Thermodynamics of the Helix-Coil Equilibrium in Oligoadenylic Acid from Hypochromicity Studies

Applequist, Jon; Damle, Vinayak N.

doi:10.1021/ja01085a007

Cited by 174 publications

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“…The theory for melting of short oligomeric doublestranded nucleic acids has been treated by several authors [3,4,8]. The simplest approach will be used here, namely the analysis of melting curves by the "all-or-none" model [3,4].…”

Section: Theoretical Backgroundmentioning

confidence: 99%

“…The simplest approach will be used here, namely the analysis of melting curves by the "all-or-none" model [3,4]. I n this model it is assumed that only completely base-paired molecules and single stranded chains are present in measurable concentrations and that any intermediate states are of negligible concentration.…”

Section: Theoretical Backgroundmentioning

confidence: 99%

“…A simple estimate shows that a t 25 "C only 2O/, of the double helical molecules will have (n-1) base pairs formed instead of n, which is a t present below the limit for experimental detection. (For relatively small s values, one has to use the ('staggered-zipper" model in the analysis [3], which takes into account also doublehelical molecules, where not all the possible base pairs are formed.) It is also considerably higher than the one extrapolated from calorimetric measurements of the melting of DNA with different base composition [25] and the reason for this discrepancy is not yet clear.…”

Section: Free Energy Of Base-pair Formationmentioning

confidence: 99%

“…On the other hand, information about the free energy and enthalpy of base pair formation and the nucleation parameters involved in the initiation of the double helix can be obtained in a rather direct way from melting experiments using short oligomers of defined length and sequence [3]. A considerable body of thermodynamic data on A .…”

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Thermodynamics of the Helix‐Coil Transition of (dG‐dC) Oligomers

Pohl

1974

European Journal of Biochemistry

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The dissociation of short double-helical DNA with the alternating sequence (dG-dC),. (dG-dC), into the corresponding single strands was studied as a function of chain length, oligomer concentration and temperature in 1.0 M NaCl, pH 7.2 by hypochromicity and equilibrium centrifugation. The melting curves are analyzed according to an "all-or-none'' model and the following thermodynamic parameters were deduced.The change in free energy for formation of a dG . dC base pair adjacent to another one, AG:, ---2.2 kcal/mol at 37 "C; the corresponding change in enthaply, AH:, = -11.1 5 0.5 kcal/mol and in entropy, AS:, = -27.9 & 1 cal . K-l * mol base pair-l. The stability constant, s, is 104 f 5 at 25 "C. The formation of the first base pair from two single strands involves a nucleation parameter, j3, = 1.6 M-l a t 25 "C, which is similar to the corresponding values determined for different RNA oligomers. The enthaply change associated with the formation of the first base pair, -AH;,, = + 3 & 5 kcal/mol which is very close to zero.These thermodynamic parameters are compared with those for the dA . dT base pair. At physiological conditions, i t is estimated that the stability of one dG * dC pair is very close to that of two dA . dT pairs. The data imply that the opening of a unique sequence of DNA in a cell is a very improbable event.The thermodynamics of base-pair formation in DNA are of considerable biological interest. Processes like replication, recombination or recognition of specific base sequences very probably involve an opening of the double helix. Experimental techniques like the hybridization of nucleic acids also depend on the relative stability of base pairs.The higher stability of the dG * dC base pair as compared to the dA * dT pair has been known for a long time and can be deduced, for example, from the dependence of the melting temperature (T,,,) on the dG . dC content of DNA's from different organism, [ 11. Quantitative thermodynamic parameters for the two base pairs involved in the helix-coil transition of natural DNA, which is essentially a mixture of many different sequences, is rather difficult t o obtain. The situation is made somewhat easier by studying the melting of corresponding polymers with simple repeating sequences [2].On the other hand, information about the free energy and enthalpy of base pair formation and the nucleation parameters involved in the initiation of the double helix can be obtained in a rather direct way from melting experiments using short oligomers of defined length and sequence [3]. A considerable body of thermodynamic data on A . U and G * C base pairs has been accumulated during the last few years by studying synthetic and natural RNA oligomers [4-lo]. With respect to DNA the situation is less satisfying and most of the results are restricted to the dA dT base pais, obtained from the melting of oligomers of the type (dA),. (dT)m [11,12] or (dA-dT), [13,14]. I n order to establish the thermodynamic parameters of the dG . dC base pair in the double helix, experiments on t...

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Section: Theoretical Backgroundmentioning

confidence: 99%

Section: Theoretical Backgroundmentioning

confidence: 99%

Section: Free Energy Of Base-pair Formationmentioning

confidence: 99%

mentioning

confidence: 99%

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Thermodynamics of the Helix‐Coil Transition of (dG‐dC) Oligomers

Pohl

1974

European Journal of Biochemistry

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“…From Eq. 8 one also has /df\ e-1 (AH) dT max 4 RT2 [9] Although they will not be used here, more precise results can be given (Eqs. 10 and 10' below) that may be useful when BH!…”

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Molecular field theory of reversible unfolding of biopolymers

Cerf¹

1978

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

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The theory of thermal transitions of nucleic acids and proteins has been developed thoroughly for various systems that exhibit some simplifying feature e.g., nucleic acids with a well-defined ordered or disordered sequence of base pairs. This subject was reviewed a few years ago by Poland and Scheraga (1). In several instances, especially in more complicated situations that involve, for example, the breaking of both tertiary and secondary structures (e.g., tRNAs and proteins), it is still a customary procedure to decompose the melting curve in the maximum number of two-state transitions compatible with the enthalpy change associated with the overall denaturation process. Explicit use of this procedure has been made recently by, among others, Privalov et al. (2) in interpreting their calorimetric investigation of the melting of tRNAIVal.I propose here a model that is an alternative to the two-state one and lends itself to accounting for cooperativeness without resort to a detailed description of the elementary steps of a transition. It will be shown that the molecular field approach-which has already been used for describing the behavior of membranes (3) and hysteresis effects in RNA and polyribonucleotide triple helices (4)-leads to remarkable properties for values of the molecular field parameter at which hysteresis just ceases to be observed, exhibiting high cooperativity in a most simple way. Molecular field theory of thermal transitionsThe model is intended to describe a particular concerted step in the unfolding of a nucleic acid or protein. We assume that one sequence of n pairs of elements that are linked together by noncovalent bonds in the folded conformation will be separated in the step we consider. A conformational change thus comprises n elementary steps. Let 0 < f < 1 be the fraction of pairs that remain united at a given stage of the transition.Following the work of Weisbuch and Neumann (4) [I]Postulate 1 is analogous to that introduced by P. Weiss in the first theory of ferromagnetism (i.e., the molecular field assumption). As in ref. 4, this postulate, which stems from the long-range nature of the force field, introduces a nonlinear relation between the separation free energy and the number fraction of units melted. In the simplest model, all pairs of elements would be considered identical. It is quite simple, however, to introduce significant heterogeneity in the composition of the pairs. For this, let us divide the united pairs of the above sequence in v classes i (i = 1, 2, . . ., P). The pairs of two different classes may differ from each other by the nature of the elements of which they are composed (e.g., in nucleic acids, A-T and G-C pairs, respectively) as well as by their environment.Call rs the fraction of pairs in class i and Ai the corresponding value of A. We assume that, throughout the transition, the relative number of united and separated pairs does not depend on the index i. This is equivalent to assuming that the molecular field is so strong that the sequence of pairs we consi...

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Cooperative Conformational Kinetics of Synthetic and Biological Chain Molecules

Cerf

1975

Advances in Chemical Physics

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Thermodynamics of the Helix-Coil Equilibrium in Oligoadenylic Acid from Hypochromicity Studies

Cited by 174 publications

References 0 publications

Thermodynamics of the Helix‐Coil Transition of (dG‐dC) Oligomers

Thermodynamics of the Helix‐Coil Transition of (dG‐dC) Oligomers

Molecular field theory of reversible unfolding of biopolymers

Cooperative Conformational Kinetics of Synthetic and Biological Chain Molecules

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