Heats of thermally induced helix–coil transitions of DNA in aqueous solution

Shiao, D. D. F.; Sturtevant, Julian M.

doi:10.1002/bip.1973.360120810

Cited by 55 publications

(16 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In accordance with the common point of view in alkaline medium only coil DNA form can be deprotonated (18)(19)(20). There is only one paper (21) known to us where it was shown that deprotonation occurs in helical DNA characterized by high GC content (GC=72%).…”

Section: Experimental Data and Results Of Calculation For Alkaline Mesupporting

confidence: 52%

See 1 more Smart Citation

Theoretical and Experimental Study of DNA Helix-Coil Transition in Acidic and Alkaline Medium

DYu

Haroutiunian

et al. 1994

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

The theoretical approach to the calculation of the influence of selective binding of small ligands on DNA helix-coil transition has been described in the previous paper (Lando D. Yu., J. Biomol. Struct. Dyn., (1994)). In the present paper that method is used for the study of DNA protonation and deprotonation in acidic and alkaline medium by theoretical analysis of pH effect on DNA heat denaturation. The mechanism of DNA protonation in acidic medium and pK values of nucleotides are well known. It gave us an opportunity to check the theory without any fitting of pK values. A good agreement between experimental and calculated functions Tm(pH) and delta T(pH) (melting temperature and melting range width) obtained for acidic medium proved the validity of the theory. However, for alkaline medium there was not even qualitative agreement when the agreed-upon mechanism of deprotonation was considered. Looking into the cause of the discrepancy, we have studied the DNA melting for different mechanisms of deprotonation by calculation of Tm(pH) and delta T(pH). As a result, it has been established that the discrepancy is due to deprotonation of bonded GC base pairs of helical DNA regions (pK = 11). It was shown that the early known protonation and newly found deprotonation of helical DNA essentially stabilised double helix in alkaline and acidic medium.

show abstract

Section: Experimental Data and Results Of Calculation For Alkaline Mesupporting

confidence: 52%

“…Let us consider the model of DNA deprotonation supposed in (18)(19)(20). I) helical DNA form cannot release protons (pK 2 ; =+co); 2) DNA deprotonation is a noncooperative process (w 1 =0); 3) guanine and thymine may be deprotonated in coil DNA form.…”

Section: Experimental Data and Results Of Calculation For Alkaline Mementioning

confidence: 99%

Theoretical and Experimental Study of DNA Helix-Coil Transition in Acidic and Alkaline Medium

DYu

Haroutiunian

et al. 1994

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

show abstract

“…Note that the size of the co-operatively melting unit cancels out of equation (6.9) for d2^/dlna± (Record, 1975). Calorimetric studies on nucleic acid conformational transitions indicate that the quantity RT^/AH^ is a con-stant (here designated fi) independent of temperature, counterion concentration, base composition and chain length, although dependent upon the strandedness of the forms involved and possibly upon the nature of the counterion and the pH (Krakauer & Sturtevant, 1968;Privalov, Ptitsyn & Birshtein, 1969;Klump & Ackermann, 1971;Shiao & Sturtevant, 1973;Breslauer, Sturtevant & Tinoco, 1975; see Record, Woodbury & Lohman, 1976 b). An experimental value for A5 M+ can be obtained for T4 DNA from the calorimetric data of Privalov et al (1969) (/?= 50 + 2 deg, independent of NaCl concentration and absolute temperature) and the melting data of Record (1975), which give d2^/dlna± = 8-9 ±0-2 over the range 2-5 x io~3 M ^ [NaCl] s$ o-1 M. Over this range (8 In y±/8 In a±) is variable but small, an average value for NaCl (Robinson & Stokes, 1959) being 0-05 ± 0-03, so a ~ 0-95.…”

Section: Transitionsmentioning

confidence: 99%

Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity

1978

Quart. Rev. Biophys.

1,653

1,047

View full text Add to dashboard Cite

The purpose of this review is to examine the various effects of low- molecular-weight electrolytes on the associations and interactions of proteins and nucleic acids. Our primary interest is in general electrostatic effects, rather than chemical effects (specific interactions) of particular ions (e.g. transition metals, protons). We consider those interactions in which a variation in salt concentration has a significant effect on the macromolecular equilibrium, and analyse the effects of salt in these situations in terms of (i) direct participation of ions in the biopolymer reaction, (ii) Debye—Hückel screening by salt ions of the charge interactions on the biopolymers, and (iii) the reduction in water activity brought about at high salt concentrations.

show abstract

“…We are not aware of such data for DNA containing MgCl 2 , but some results in the presence of only monovalent counterions do exist in the literature. Experimental values of ⌬G m,0 (C Na ) at the standard temperature T o can be determined from the dependence of melting enthalpy (⌬H m ) on melting temperature from the following relation (Shiao and Sturtevant, 1973):…”

Section: Dependence Of ⌬G M On Nacl Concentrationmentioning

confidence: 99%

Application of Polyelectrolyte Theories for Analysis of DNA Melting in the Presence of Na+ and Mg2+ Ions

Korolev

Lyubartsev

Nordenskiöld

1998

Biophysical Journal

View full text Add to dashboard Cite

Numerical calculations, using Poisson-Boltzmann (PB) and counterion condensation (CC) polyelectrolyte theories, of the electrostatic free energy difference, DeltaGel, between single-stranded (coil) and double-helical DNA have been performed for solutions of NaDNA + NaCl with and without added MgCl2. Calculations have been made for conditions relevant to systems where experimental values of helix coil transition temperature (Tm) and other thermodynamic quantities have been measured. Comparison with experimental data has been possible by invoking values of Tm for solutions containing NaCl salt only. Resulting theoretical values of enthalpy, entropy, and heat capacity (for NaCl salt-containing solutions) and of Tm as a function of NaCl concentration in NaCl + MgCl2 solutions have thus been obtained. Qualitative and, to a large extent, quantitative reproduction of the experimental Tm, DeltaHm, DeltaSm, and DeltaCp values have been found from the results of polyelectrolyte theories. However, the quantitative resemblance of experimental data is considerably better for PB theory as compared to the CC model. Furthermore, some rather implausible qualitative conclusions are obtained within the CC results for DNA melting in NaCl + MgCl2 solutions. Our results argue in favor of the Poisson-Boltzmann theory, as compared to the counterion condensation theory.

show abstract

Heats of thermally induced helix–coil transitions of DNA in aqueous solution

Cited by 55 publications

References 26 publications

Theoretical and Experimental Study of DNA Helix-Coil Transition in Acidic and Alkaline Medium

Theoretical and Experimental Study of DNA Helix-Coil Transition in Acidic and Alkaline Medium

Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity

Application of Polyelectrolyte Theories for Analysis of DNA Melting in the Presence of Na+ and Mg2+ Ions

Contact Info

Product

Resources

About