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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
Author(s) -
Oliver Adrian L.,
Wartell Roger M.,
Ratliff Robert L.
Publication year - 1977
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1977.360160512
Subject(s) - exponent , chemistry , stacking , dimer , crystallography , entropy (arrow of time) , thermodynamics , physics , philosophy , linguistics , organic chemistry
The thermally induced helix‐coil transitions of three A‐T DNAs, 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 , were studied. Experimental transition curves of the DNAs were analyzed using the loop entropy model of DNA melting. The calculation of the melting curve of d(A‐A‐T) n ·d(A‐T‐T) n 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 ± 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) n ·d(T) n and d(A‐A‐T) n ·d(A‐T‐T) n differ. The last result is consistent with different conformations for the dimer in these two polymers.