Mg2+ recognizes the sequence of DNA through its hydration shell

Buckin, Vitaly; Kankiya, B. I.; Rentzeperis, Dionisios; Marky, Luis A.

doi:10.1021/ja00100a003

Cited by 87 publications

(90 citation statements)

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“…DNase I and cyclization, are performed in the presence of Mg 2ϩ and yet their results are consistent with the other experiments described here. The dehydrating effect of Mg 2ϩ binding is lowest for the most hydrated DNA sequences, namely for regions rich in A⅐T base pairs (73). A similar effect was observed in gel mobility experiments on sequences with and without A-tracts (33,43).…”

Section: Fig 4 Probabilities Of Cleavage (Ln P) For the Complementasupporting

confidence: 68%

The Organic Crystallizing Agent 2-Methyl-2,4-pentanediol Reduces DNA Curvature by Means of Structural Changes in A-tracts

Dlakić

Park

Griffith

et al. 1996

Journal of Biological Chemistry

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Contemporary predictive models for sequencedependent DNA structure provide a good estimation of overall DNA curvature in most cases. However, the two current models differ fundamentally in their view of the origin of DNA curvature. An earlier model that associates DNA bending primarily, although not exclusively, with stretches of adenines (A-tracts) is based on results of comparative gel retardation, cyclization kinetics, hydroxyl radical cutting, and other solution measurements. It represents an intersection of wedge and junction models. More recently, a non-A-tract bending model has been proposed, built on structural results from x-ray crystallography and molecular modeling. In this view, A-tracts are proposed to be straight and rigid, whereas mixed sequence DNA is bent. Because a key premise of the non-A-tract bending model is the crystallographic observation that A-tracts are straight, we have examined the effect in solution of 2-methyl-2,4-pentanediol (MPD), an organic solvent used in crystal preparation for crystallographic DNA structure determinations. Using cyclization analysis, DNase I cutting, chemical probing, and electron microscopy on DNA oligomers with and without A-tracts, we show that the presence of MPD in solution dramatically affects A-tracts and that the effect is specific to these sequence elements. Combined with the previous observation that MPD affects gel mobility of curved sequences with A-tracts, our findings support the bent A-tract model and call for caution in the interpretation of crystallographic results on DNA structure as these are presently obtained.Although the origin of DNA curvature has been extensively investigated over the past decade and a half, it remains elusive and highly controversial. Early attempts to rationalize DNA curvature were based upon the observation that short runs of helically phased adenine tracts (A-tracts) are necessary and sufficient to produce experimental results consistent with macroscopic DNA curvature. Thus, it was proposed that DNA bending is an intrinsic attribute of only certain DNA sequences, primarily AA⅐TT dinucleotide elements (1) or A n T m -tracts (n ϩ m ϭ 3-6) (2-6), and that macroscopic DNA curvature arises from additive, coherent contributions of these sequences phased with helical periodicity along the DNA. Two models were then proposed to explain the observed DNA curvature which differ primarily in the basic unit of DNA that is assumed responsible for the bending. The wedge model defines bending as a result of axial deflections (wedges) of successive AA⅐TT dinucleotides, whose vectorial sum describes the global DNA trajectory (1, 6 -8). The junction model proposes that the bending arises from structural discontinuities at the junction of A-tracts, assumed to be in a modified B-DNA structure, with the adjacent B-form DNA (3, 9 -11). At first, contributions of other DNA sequence elements were considered small and hence were ignored. More recently, however, evidence has accumulated suggesting that DNA curvature may involve additional seq...

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Section: Fig 4 Probabilities Of Cleavage (Ln P) For the Complementasupporting

confidence: 68%

The Organic Crystallizing Agent 2-Methyl-2,4-pentanediol Reduces DNA Curvature by Means of Structural Changes in A-tracts

Dlakić

Park

Griffith

et al. 1996

Journal of Biological Chemistry

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“…This sequence specific behavior is consistent with a study of repeating polymers using 25 Mg NMR spectroscopy (55), in which G · C base pairs were found to bind Mg 2+ up to 100-fold more strongly than A · T base pairs. Sequence dependent Mg 2+ binding was also detected when hydration of DNA duplexes was investigated using ultrasonic velocity measurements (56). DNA A · T base pairs were proposed to interact with magnesium ions by outer-sphere complex formation, while G · C base pairs exhibited substantial dehydration changes typical for innersphere complexes.…”

Section: Discussionmentioning

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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“…Ultrasonic velocimetric titrations of 3 mM poly[r(A)] with 12 mM poly[r(U)], at 20, 30, and 40°C, were performed as previously described (23)(24)(25)(26). …”

Section: Methodsmentioning

confidence: 99%

A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques

Chalikian

Völker

Plum

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

235

219

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We use a combination of calorimetric and volumetric techniques to detect and to characterize the thermodynamic changes that accompany helix-to-coil transitions for five polymeric nucleic acid duplexes. Our calorimetric measurements reveal that melting of the duplexes is accompanied by positive changes in heat capacity (⌬C P ) of similar magnitude, with an average ⌬C P value of 64.6 ؎ 21.4 cal deg ؊1 mol ؊1 . When this heat capacity value is used to compare significantly different transition enthalpies (⌬H o ) at a common reference temperature, T ref , we find ⌬H T ref for duplex melting to be far less dependent on duplex type, base composition, or base sequence than previously believed on the basis of the conventional assumption of a near-zero value for ⌬C P . Similarly, our densimetric and acoustic measurements reveal that, at a given temperature, all the ATand AU-containing duplexes studied here melt with nearly the same volume and compressibility changes. In the aggregate, our results, in conjunction with literature data, suggest a more unified picture for the thermodynamics of nucleic acid duplex melting. Specifically, when compared at a common temperature, the apparent large differences present in the literature for the transition enthalpies of different duplexes become much more compressed, and the melting of all-AT-and all-AU-containing duplexes exhibits similar volume and compressibility changes despite differences in sequence and conformation. Thus, insofar as thermodynamic properties are concerned, when comparing duplexes, the temperature under consideration is as important as, if not more important than, the duplex type, the base composition, or the base sequence. This general behavior has significant implications for our basic understanding of the forces that stabilize nucleic acid duplexes. This behavior also is of practical significance in connection with the use of thermodynamic databases for designing probes and for assessing the affinity and specificity associated with hybridization-based protocols used in a wide range of sequencing, diagnostic, and therapeutic applications.Thermodynamic studies of nucleic acids have produced data of both fundamental and practical importance. On the fundamental side, such studies have provided insight into the nature and strength of the forces that stabilize nucleic acids in the myriad of structural states they can assume (1-7). On the practical side, such studies have produced databases that are used to predict the stability and selectivity of hybridization events required in a broad range of nucleic acid-based diagnostic and therapeutic protocols (3, 8-11, 19, 42-44).Three aspects of the current nucleic acid thermodynamic library that are conspicuously deficient are values for the heat capacity change(s), ⌬C P , the volume changes, ⌬V, and the compressibility changes, ⌬K s , which accompany nucleic acid conformational transitions. These deficiencies are of particular concern because ⌬C P , ⌬V, and ⌬K s provide unique insights into the role of solvent i...

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Mg2+ recognizes the sequence of DNA through its hydration shell

Cited by 87 publications

References 0 publications

The Organic Crystallizing Agent 2-Methyl-2,4-pentanediol Reduces DNA Curvature by Means of Structural Changes in A-tracts

The Organic Crystallizing Agent 2-Methyl-2,4-pentanediol Reduces DNA Curvature by Means of Structural Changes in A-tracts

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

A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques

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