DSC Deconvolution of the Structural Complexity of c-MYC P1 Promoter G-Quadruplexes

Dettler, Jamie M.; Buscaglia, Robert; Le, Vu; Lewis, Edwin A.

doi:10.1016/j.bpj.2011.01.068

Cited by 31 publications

(24 citation statements)

References 42 publications

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“…According to data [6][7][8][9][10][11][12][13][14], the cation porphyrins TOEPyP4, Me-TOEPyP4, and TMPyP4 are strong stabilizing agents of DNA, its synthetic analogues and G-quadruplexes [15]. These porphyrins bind to DNA and polynucleotides, and form two main binding modes-intercalation into GCrich regions and external groove binding in AT-rich regions [8,13,16].…”

Section: Discussionmentioning

confidence: 99%

Zn Ions Change Binding Mode of TOEPyP4 with DNA and Cause DNA Transition from B to C and Zn-Like Conformations

Monaselidze¹,

Gorgoshidze²,

Khachidze³

et al. 2013

AJAC

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It is known that at low concentrations of TMPyP4, this porphyrin predominantly intercalates between GC pairs at GC-rich sites of duplex DNA and G-quadruplexes of various constructions, and stabilizes these structures. However, there are still some arguable suggestions about the exact binding sites and modes of TMPyP4 to GC-rich regions of DNA in case of helation of divalent ions with help of the porphrin, which makes porphyrin structure asymmetric. We examined TOEPyP4-analogue of TMPyP4-and studied interaction of TOEPyP4 into the calf thymus DNA at presence of nanomole concentrations of one of the most important microelements in cell vital function-Zn ion. On the basis of CD and absorption spectra of the DNA-TOEPyP4 mixture, it was determined that nanomole concentrations of Zn ions changed porphyrin intercalative binding mode to some external binding modes, which initiated transition of the canonic B conformation of DNA into C-like conformation, and incubation of the (DNA-TOEP4) + Zn mixture at 37˚C caused B-Z-like transition, but no transition was observed for the DNA-TOEPyP4 mixture. In particular, at 10 mM·NaCl, TOEPyP4/DNA = 0.02, the binding mode change was observed in the concentration range from 150 to 300 nM·Zn, and the B-C-like transition occurred from 150 to 600 nM·Zn. The B-Z transition at TOEPyP4/DNA = 0.015, Zn/DNA = 0.015, NaCI 10 mM, T = 37˚C was observed within incubation time interval from 0.3 to 20 hours, and maximal percents of Z-like form was seen when incubation time interval was from 5 to 6 hours.

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Section: Discussionmentioning

confidence: 99%

Zn Ions Change Binding Mode of TOEPyP4 with DNA and Cause DNA Transition from B to C and Zn-Like Conformations

Monaselidze¹,

Gorgoshidze²,

Khachidze³

et al. 2013

AJAC

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“…The melting temperature was determined as the T max of each transition. In cases where there is overlap between the lower and higher temperature transitions, the data were deconvoluted using Origin software, assuming each transition follows the two-state model of unfolding, 21 to determine Δ H for the transition of interest (Figure S2). …”

Section: Methodsmentioning

confidence: 99%

Unique Length-Dependent Biophysical Properties of Repetitive DNA

Huang

Delaney

2016

J. Phys. Chem. B

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Expansion of a trinucleotide repeat (TNR) sequence is the molecular signature of several neurological disorders. Formation of non-canonical structures by the TNR sequence is proposed to contribute to the expansion mechanism. Furthermore, it is known that the propensity for expansion increases with repeat length. In this work we use calorimetry to describe the thermodynamic parameters (ΔH, TΔS, and ΔG) of the non-canonical stem-loop hairpins formed by the TNR sequences (CAG)n and (CTG)n, and also the canonical (CAG)n/(CTG)n duplexes, for n = 6–14. Using a thermodynamic cycle, we calculated the same thermodynamic parameters describing the process of converting from non-canonical stem-loop hairpins to canonical duplex. In addition to these thermodynamic analyses, we used spectroscopic techniques to determine the rate at which the non-canonical structures convert to duplex, and the activation enthalpy ΔH‡ describing this process. We report that the thermodynamic parameters of unfolding the stem-loop (CTG)n and (CAG)n hairpins, along with the thermodynamic and kinetic properties of hairpin to duplex conversion, do not proportionally corresponding to the increase of length, but rather show a unique pattern that depends on whether the sequence has an even or odd number of repeats.

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“…Detailed computational and experimental (thermodynamic, kinetic) investigation of folding and ligand binding pathways of quadruplex DNA has begun very recently (17)(18)(19)(20)(21)(22). These studies leave no doubt that in solution, the Tel22 folding/unfolding process may consist of several structural steps, meaning that such solutions should be considered as equilibrium mixtures of Tel22 molecules in their folded (Q), unfolded (U), and intermediate (I) states.…”

Section: Introductionmentioning

confidence: 99%

Dominant Driving Forces in Human Telomere Quadruplex Binding-Induced Structural Alterations

Bončina

Hamon

Islam

et al. 2015

Biophysical Journal

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Recently various pathways of human telomere (ht) DNA folding into G-quadruplexes and of ligand binding to these structures have been proposed. However, the key issue as to the nature of forces driving the folding and recognition processes remains unanswered. In this study, structural changes of 22-mer ht-DNA fragment (Tel22), induced by binding of ions (K(+), Na(+)) and specific bisquinolinium ligands, were monitored by calorimetric and spectroscopic methods and by gel electrophoresis. Using the global model analysis of a wide variety of experimental data, we were able to characterize the thermodynamic forces that govern the formation of stable Tel22 G-quadruplexes, folding intermediates, and ligand-quadruplex complexes, and then predict Tel22 behavior in aqueous solutions as a function of temperature, salt concentration, and ligand concentration. On the basis of the above, we believe that our work sets the framework for better understanding the heterogeneity of ht-DNA folding and binding pathways, and its structural polymorphism.

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DSC Deconvolution of the Structural Complexity of c-MYC P1 Promoter G-Quadruplexes

Cited by 31 publications

References 42 publications

Zn Ions Change Binding Mode of TOEPyP4 with DNA and Cause DNA Transition from B to C and Zn-Like Conformations

Zn Ions Change Binding Mode of TOEPyP4 with DNA and Cause DNA Transition from B to C and Zn-Like Conformations

Unique Length-Dependent Biophysical Properties of Repetitive DNA

Dominant Driving Forces in Human Telomere Quadruplex Binding-Induced Structural Alterations

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