Helix–coil transitions of compositionally heterogeneous DNA

Pritchard, A. E.; Eichinger, B. E.

doi:10.1002/bip.1975.360140705

Cited by 7 publications

(3 citation statements)

References 32 publications

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“…Theoretically, a phase transition is forbidden in two-stranded homopolynucleotides because the contribution of the rings to the entropy may increase due to the possible displacement of strands in the homopolynucleotide. [17,18] The data in ref. [16] and in Figure 2 suggest there is no chain slip in the real situation.…”

Section: Resultsmentioning

confidence: 99%

Effect of Mg2+ Ions on the Stability of PolyA/2PolyU Three-Stranded Helices in Aqueous Solutions

et al. 2002

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Section: Resultsmentioning

confidence: 99%

Effect of Mg2+ Ions on the Stability of PolyA/2PolyU Three-Stranded Helices in Aqueous Solutions

et al. 2002

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“…The theoretical curves were generated by numerically solving Eqs. (15) and (16) of the preceding sections. , by varying k and U11 or U22, respectively.…”

Section: Evaluation Of the Thermodynamic Parametersmentioning

confidence: 95%

Helix coil transitions of d (A)_n·d(T)_n, d(A‐T)_n·d(A‐T)_n, and d(A‐A‐T)_n·d(A‐T‐T)_n; evaluation of parameters governing DNA stability

1977

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SynopsisT h e thermally induced helix-coil transitions of three A-T DNAs, d(A),,.d(T),, d(A-T),. d(A-T),,, and d(A-A-T),-d(A-T-T),, were studied. Experimental transition curves of the DNAs were analyzed using the loop entropy model of DNA melting. T h e calculation of the melting curve of d(A-A-T),-d(A-T-T)" is presented using the integral equation formalism of Goel and Montroll. The aim of this work was to evaluate thermodynamic parameters which govern DNA stability and to test the theoretical model employed in the analysis. Our results show 1) an excellent over-all agreement between theory and experiment, 2) a loop entropy exponent k = 1.55 f 0.05 provided the best fit to all the polymer transition curves, 3) the evaluated stacking free energies reflect the relative stability of the DNAs, and 4) the stacking energies of the ApA-TpT dimer evaluated from d(A),-d(T), and d(A-A-T),.d(A-T-T), differ.T h e last result is consistent with different conformations for the dimer in these two polymers.

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“…Theory [42,43] however forbids a phase transition in double-stranded homopolynucleotides because of a possible transitional shift of the strands. Such a shift increases the contribution of the ring to entropy and the end of the transition becomes smeared at T = T f .…”

Section: Polya/2 Polyumentioning

confidence: 99%

Ni2+ Ion Effect of Conformations on Single-, Double- and Three-Stranded Homopolynucleotides Containing Adenine and Uracil

Sorokin¹,

Valeev

Gladchenko

et al. 2001

Macromol. Biosci.

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Differential UV and visible spectroscopy and thermal denaturation were used to study the interaction of Ni2+ ions with adenosine 5′‐monophosphate (AMP), uridine 5′‐monophosphate (UMP), single‐stranded polyadenylic acid (polyA) and polyuridylic (polyU), double‐stranded polyA/polyU (AU) and three‐stranded polyA/2 polyU (A2U). The coil → helix transition observed in polyA, AU and A2U at room temperature is induced by Ni2+ binding to the oxygen atoms of the phosphate groups which belong to the disordered single‐stranded parts of the polynucleotides. Ni2+ ions coordinate with bases only in individual AMP and single‐stranded polyA. This coordination causes disordering of the helical parts of the strands. The disordered single strands form thermally stable compact particles with effective radii of ˜100 Å. Diagrams of the phase equilibrium between single‐, double‐ and three‐stranded conformations as a function of temperature and Ni2+ concentration have been obtained. The melting ranges of A2U and AU differ considerably, mainly due to different enthalpies of their helix–coil transitions. The behaviour of the transition parameters in the presence of Ni2+ ions agrees with the data obtained from the theory of equilibrium binding. The constants of the Ni2+ binding to AU and A2U are found. The effect of Ni2+ ions upon the thermal stability of AU and A2U is connected mainly with their different binding to multi‐stranded helices and polyU. The end of melting of the double‐stranded AU formed due to the A2U → AU + U transition has the character of a second‐order phase transition.

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Helix–coil transitions of compositionally heterogeneous DNA

Cited by 7 publications

References 32 publications

Effect of Mg2+ Ions on the Stability of PolyA/2PolyU Three-Stranded Helices in Aqueous Solutions

Effect of Mg2+ Ions on the Stability of PolyA/2PolyU Three-Stranded Helices in Aqueous Solutions

Helix coil transitions of d (A)_n·d(T)_n, d(A‐T)_n·d(A‐T)_n, and d(A‐A‐T)_n·d(A‐T‐T)_n; evaluation of parameters governing DNA stability

Ni2+ Ion Effect of Conformations on Single-, Double- and Three-Stranded Homopolynucleotides Containing Adenine and Uracil

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Helix–coil transitions of compositionally heterogeneous DNA

Cited by 7 publications

References 32 publications

Effect of Mg2+ Ions on the Stability of PolyA/2PolyU Three-Stranded Helices in Aqueous Solutions

Effect of Mg2+ Ions on the Stability of PolyA/2PolyU Three-Stranded Helices in Aqueous Solutions

Helix coil transitions of d (A)n·d(T)n, d(A‐T)n·d(A‐T)n, and d(A‐A‐T)n·d(A‐T‐T)n; evaluation of parameters governing DNA stability

Ni2+ Ion Effect of Conformations on Single-, Double- and Three-Stranded Homopolynucleotides Containing Adenine and Uracil

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Helix coil transitions of d (A)_n·d(T)_n, d(A‐T)_n·d(A‐T)_n, and d(A‐A‐T)_n·d(A‐T‐T)_n; evaluation of parameters governing DNA stability