Recherches sur la d'enaturation des acides desoxyribonucléiques

doi:10.1016/0006-3002(54)90163-8

Biochimica et Biophysica Acta

Volume 14, 1954, Pages 231-240

https://doi.org/10.1016/0006-3002(54)90163-8 Get rights and content

Résumé

L'absorption ultra-violette des acide desoxyribonucléiques (ADN) en solution saline neutre est de loin inférieure à celle que l'on peut calculer par la sommation des absorptions de leurs constituants. Le spectre observé s'approche du spectre calculé sous l'action de traitements doux (changements du pH, de la température, ou de la Force ionique) qui sont probablement sans action sur les liaisons phosphoester. Les rapports de ces phénomènes avec la structure chimique et les propriétés biologiques des ADN sont discutés. Les résultats sont interprêtés comme résultant d'une dénaturation des ADN, c'est-à-dire de la destruction d'une structure secondaire de liaisions labiles impliquant les cycles puriques et pyrimidiques.

Abstract

The ultraviolet absorption of desoxyribonucleic acids (DNA) in neutral solution is much less than expected from the sum of the absorptions of its constituents. The observed spectrum can be made to approach the calculated one by applying mild treatments which are presumably without action on phosphoester linkages (pH, temperature and salt concentration changes). The incidence of these facts on the questions of the chemical structure and biological properties of DNA is discussed. The results are interpreted as reflecting a denaturation of the DNA, i.e. the destruction of a secondary molecular structure constituted by labile bounds involving the puric and pyrimidic rings.

Zusammenfassung

Die Ultraviolettabsorption von Desoxyribonucleinsäuren (DNS) in neutralen Salzlösungen ist weitaus geringer als die sich aus der Absorption der Bestandteile errechnende Summe. Nach milder Behandlung (Änderung des pH's, der Temperatur oder der Salzkonzentration), die wahrscheinlich ohne Wirkung auf die Phosphoesterbindung ist, nähert sich das beobachtete Spektrum dem berechneten. Der Einfluss dieser Erscheinungen auf die Frage der chemischen Struktur und die biologischen Eigenschaften der DNA werden besprochen. Die Resultate werden als ein Ergebnis einer Denatu rierung der DNA interpretiert, d.h. einem Abbau einer sekundären Molekülstruktur von labilen Bindungen mit Purin und Pyrimidinringen.

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Citation Excerpt :
As a result, the denaturation temperature in the presence of MgCl2 is higher than NaCl at the same cation concentration [4]. This was already seen in early reports by Thomas [5] who found that to maintain native DNA at room temperature, the concentration of NaCl should be 100 times higher than that of MgCl2. Similar conclusions were reached in several comparative studies of how Na+ and Mg2+ influences the denaturation [6–8].
Monovalent and divalent cations play a crucial role in living cells and for molecular techniques such as PCR. Here we evaluate DNA melting temperatures in magnesium (Mg²⁺) and magnesium‑potassium (Mg²⁺+ K⁺) buffers with a mesoscopic model that allows us to estimate hydrogen bonds and stacking interaction potentials. The Mg²⁺ and Mg²⁺+ K⁺ results are compared to previous calculations for sodium ions (Na⁺), in terms of equivalent sodium concentration and ionic strength. Morse potentials, related to hydrogen bonding, were found to be essentially constant and unaffected by cation conditions. However, for stacking interactions we find a clear dependence with ionic strength and cation valence. The highest ionic strength variations, for both hydrogen bonds and stacking interactions, was found at the sequence terminals. This suggests that end-to-end interactions in DNA will be strongly dependent on cation valence and ionic strength.
Prologue to the special issue of JTB dedicated to the memory of René Thomas (1928–2017): A journey through biological circuits, logical puzzles and complex dynamics
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DNA melting and energetics of the double helix
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Studying melting and energetics of the DNA double helix has been one of the major topics of molecular biophysics over the past six decades. The main objective of this article is to overview the current state of the field and to emphasize that there are still serious gaps in our understanding of the issue. We start with a concise description of the commonly accepted theoretical model of the DNA melting. We then concentrate on studies devoted to the comparison with experiment of theoretically predicted melting profiles of DNAs with known sequences. For long DNA molecules, such comparison is significant from the basic-science viewpoint while an accurate theoretical description of melting of short duplexes is necessary for various very important applications in biotechnology. Several sets of DNA melting parameters, proposed within the framework of the nearest neighbor model, are compared and analyzed. The analysis leads to a conclusion that in case of long DNA molecules the consensus set of nearest neighbor parameters describes well the experimental melting profiles. Unexpectedly, for short DNA duplexes the same set of parameters hardly yields any improvement as compared to the simplest model, which completely ignores the effect of heterogeneous stacking. Possible causes of this striking observation are discussed. We then overview the issue of separation of base-pairing and base-stacking contributions into the double helix stability. The recent experimental attempts to solve the problem are extensively analyzed. It is concluded that the double helix is essentially stabilized by stacking interaction between adjacent base pairs. Base pairing between complementary pairs does not appreciably contribute into the duplex stability. In the final section of the article, kinetic aspects of the DNA melting phenomenon are discussed. The main emphasis is made on the hysteresis effects often observed in melting of long DNA molecules. It is argued that the phenomenon can be well described via an accurate theoretical treatment of the random-walk model of melting kinetics of an isolated helical segment in DNA.
Comparison of DNA quality in raw and reconstituted milk during sterilization
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In the present study, the increased DNA yield observed in heat-treated FM and RM probably represents an overestimation because of DNA degradation, given that agarose gel electrophoresis analysis confirmed that the level of DNA degradation was greater in heat-treated than in unheated samples. The partial degradation of double-stranded DNA partially degraded to single-stranded DNA results in an increase in absorbance value of UV light (at 260 nm) of DNA solutions, a phenomenon long recognized as the hyperchromic effect (Thomas, 1954; Benight et al., 2001). It has been demonstrated that DNA can be degraded into smaller fragments in processed food products (Novak et al., 2007).
Responses to milk sterilization are usually evaluated only in terms of physicochemical properties and microbial safety, thus undervaluing the importance of DNA quality in an authentication process by methods based on PCR. Because DNA is a heat-sensitive molecule, we hypothesized that the heating process may impair the detection or quantification of DNA in raw fresh milk (FM) or reconstituted milk (RM), and that differences in DNA quality might exist between FM and RM. We thus investigated the effects of sterilization on the quality of DNA extracted from FM or RM; differences in DNA quality between FM and RM were also evaluated. The quality of extracted DNA from FM or RM was assessed by the specific detection of FM or RM composition in goat milk mixtures using primers targeting the bovine 12S gene, as well as by monitoring DNA yield, purity, ratio of mitochondrial (mt) to nuclear (n) DNA, and the level of DNA degradation. Polymerase chain reaction readily detected both untreated and heat-treated FM or RM in cow-goat milk mixtures, and gave a good sensitivity threshold (0.1%) under all sterilization conditions. The DNA yield and mtDNA:nDNA ratio of FM and RM varied significantly during the sterilization process. These results demonstrated that the sterilization altered the quantification of DNA in FM or RM during sterilization, but DNA could still be readily detected in sterilized FM or RM by PCR. Furthermore, we noted significant differences in DNA integrity, yield, and mtDNA:nDNA ratio between FM and RM during sterilization, which may have potential as a means to distinguish FM and RM.
Twist versus nonlinear stacking in short DNA molecules
2014, Journal of Theoretical Biology
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous short sequences of DNA, i.e. $~ 100$ base pairs, in the framework of a mesoscopic Hamiltonian model which accounts for the helicoidal geometry of the molecule. The theoretical background for the application of the path integral formalism to predictive analysis of the molecule thermodynamical properties is discussed. The base pair displacements with respect to the ground state are treated as paths whose temperature dependent amplitudes are governed by the thermal wavelength. The ensemble of base pairs paths is selected, at any temperature, consistently with both the model potential and the second law of thermodynamics. The partition function incorporates the effects of the base pair thermal fluctuations which become stronger close to the denaturation. The transition appears as a gradual phenomenon starting from the molecule segments rich in adenine–thymine base pairs. Computing the equilibrium thermodynamics, we focus on the interplay between twisting of the complementary strands around the molecule axis and nonlinear stacking potential: it is shown that the latter affects the melting profiles only if the rotational degrees of freedom are included in the Hamiltonian. The use of ladder Hamiltonian models for the DNA complementary strands in the pre-melting regime is questioned.
Mapping between the order of thermal denaturation and the shape of the critical line of mechanical unzipping in one-dimensional DNA models
2010, Chemical Physics Letters
Citation Excerpt :
Several fundamental biological processes, like transcription and replication, involve the separation and recombination of the two strands that compose double-stranded (zipped) DNA molecules. Since transcription and replication are quite complex mechanisms, many early studies focused on thermal denaturation, that is the separation of the two strands upon heating [1–7]. In cells, unzipping is however not mediated by thermal activation but rather by proteins, which apply forces to separate and stretch complementary DNA strands.
In this Letter, we investigate the link between thermal denaturation and mechanical unzipping for two models of DNA, namely the Dauxois–Peyrard–Bishop model and a variant thereof we proposed recently. We show that the critical line that separates zipped from unzipped DNA sequences in mechanical unzipping experiments is a power-law in the temperature-force plane. We also prove that for the investigated models the corresponding critical exponent is proportional to the critical exponent α, which characterizes the behaviour of the specific heat in the neighbourhood of the critical temperature for thermal denaturation.

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Recherches sur la d'enaturation des acides desoxyribonucléiques

Résumé

Abstract

Zusammenfassung

J. Biol. Chem.

J. Biol. Chem.

Biochim. Biophys. Acta

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

Biochim. Biophys. Acta

Biochim. Biophys. Acta

Biochim. Biophys. Acta

J. Chem. Soc.

J. Am. Chem. Soc.

J. Chem. Soc.

Nature

J. Chem. Soc.

Biochim. Biophys. Acta

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