DNA melting transition in aqueous magnesium salt solutions

Ott, Gary; Ziegler, Robert C.; Bauer, William R.

doi:10.1021/bi00686a022

Cited by 25 publications

(16 citation statements)

References 31 publications

(23 reference statements)

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“…(c) At high concentration (10 -2 M), Mg 2+ destabilizes free DNA (33,36), perhaps by "charge reversal", i.e. by extensive binding to all phosphates.…”

Section: Discussionmentioning

confidence: 99%

DNA denaturation in situ. Effect of divalent cations and alcohols.

Darżynkiewicz¹,

Traganos²,

Sharpless³

et al. 1976

The Journal of Cell Biology

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Heat denaturation profiles of rat thymus DNA, in intact cells, reveal the presence of two main DNA fractions differing in sensitivities to heat. The thermosensitive DNA fraction shows certain properties similar to those of free DNA: its stability to heat is decreased by alcohols and is increased in the presence of the divalent cations Ca 2+, Mn 2+, or Mg 2+ at, concentrations of 0.1-! .0 mM. Unlike free DNA, however, this fraction denatures over a wide range of temperature, and is heterogeneous, consisting of at least two subfractions with different melting points.The thermoresistant DNA fraction shows lowered stability to heat in the presence of Ca 2 § Mn 2+, or Mg 2+ and increased stability in the presence of alcohols. It denatures within a relatively narrow range of temperature, consists of at least three subfractions, and, most likely, represents DNA masked by histones.The effect of Ca 2+, Mn 2+, or Mg 2+ in lowering the melting point of the thermoresistant DNA fraction is seen at cation concentrations comparable to those required to maintain gross chromatin structure in cell nuclei or to support superhelical DNA conformation in isolated chromatin (0.5-1.0 mM). It is probable that factors involved in the maintenance of gross chromatin organization in situ and/or related to DNA superhelicity also have a role in modulating DNA-histone interactions, and that DNA-protein interactions as revealed by conventional methods using isolated chromatin may be different from those revealed when gross chromatin morphology remains intact.

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“…(c) At high concentration (10 -2 M), Mg 2+ destabilizes free DNA (33,36), perhaps by "charge reversal", i.e. by extensive binding to all phosphates.…”

Section: Discussionmentioning

confidence: 99%

DNA denaturation in situ. Effect of divalent cations and alcohols.

Darżynkiewicz¹,

Traganos²,

Sharpless³

et al. 1976

The Journal of Cell Biology

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“…When the value of R falls below ∼6, bound magnesium ions are being displaced by K + . As a result, parameters of eq 16 change (eqs [18][19][20]. The melting temperature decreases slightly when potassium ions are added to solutions of magnesium ions under these conditions.…”

Section: Binding Of Magnesium Cations To Single Strandedmentioning

confidence: 99%

Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations

et al. 2008

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Accurate predictions of DNA stability in physiological and enzyme buffers are important for the design of many biological and biochemical assays. We therefore investigated the effects of magnesium, potassium, sodium, Tris ions, and deoxynucleoside triphosphates on melting profiles of duplex DNA oligomers and collected large melting data sets. An empirical correction function was developed that predicts melting temperatures, transition enthalpies, entropies, and free energies in buffers containing magnesium and monovalent cations. The new correction function significantly improves the accuracy of predictions and accounts for ion concentration, G-C base pair content, and length of the oligonucleotides. The competitive effects of potassium and magnesium ions were characterized. If the concentration ratio of [Mg 2+ ] 0.5 /[Mon + ] is less than 0.22 M -1/2 , monovalent ions (K + , Na + ) are dominant. Effects of magnesium ions dominate and determine duplex stability at higher ratios. Typical reaction conditions for PCR and DNA sequencing (1.5-5 mM magnesium and 20-100 mM monovalent cations) fall within this range. Conditions were identified where monovalent and divalent cations compete and their stability effects are more complex. When duplexes denature, some of the Mg 2+ ions associated with the DNA are released. The number of released magnesium ions per phosphate charge is sequence dependent and decreases surprisingly with increasing oligonucleotide length.Interactions of magnesium, sodium and potassium ions with DNA 1 and RNA molecules are important for essential functions of living cells and for molecular biology applications. Both divalent and monovalent cations bind to nucleic acid molecules and affect their physical properties (1). Magnesium cations stabilize nucleic acid duplexes and facilitate their folding into secondary and tertiary structures (2), which are biologically active. Mg 2+ ions are also necessary cofactors of many enzymatic reactions involving nucleic acids (3). The total magnesium concentrations in various cells range from 5 to 30 mM; however, free Mg 2+ concentrations are tightly controlled between 0.4 and 1.2 mM (4). Binding of monovalent cations also increases duplex stability. The major intracellular monovalent cation is K + , while the major monovalent cation in extracellular fluid is Na + .Several theoretical models have been proposed to describe the complex phenomena of associations between cations and nucleic acids. The most widely used approaches are the mean-field approximation of the Poisson-Boltzmann equation (5-8), the counterion condensation model (9, 10), and Monte Carlo simulations (11,12). There have been few experimental studies addressing effects of Mg 2+ ion on the stability of short DNA duplexes (13-16), and comprehensive experimental melting data are not available. The majority of melting studies in magnesium buffers investigated genomic DNAs (e.g., calf thymus) (5,(17)(18)(19), long polymeric repeats (20-22), or biologically active RNA molecules (2, 23). Pione...

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“…It follows from Eqs. (l), (2), and (6) that the quantity 6tf largely depends on the ion-denatured DNA binding, i.e., on K 1 ; hence the study of the final melting stage could be a sensitive technique for determining this binding constant. An increase in Na+ concentration in the solution to 10-2M significantly cuts down the binding constants of Mg++ to DNA, thus reducing the theoretical values of &, , , and A&, which is in good agreement with the data obtained (Fig.…”

Section: Atmentioning

confidence: 99%

Magnesium ion effect on the helix‐coil transition of DNA

Blagoı̆¹,

Sorokin²,

Valeyev³

et al. 1978

Biopolymers

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SynopsisThe effect of magnesium ions on the parameters of the DNA helix-coil transition has been studied for the concentration range 10-6-10-lM at the ionic strengths of 10-3M Na+. Special attention has been given to the region of low ion concentrations and to the effect of polyvalent metallic impurities present in DNA. I t has been shown that binding with Mg++ increases the DNA stability, the effect being observed mainly in the concentration range 10-6-10-4M.At [Mg++] > 10-W the thermal stability of DNA starts to decrease. The melting range extends to concentrations -10-5M and then decreases to 7-8OC a t the ion content of lO-3M. Asymmetry of the melting curves is observed at low ionic strengths ("a+] = lO-3M) and [Mg++] Q 10-5M. The results, analyzed in terms of the statistical thermodynamic theory of double-stranded homopolymers melting in the presence of ligands, suggest that the effects observed might be due to the ion redistribution from denatured to native DNA. An experimental DNA-Mg++ phase diagram has been obtained which is in good agreement with the theory. It has been shown that thermal denaturation of the system may be an efficient method for determining the ion-binding constants for both native and denatured DNA.

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DNA melting transition in aqueous magnesium salt solutions

Cited by 25 publications

References 31 publications

DNA denaturation in situ. Effect of divalent cations and alcohols.

DNA denaturation in situ. Effect of divalent cations and alcohols.

Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations

Magnesium ion effect on the helix‐coil transition of DNA

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