples of such transition curves transformed in a variety of ways. Figure 6A shows raw absorbance data collected at 295 nm, a wavelength particularly sensitive to disruption of G-quadruplexes (138). Figure 6B shows the same data after transformation and normalization to show the fraction denatured (α) as a function of temperature. The first derivative of the transition curve in panel B is shown in Figure 6C. This is a common approach to directly estimating the Tm of a transition, and also for enhancing the detection of multiple intermediates that differ in their Tm-values. Specific analytical equations are available for extracting thermodynamic parameters from each of these curves are available, as is described in detail in (135,136). Application of these equations yield a thermodynamic profile for the denaturation process that includes the free-energy change (ΔG), the enthalpy change (ΔH) and the entropy change (ΔS). In principle, but rarely in practice, the change in heat capacity [ΔCp, cf. Equation (3)] might also be obtained from thermal denaturation curves. There are, however, numerous potential pitfalls in reliably obtaining these thermodynamic parameters.Figure 6.


Stability and kinetics of G-quadruplex structures.

Lane AN, Chaires JB, Gray RD, Trent JO - Nucleic Acids Res. (2008)

Thermal unfolding curves for the human intramolecular quadruplex. Transition curves for the denaturation of the Na+ form of the human telomere quadruplex sequence 5′AGGG(TTAGGG)3 in phosphate buffer (pH 7.0) containing 200 mM NaCl. (A) Absorbance at 295 nm versus temperature. The lines were calculated to fit the pre- and post-transition baselines. (B) Fraction of unfolded molecules (α) versus temperature after correction of the data in panel (A) for the sloping baselines and normalization. The straight line indicates the slope at the transition midpoint. (C) First derivative of the data in panel (B).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553573&req=5

Figure 6: Thermal unfolding curves for the human intramolecular quadruplex. Transition curves for the denaturation of the Na+ form of the human telomere quadruplex sequence 5′AGGG(TTAGGG)3 in phosphate buffer (pH 7.0) containing 200 mM NaCl. (A) Absorbance at 295 nm versus temperature. The lines were calculated to fit the pre- and post-transition baselines. (B) Fraction of unfolded molecules (α) versus temperature after correction of the data in panel (A) for the sloping baselines and normalization. The straight line indicates the slope at the transition midpoint. (C) First derivative of the data in panel (B).
Mentions: Monitoring any of these spectroscopic signals as a function of temperature provides a denaturation transition curve (‘melting curve’), which contains thermodynamic information. Figure 6 shows examples of such transition curves transformed in a variety of ways. Figure 6A shows raw absorbance data collected at 295 nm, a wavelength particularly sensitive to disruption of G-quadruplexes (138). Figure 6B shows the same data after transformation and normalization to show the fraction denatured (α) as a function of temperature. The first derivative of the transition curve in panel B is shown in Figure 6C. This is a common approach to directly estimating the Tm of a transition, and also for enhancing the detection of multiple intermediates that differ in their Tm-values. Specific analytical equations are available for extracting thermodynamic parameters from each of these curves are available, as is described in detail in (135,136). Application of these equations yield a thermodynamic profile for the denaturation process that includes the free-energy change (ΔG), the enthalpy change (ΔH) and the entropy change (ΔS). In principle, but rarely in practice, the change in heat capacity [ΔCp, cf. Equation (3)] might also be obtained from thermal denaturation curves. There are, however, numerous potential pitfalls in reliably obtaining these thermodynamic parameters.Figure 6.

Bottom Line: Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes.Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium.The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology Program, JG Brown Cancer Center, University of Louisville, KY 40202, USA. anlane01@gwise.louisville.edu

ABSTRACT
In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.

Show MeSH